Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 89 of 310
Found at i:28596292 original size:28 final size:28
Alignment explanation
Indices: 28596232--28596292 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
28596222 TAAAACAAAT
28596232 CCTAATTTATTTTTAAAAAACCCTAAAC
1 CCTAATTTATTTTTAAAAAACCCTAAAC
* *
28596260 TCTAATTTATTTTTTCAAAAACCCT-AAC
1 CCTAATTTA-TTTTTAAAAAACCCTAAAC
28596288 CCTAA
1 CCTAA
28596293 CCTTAAGTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 15 0.52
29 14 0.48
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.38
Consensus pattern (28 bp):
CCTAATTTATTTTTAAAAAACCCTAAAC
Found at i:28603977 original size:13 final size:13
Alignment explanation
Indices: 28603959--28603983 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28603949 AGGCCGTGTG
28603959 AAGGACACGGGCC
1 AAGGACACGGGCC
28603972 AAGGACACGGGC
1 AAGGACACGGGC
28603984 ATGTGCTCGG
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:0.28, G:0.40, T:0.00
Consensus pattern (13 bp):
AAGGACACGGGCC
Found at i:28604672 original size:74 final size:74
Alignment explanation
Indices: 28604583--28604730 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
28604573 AATATACTCC
28604583 AATGTTCCCTTCGTGTTATGGATTCCTCTAGTGAATCGAACTCTTTTTCTCTTTCCAAAAACACA
1 AATGTTCCCTTCGTGTTATGGATTCCTCTAGTGAATCGAACTCTTTTTCTCTTTCCAAAAACACA
28604648 GTGCTCACT
66 GTGCTCACT
28604657 AATGTTCCCTTCGTGTTATGGATTCCTCTAGTGAATCGAACTCTTTTTCTCTTTCCAAAAACACA
1 AATGTTCCCTTCGTGTTATGGATTCCTCTAGTGAATCGAACTCTTTTTCTCTTTCCAAAAACACA
28604722 GTGCTCACT
66 GTGCTCACT
28604731 GAAATTCAGT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.38
Consensus pattern (74 bp):
AATGTTCCCTTCGTGTTATGGATTCCTCTAGTGAATCGAACTCTTTTTCTCTTTCCAAAAACACA
GTGCTCACT
Found at i:28604889 original size:25 final size:25
Alignment explanation
Indices: 28604855--28604906 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
28604845 ATCTGACAAG
28604855 AAAGAAGAAGCAAAAATTGCATTGT
1 AAAGAAGAAGCAAAAATTGCATTGT
28604880 AAAGAAGAAGCAAAAATTGCATTGT
1 AAAGAAGAAGCAAAAATTGCATTGT
28604905 AA
1 AA
28604907 CACCCTTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.54, C:0.08, G:0.19, T:0.19
Consensus pattern (25 bp):
AAAGAAGAAGCAAAAATTGCATTGT
Found at i:28623185 original size:47 final size:47
Alignment explanation
Indices: 28623107--28626111 Score: 5767
Period size: 47 Copynumber: 63.6 Consensus size: 47
28623097 CCCTTCGGGA
* * * * * *
28623107 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28623154 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28623201 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28623250 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28623299 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28623348 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28623397 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28623446 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28623495 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28623544 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28623591 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28623638 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28623685 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28623732 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28623779 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28623826 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28623873 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28623920 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28623967 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28624016 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28624063 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28624110 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28624157 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28624204 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28624251 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28624298 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28624345 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28624392 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28624439 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28624486 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28624533 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28624580 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28624627 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28624674 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28624721 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28624768 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28624815 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28624862 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28624909 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28624956 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625003 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625050 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625097 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625144 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625191 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625238 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625285 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625332 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625379 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625428 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625475 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625522 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625569 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625616 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625663 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625710 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625757 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625804 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625851 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625898 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625945 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28625992 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28626039 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28626086 CTTATCACATATATATACTTTCACAT
1 CTTATCACATATATACACTTTCACAT
28626112 CACAATTATC
Statistics
Matches: 2941, Mismatches: 11, Indels: 12
0.99 0.00 0.00
Matches are distributed among these distances:
47 2506 0.85
49 435 0.15
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28630197 original size:40 final size:40
Alignment explanation
Indices: 28630165--28630596 Score: 783
Period size: 40 Copynumber: 10.8 Consensus size: 40
28630155 CCAGCATGAT
* * * *
28630165 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** * *
28630205 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28630245 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28630285 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28630325 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28630365 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28630405 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28630445 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28630485 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28630525 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28630565 TGCTCTTCGGGACTTAGCCCGGATATATCACT
1 TGCTCTTCGGGACTTAGCCCGGATACATCACT
28630597 CTCAATTCTC
Statistics
Matches: 381, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 381 1.00
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:28631861 original size:37 final size:37
Alignment explanation
Indices: 28631811--28631889 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
28631801 TTATTACGAA
* * *
28631811 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
28631848 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
28631885 GTCTT
1 GTCTT
28631890 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:28632086 original size:47 final size:47
Alignment explanation
Indices: 28632008--28632691 Score: 1287
Period size: 47 Copynumber: 14.6 Consensus size: 47
28631998 CCCTTCGGGA
* * * * * *
28632008 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28632055 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28632102 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28632149 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28632196 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28632243 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28632290 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28632337 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28632384 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28632431 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28632478 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28632525 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28632572 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28632619 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28632666 CTTATCACATATATATACTTTCACAT
1 CTTATCACATATATACACTTTCACAT
28632692 CACAATTATC
Statistics
Matches: 626, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 626 1.00
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28635835 original size:6 final size:6
Alignment explanation
Indices: 28635824--28635862 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
28635814 TTTTGAAGAC
* *
28635824 TTTTTA TTTTTA TTTTTA TTTTTA CTTTTA TCTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
28635863 ATCTTTTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:28635870 original size:18 final size:19
Alignment explanation
Indices: 28635830--28635870 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
28635820 AGACTTTTTA
* *
28635830 TTTTTATTTTTATTTTTAC
1 TTTTTATCTTTATTTATAC
28635849 -TTTTATCTTTATTTAT-C
1 TTTTTATCTTTATTTATAC
28635866 TTTTT
1 TTTTT
28635871 CAATTACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTATCTTTATTTATAC
Found at i:28656243 original size:16 final size:16
Alignment explanation
Indices: 28656224--28656254 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28656214 CTTACATTTA
*
28656224 GACAGGCTCTCACTTT
1 GACAGGCTCGCACTTT
28656240 GACAGGCTCGCACTT
1 GACAGGCTCGCACTT
28656255 GGTTTACTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.32, G:0.23, T:0.26
Consensus pattern (16 bp):
GACAGGCTCGCACTTT
Found at i:28657616 original size:26 final size:26
Alignment explanation
Indices: 28657580--28657630 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
28657570 CTTTGACATC
28657580 TTGCTGAGCTTGCAACTTGCACATTT
1 TTGCTGAGCTTGCAACTTGCACATTT
*
28657606 TTGCTGAGCTTGCAGCTTGCACATT
1 TTGCTGAGCTTGCAACTTGCACATT
28657631 GGAAAGCTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.37
Consensus pattern (26 bp):
TTGCTGAGCTTGCAACTTGCACATTT
Found at i:28660959 original size:16 final size:16
Alignment explanation
Indices: 28660940--28660970 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28660930 CTTACATTTA
*
28660940 GACAGGCTCTCACTTT
1 GACAGGCTCGCACTTT
28660956 GACAGGCTCGCACTT
1 GACAGGCTCGCACTT
28660971 GGTTTACTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.32, G:0.23, T:0.26
Consensus pattern (16 bp):
GACAGGCTCGCACTTT
Found at i:28664531 original size:2 final size:2
Alignment explanation
Indices: 28664519--28664570 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
28664509 ATTCAGCTAT
*
28664519 CA CA CA TA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28664561 CA CA CA CA CA
1 CA CA CA CA CA
28664571 TATATATTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.48, G:0.00, T:0.02
Consensus pattern (2 bp):
CA
Found at i:28666883 original size:19 final size:19
Alignment explanation
Indices: 28666859--28666897 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
28666849 AAAAATAGAG
28666859 TAAGGAAGTCATCCTTACC
1 TAAGGAAGTCATCCTTACC
28666878 TAAGGAAGTCATCCTTACC
1 TAAGGAAGTCATCCTTACC
28666897 T
1 T
28666898 GAAGCCTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (19 bp):
TAAGGAAGTCATCCTTACC
Found at i:28667993 original size:22 final size:22
Alignment explanation
Indices: 28667968--28668010 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28667958 TTTAAAAGTG
28667968 TTTTATTAGTATTTTTATATTT
1 TTTTATTAGTATTTTTATATTT
* * *
28667990 TTTTGTTATTGTTTTTATATT
1 TTTTATTAGTATTTTTATATT
28668011 AATATGTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (22 bp):
TTTTATTAGTATTTTTATATTT
Found at i:28668026 original size:22 final size:23
Alignment explanation
Indices: 28667978--28668027 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
28667968 TTTTATTAGT
** *
28667978 ATTTTTATATTTTTTTGTTATTG
1 ATTTTTATATTAATATGTTATTG
28668001 -TTTTTATATTAATATGTTA-TG
1 ATTTTTATATTAATATGTTATTG
28668022 ATTTTT
1 ATTTTT
28668028 TAAATTTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.70
Consensus pattern (23 bp):
ATTTTTATATTAATATGTTATTG
Found at i:28668379 original size:25 final size:25
Alignment explanation
Indices: 28668351--28668401 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
28668341 AATAAGAAAG
28668351 ATCTAAATGCTACACTAAAAAAAAA
1 ATCTAAATGCTACACTAAAAAAAAA
28668376 ATCTAAATGCTACACTAAAAAAAAA
1 ATCTAAATGCTACACTAAAAAAAAA
28668401 A
1 A
28668402 GTTATATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.61, C:0.16, G:0.04, T:0.20
Consensus pattern (25 bp):
ATCTAAATGCTACACTAAAAAAAAA
Found at i:28669289 original size:22 final size:22
Alignment explanation
Indices: 28669264--28669307 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
28669254 CTTGAATATC
28669264 CAATTTATTCAACACATTTAAT
1 CAATTTATTCAACACATTTAAT
28669286 CAATTTATTCAACACATTTAAT
1 CAATTTATTCAACACATTTAAT
28669308 AATACAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (22 bp):
CAATTTATTCAACACATTTAAT
Found at i:28670005 original size:20 final size:20
Alignment explanation
Indices: 28669980--28670017 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28669970 TCGGAAGTGT
*
28669980 CAACACCTAACAAATATTGG
1 CAACACCCAACAAATATTGG
28670000 CAACACCCAACAAATATT
1 CAACACCCAACAAATATT
28670018 TTTTCTTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.29, G:0.05, T:0.18
Consensus pattern (20 bp):
CAACACCCAACAAATATTGG
Found at i:28671821 original size:20 final size:20
Alignment explanation
Indices: 28671792--28671830 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28671782 ATAGTATAAT
*
28671792 AAAAAGGAAAAGAAAAAAAG
1 AAAAAAGAAAAGAAAAAAAG
28671812 AAAAAAGAAAAGAAAAAAA
1 AAAAAAGAAAAGAAAAAAA
28671831 CTTTAACCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAAAGAAAAAAAG
Found at i:28671829 original size:12 final size:12
Alignment explanation
Indices: 28671792--28671830 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
28671782 ATAGTATAAT
*
28671792 AAAAAGGAAAAGA
1 AAAAAAGAAAA-A
28671805 AAAAAAGAAAAA
1 AAAAAAGAAAAA
*
28671817 AGAAAAGAAAAA
1 AAAAAAGAAAAA
28671829 AA
1 AA
28671831 CTTTAACCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:28671923 original size:7 final size:7
Alignment explanation
Indices: 28671911--28671943 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
28671901 GCCCCCAGCT
28671911 CCCTCTC
1 CCCTCTC
28671918 CCCTCTC
1 CCCTCTC
28671925 CCCTCTC
1 CCCTCTC
28671932 CCCTCTC
1 CCCTCTC
28671939 TCCCT
1 -CCCT
28671944 TTTTTTTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.84
8 4 0.16
ACGTcount: A:0.00, C:0.70, G:0.00, T:0.30
Consensus pattern (7 bp):
CCCTCTC
Found at i:28671928 original size:14 final size:15
Alignment explanation
Indices: 28671909--28671943 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
28671899 TCGCCCCCAG
28671909 CTCCCTCTCCCCTCT
1 CTCCCTCTCCCCTCT
28671924 C-CCCTCTCCCCTCT
1 CTCCCTCTCCCCTCT
28671938 CTCCCT
1 CTCCCT
28671944 TTTTTTTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (15 bp):
CTCCCTCTCCCCTCT
Found at i:28672362 original size:3 final size:3
Alignment explanation
Indices: 28672354--28672386 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
28672344 TCCTTTTTAT
*
28672354 TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28672387 GTATATGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:28672407 original size:14 final size:15
Alignment explanation
Indices: 28672382--28672410 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28672372 TTATTATTAG
28672382 TATTAGTATATGTTT
1 TATTAGTATATGTTT
28672397 TATTA-TATATGTTT
1 TATTAGTATATGTTT
28672411 ATATCTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (15 bp):
TATTAGTATATGTTT
Found at i:28672561 original size:24 final size:26
Alignment explanation
Indices: 28672516--28672563 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
28672506 TATGTTATGA
*
28672516 ATATATTTTTTATATATGTTATATAC
1 ATATATTTTTTATATATATTATATAC
28672542 ATATATTTTTT-TA-ATATTATAT
1 ATATATTTTTTATATATATTATAT
28672564 TTTTTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 2 0.10
26 11 0.52
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (26 bp):
ATATATTTTTTATATATATTATATAC
Found at i:28672564 original size:16 final size:18
Alignment explanation
Indices: 28672542--28672579 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
28672532 TGTTATATAC
28672542 ATATATTTTTTTA-ATATT
1 ATAT-TTTTTTTATATATT
28672560 ATATTTTTTTTATATATT
1 ATATTTTTTTTATATATT
28672578 AT
1 AT
28672580 TATGTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
ATATTTTTTTTATATATT
Found at i:28672580 original size:16 final size:16
Alignment explanation
Indices: 28672543--28672579 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
28672533 GTTATATACA
28672543 TATATTTTTTTAATAT
1 TATATTTTTTTAATAT
28672559 TATATTTTTTTTATATAT
1 TATA-TTTTTTTA-ATAT
28672577 TAT
1 TAT
28672580 TATGTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.21
17 8 0.42
18 7 0.37
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATATTTTTTTAATAT
Found at i:28672598 original size:24 final size:24
Alignment explanation
Indices: 28672480--28672685 Score: 93
Period size: 24 Copynumber: 8.8 Consensus size: 24
28672470 TTCTAATACG
*
28672480 TATA-TATTATGTAAATATTTTAA
1 TATATTATTATGTATATATTTTAA
* * *
28672503 TACTA-TGTTATGAATATATTTTTTA
1 TA-TATTATTATGTATATA-TTTTAA
** **
28672528 TATATGT-TATATACATATATTTTTT
1 TATAT-TAT-TATGTATATATTTTAA
28672553 TAATATTA-TAT-T-T-T-TTTT-A
1 T-ATATTATTATGTATATATTTTAA
28672572 TATATTATTATGTATATATTTTAA
1 TATATTATTATGTATATATTTTAA
*
28672596 TATCATTA--AT-TATATATTTTTA
1 TAT-ATTATTATGTATATATTTTAA
28672618 TACTATT-TTATGTATATATTTCT-A
1 TA-TATTATTATGTATATATTT-TAA
*
28672642 -ATATTATATATTGAATAT-TTTTAA
1 TATATTAT-TA-TGTATATATTTTAA
* *
28672666 TACCATTATTATTTATATAT
1 TA-TATTATTATGTATATAT
28672686 ATACGTACGT
Statistics
Matches: 143, Mismatches: 14, Indels: 50
0.69 0.07 0.24
Matches are distributed among these distances:
18 6 0.04
19 4 0.03
20 5 0.03
21 2 0.01
22 22 0.15
23 14 0.10
24 42 0.29
25 30 0.21
26 18 0.13
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (24 bp):
TATATTATTATGTATATATTTTAA
Found at i:28672603 original size:22 final size:22
Alignment explanation
Indices: 28672567--28672674 Score: 78
Period size: 23 Copynumber: 4.7 Consensus size: 22
28672557 ATTATATTTT
*
28672567 TTTTATATATTATTATGTATATA
1 TTTTA-ATATCATTATGTATATA
28672590 TTTTAATATCATTAAT-TATATA
1 TTTTAATATCATT-ATGTATATA
*
28672612 TTTTTATACTAT-TTTATGTATATA
1 -TTTTA-A-TATCATTATGTATATA
* *
28672636 TTTCTAATATTATATATTGAATAT-
1 TTT-TAATATCAT-TA-TGTATATA
*
28672660 TTTTAATACCATTAT
1 TTTTAATATCATTAT
28672675 TATTTATATA
Statistics
Matches: 70, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
21 1 0.01
22 18 0.26
23 26 0.37
24 16 0.23
25 9 0.13
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (22 bp):
TTTTAATATCATTATGTATATA
Found at i:28672644 original size:47 final size:47
Alignment explanation
Indices: 28672555--28672685 Score: 153
Period size: 47 Copynumber: 2.8 Consensus size: 47
28672545 TATTTTTTTA
*
28672555 ATATTATATTTTTTTTATA-TATTATTATGTATATATTTTAATATCAT
1 ATATTATA-TATTTTTATACTATTATTATGTATATATTTTAATATCAT
*
28672602 -TAATTATATATTTTTATACTATT-TTATGTATATATTTCTAATATTAT
1 AT-ATTATATATTTTTATACTATTATTATGTATATATTT-TAATATCAT
* *
28672649 ATATTGA-ATATTTTTAATACCATTATTATTTATATAT
1 ATATT-ATATATTTTT-ATACTATTATTATGTATATAT
28672686 ATACGTACGT
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
46 24 0.33
47 29 0.40
48 9 0.12
49 11 0.15
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (47 bp):
ATATTATATATTTTTATACTATTATTATGTATATATTTTAATATCAT
Found at i:28672773 original size:22 final size:22
Alignment explanation
Indices: 28672748--28673232 Score: 90
Period size: 23 Copynumber: 21.4 Consensus size: 22
28672738 ATTTCTAATG
*
28672748 TATATATA-TATCGTATATGTTT
1 TATATATATTAT-GTATATATTT
*
28672770 TATAAATATTATGTATATATTT
1 TATATATATTATGTATATATTT
*
28672792 TA-ATATTATTAGTTATATATATTT
1 TATATA-TATTA--TGTATATATTT
28672816 TATACTAT-TTCATGTATATATTT
1 TATA-TATATT-ATGTATATATTT
** *
28672839 T-TATATTATCCT-TAT-TATTAG
1 TATATA-TATTATGTATATATT-T
***
28672860 TAT-TAATATTA-GTAT-GCGTT
1 TATAT-ATATTATGTATATATTT
28672880 T-TAT-TA-TATGTATATATCTT
1 TATATATATTATGTATATAT-TT
28672900 TA-ATATATATATGTATATA-TT
1 TATATATAT-TATGTATATATTT
*
28672921 TATGTAATATTAT-TAATAGTTATTT
1 TATAT-ATATTATGT-ATA--TATTT
* *
28672946 TTTA-ACATTAT-TAT-TATTT
1 TATATATATTATGTATATATTT
*
28672965 CTAATATGTATATACTATGTAAATATTT
1 -T-ATA--TATAT--TATGTATATATTT
*
28672993 TAATACTATATTATGTATACATTT
1 T-ATA-TATATTATGTATATATTT
** *
28673017 TACATATATATTACATATATATATG
1 T--ATATATATTATGTATATAT-TT
* * * *
28673042 TCT-TTTAATAT-TGTAT-TTT
1 TATATATATTATGTATATATTT
*
28673061 TATATATA--ATATATATATTT
1 TATATATATTATGTATATATTT
* * *
28673081 CGAATACTATATTA--TATTTTTTT
1 --TATA-TATATTATGTATATATTT
* *
28673104 TACATATTATCTTATGTCTATATTT
1 T--ATA-TATATTATGTATATATTT
* *
28673129 AATACTATATTATGTATGTATTT
1 TATA-TATATTATGTATATATTT
* * *
28673152 TTTAACGCCATATTATGTACATATTT
1 TAT-A---TATATTATGTATATATTT
*
28673178 T-TA-ATACTATGTATATACTTT
1 TATATATATTATGTATATA-TTT
*
28673199 GTAATACTATTATTATGTTTATATTT
1 -T-ATA-TA-TATTATGTATATATTT
28673225 TA-ATATAT
1 TATATATAT
28673233 GTACGTATGT
Statistics
Matches: 339, Mismatches: 64, Indels: 121
0.65 0.12 0.23
Matches are distributed among these distances:
17 2 0.01
18 8 0.02
19 13 0.04
20 31 0.09
21 35 0.10
22 49 0.14
23 77 0.23
24 49 0.14
25 21 0.06
26 31 0.09
27 18 0.05
28 5 0.01
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (22 bp):
TATATATATTATGTATATATTT
Found at i:28672788 original size:24 final size:22
Alignment explanation
Indices: 28672761--28672843 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 22
28672751 ATATATATCG
28672761 TATATGTTTTATAAATATTATGTA
1 TATAT-TTTTAT-AATATTATGTA
* *
28672785 TATATTTTAATATTATTA-GTTA
1 TATATTTTTATAATATTATG-TA
*
28672807 TATATATTTTATACTATTTCATGTA
1 TATAT-TTTTATAATA-TT-ATGTA
28672832 TATATTTTTATA
1 TATATTTTTATA
28672844 TTATCCTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
21 1 0.02
22 13 0.26
23 13 0.26
24 14 0.28
25 8 0.16
26 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (22 bp):
TATATTTTTATAATATTATGTA
Found at i:28673007 original size:24 final size:24
Alignment explanation
Indices: 28672973--28673029 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
28672963 TTCTAATATG
* *
28672973 TATATACTATGTAAATATTTTA-A
1 TATATATTATGTAAACATTTTACA
*
28672996 TACTATATTATGTATACATTTTACA
1 TA-TATATTATGTAAACATTTTACA
28673021 TATATATTA
1 TATATATTA
28673030 CATATATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.07
24 24 0.83
25 3 0.10
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (24 bp):
TATATATTATGTAAACATTTTACA
Found at i:28673035 original size:24 final size:24
Alignment explanation
Indices: 28672989--28673035 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
28672979 CTATGTAAAT
**
28672989 ATTTTAATACTATATTATGTATAC
1 ATTTTAATACTATATTACATATAC
28673013 ATTTTACATA-TATATTACATATA
1 ATTTTA-ATACTATATTACATATA
28673036 TATATGTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (24 bp):
ATTTTAATACTATATTACATATAC
Found at i:28673190 original size:20 final size:21
Alignment explanation
Indices: 28673165--28673208 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
28673155 AACGCCATAT
*
28673165 TATGTACATA-TTTTTAATAC
1 TATGTACATACTTTGTAATAC
*
28673185 TATGTATATACTTTGTAATAC
1 TATGTACATACTTTGTAATAC
28673206 TAT
1 TAT
28673209 TATTATGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.50
Consensus pattern (21 bp):
TATGTACATACTTTGTAATAC
Found at i:28681553 original size:26 final size:24
Alignment explanation
Indices: 28681524--28681572 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
28681514 TTATTATAAT
28681524 GAATTAACATTGGCACTATGTGTGCG
1 GAATTAA-A-TGGCACTATGTGTGCG
* *
28681550 GAATTAAATGTCACTTTGTGTGC
1 GAATTAAATGGCACTATGTGTGC
28681573 AGATTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 13 0.62
25 1 0.05
26 7 0.33
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (24 bp):
GAATTAAATGGCACTATGTGTGCG
Found at i:28685632 original size:72 final size:72
Alignment explanation
Indices: 28685515--28685655 Score: 273
Period size: 72 Copynumber: 2.0 Consensus size: 72
28685505 AAGGGAACCG
28685515 TTATCCGTTCACTGCTAGGCTGAATTTCTTCTGTACCAATAACATAGCAGAATATGAGGCCTGTA
1 TTATCCGTTCACTGCTAGGCTGAATTTCTTCTGTACCAATAACATAGCAGAATATGAGGCCTGTA
28685580 TCATCCA
66 TCATCCA
*
28685587 TTATCTGTTCACTGCTAGGCTGAATTTCTTCTGTACCAATAACATAGCAGAATATGAGGCCTGTA
1 TTATCCGTTCACTGCTAGGCTGAATTTCTTCTGTACCAATAACATAGCAGAATATGAGGCCTGTA
28685652 TCAT
66 TCAT
28685656 GGGACTTTGT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (72 bp):
TTATCCGTTCACTGCTAGGCTGAATTTCTTCTGTACCAATAACATAGCAGAATATGAGGCCTGTA
TCATCCA
Found at i:28688290 original size:78 final size:75
Alignment explanation
Indices: 28688099--28688452 Score: 448
Period size: 78 Copynumber: 4.6 Consensus size: 75
28688089 TTTATTTCTA
* ** *
28688099 TTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAAGACACGTTGAGTTATTTTC
1 TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGTTATTTTC
28688163 AATTTCTGTC
66 AATTTCTGTC
*
28688173 -TTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTT
1 TTTTC--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGA-G---TT
*
28688237 CTTTTCAATTTCT-TC
60 ATTTTCAATTTCTGTC
* *
28688252 TTTTCAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTCT
1 TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGA-G---TTAT
28688317 TTTCAATTTCT-TC
62 TTTCAATTTCTGTC
* * ** *
28688330 TTTTCAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCTTCAAGACACGTTGAGTTATTTTC
1 TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGTTATTTTC
28688395 AATTTCTGTC
66 AATTTCTGTC
28688405 -TTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
1 TTTTC--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
28688453 TCACATGCCG
Statistics
Matches: 252, Mismatches: 17, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
73 4 0.02
74 18 0.07
75 2 0.01
76 83 0.33
77 2 0.01
78 123 0.49
79 2 0.01
80 18 0.07
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (75 bp):
TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGTTATTTTC
AATTTCTGTC
Found at i:28688415 original size:154 final size:151
Alignment explanation
Indices: 28688099--28688452 Score: 450
Period size: 154 Copynumber: 2.3 Consensus size: 151
28688089 TTTATTTCTA
* ** *
28688099 TTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAAGACACGTTGAGTTATTTTC
1 TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGTTATTTTC
** *
28688163 AATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCT
66 AATTTCTGTCTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCT
*
28688228 GAGGTATTTCTTTTCAATTTCTTC
130 GAGG--TTTATTTTCAATTTCTTC
* *
28688252 TTTTCAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTCT
1 TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGA-G---TTAT
* *
28688317 TTTCAATTTCT-TCTTTTC-AAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCTTCAAGACA
62 TTTCAATTTCTGTC-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
28688380 CGTTGA-G-TTATTTTCAATTTCTGTC
126 CGCTGAGGTTTATTTTCAATTTCT-TC
28688405 -TTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
1 TTTTC--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
28688453 TCACATGCCG
Statistics
Matches: 178, Mismatches: 14, Indels: 17
0.85 0.07 0.08
Matches are distributed among these distances:
152 18 0.10
153 7 0.04
154 86 0.48
155 2 0.01
156 45 0.25
157 2 0.01
158 18 0.10
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (151 bp):
TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGTTATTTTC
AATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTG
AGGTTTATTTTCAATTTCTTC
Found at i:28688490 original size:14 final size:14
Alignment explanation
Indices: 28688467--28688516 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
28688457 ATGCCGAGGT
*
28688467 TTTTTAAAATTTTG
1 TTTTTCAAATTTTG
* *
28688481 TTTTTCAAATTCTA
1 TTTTTCAAATTTTG
28688495 TTTTT--AATTTCTG
1 TTTTTCAAATTT-TG
28688508 TTTTTCAAA
1 TTTTTCAAA
28688517 AATTAAGTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
12 4 0.14
13 6 0.21
14 16 0.57
15 2 0.07
ACGTcount: A:0.26, C:0.08, G:0.04, T:0.62
Consensus pattern (14 bp):
TTTTTCAAATTTTG
Found at i:28688546 original size:102 final size:103
Alignment explanation
Indices: 28688388--28688663 Score: 360
Period size: 102 Copynumber: 2.7 Consensus size: 103
28688378 CACGTTGAGT
* * *
28688388 TATTTTCAATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTAATTTCTGTTTTTC--AAAAAATCAAGTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
* * *
28688453 TCACATGCCGAGGT-TTTTTAAAATTTTGTTTTTCAAATTC
64 TCACATGCCGAGGTATTTTCAAAA-TCTGTTTTTCAAAATC
*
28688493 TATTTTTAATTTCTGTTTTTC-AAAAATTAAGTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 TATTTTTAATTTCTGTTTTTCAAAAAATCAAGTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
*
28688557 ACATGCTGAGGTATTTTCAAAATCTGTTTTTCAAAATC
66 ACATGCCGAGGTATTTTCAAAATCTGTTTTTCAAAATC
* * * * *
28688595 TGTTTTTAATTTCTTTTTTTTCAAAAAAACAACG-CATATTGTGAGATGTGAGTTGAGCCTCGGG
1 TATTTTTAATTTC-TGTTTTTCAAAAAATCAA-GTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
*
28688659 ACACA
64 TCACA
28688664 CTGAGGTATT
Statistics
Matches: 152, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
102 78 0.51
103 15 0.10
104 39 0.26
105 20 0.13
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (103 bp):
TATTTTTAATTTCTGTTTTTCAAAAAATCAAGTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
ACATGCCGAGGTATTTTCAAAATCTGTTTTTCAAAATC
Found at i:28688600 original size:13 final size:14
Alignment explanation
Indices: 28688570--28688601 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
28688560 TGCTGAGGTA
28688570 TTTTCAAAATCTGT
1 TTTTCAAAATCTGT
28688584 TTTTCAAAATCTGT
1 TTTTCAAAATCTGT
28688598 TTTT
1 TTTT
28688602 AATTTCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.25, C:0.12, G:0.06, T:0.56
Consensus pattern (14 bp):
TTTTCAAAATCTGT
Found at i:28688733 original size:79 final size:74
Alignment explanation
Indices: 28688612--28688842 Score: 270
Period size: 79 Copynumber: 3.1 Consensus size: 74
28688602 AATTTCTTTT
* * *
28688612 TTTTCAAAAAAA-CAACGCATATTGTGAGATGTGAGTTGAGCCTCGGGACACACTGAGGTATTTC
1 TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTA----
28688676 TTTTCAATTTCTG
62 TTTTCAATTTCTG
* *
28688689 CTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTT
1 -TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTATTT
28688754 TCAATTTCTG
65 TCAATTTCTG
* * * * *
28688764 TGCTTC--AAGAATCAACTGATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTAT
1 T-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACA--CTGAGGTAT
*
28688827 TTTCAAATTCTG
63 TTTCAATTTCTG
28688839 TTTT
1 TTTT
28688843 TAATTTATAT
Statistics
Matches: 135, Mismatches: 14, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
73 41 0.30
74 3 0.02
75 36 0.27
78 12 0.09
79 43 0.32
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (74 bp):
TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTATTTT
CAATTTCTG
Found at i:28688879 original size:344 final size:343
Alignment explanation
Indices: 28688238--28689558 Score: 1668
Period size: 344 Copynumber: 3.8 Consensus size: 343
28688228 GAGGTATTTC
* * ** * *
28688238 TTTTCAATTTCTTCTTTTCAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
1 TTTTTAATTTCTTTTTTTCAAAAAAACAACGCATATTGTGAGAGGTGAGTTGAGCCTCGGGACAC
* *
28688303 GCTGAGGTATTTCTTTTCAATTTCTTCTTTTC-AAAAAATTAACTCATATTGCGAGAGGTGAGTT
66 GCTGAGGTATTTCTTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
* * * * * ***
28688367 GAGCTTCAAGACACGTTGAGTTATTTTCAATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCG
131 GAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGT-TGTCTTCAAAAATCAACTCATATTGCG
*
28688432 AGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTTTTTTAAAATTTTGTTTTTCAAATTCTATT
195 AGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGG-----T---A------TTTTCAAATTCTGTT
* * *
28688497 TTTAATTTCTGTTTTTCAAAAATTAAGTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATG
246 TTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACATG
*
28688562 CTGAGGTATTTTCAAAATCTGTTTTTCAAAATCTG
311 CCGAGGTATTTTCAAAAT-TGTTTTTC-AAATCTG
*
28688597 TTTTTAATTTCTTTTTTTTCAAAAAAACAACGCATATTGTGAGATGTGAGTTGAGCCTCGGGACA
1 TTTTTAATTTC-TTTTTTTCAAAAAAACAACGCATATTGTGAGAGGTGAGTTGAGCCTCGGGACA
*
28688662 CACTGAGGTATTTCTTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGT
65 CGCTGAGGTATTTCTTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGT
* *
28688727 TGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTG-TG-CTTCAAGAATCAACTGATATTGCG
130 TGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCTTCAAAAATCAACTCATATTGCG
* *
28688790 AGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAAATTCTGTTTTTAATTTATATTT
195 AGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAAATTCTGTTTTTAATTTCTGTTT
*
28688855 TTCAAAAACCAACTCATATTGCGAG-GGTGAGTTGAGCCTTGGGTCACATGCCGAGGTATTTTCA
260 TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACATGCCGAGGTATTTTCA
28688919 AAATTTGTTTTTCAAATTCTG
325 AAA-TTGTTTTTCAAA-TCTG
* * * *
28688940 TTTTTAATTTCTGTTTTTCAAAAAAACAACGCATATTGTGAAAAGTGAGTTGAGCCTCGGGACAT
1 TTTTTAATTTCTTTTTTTCAAAAAAACAACGCATATTGTGAGAGGTGAGTTGAGCCTCGGGACAC
*
28689005 GCTAAGGTATTTCTTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
66 GCTGAGGTATTTCTTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
*
28689070 GAGCCTCAGAACACGCTGAGGTATTTTCAATTTCTGTTTTTTCAATTTCTGTTCTTCAAAAATCA
131 GAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTG-----------T-TG-TCTTCAAAAATCA
* *
28689135 ACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGTATTTTTAAATTCTGTTTT
183 ACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAAATTCTGTTTT
28689200 TAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACATGCC
248 TAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACATGCC
28689265 GAGGTATTTTC-AAA-------T----TCTG
313 GAGGTATTTTCAAAATTGTTTTTCAAATCTG
* **
28689284 TTTTTAATTTCTATTTAGCAAAAAAACAACGCATATTGTGAGAGGTGAGTTGAGCCTCGGGACAC
1 TTTTTAATTTCTTTTTTTCAAAAAAACAACGCATATTGTGAGAGGTGAGTTGAGCCTCGGGACAC
28689349 GCTGAGGTATTTCTTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
66 GCTGAGGTATTTCTTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
* * * * *
28689414 GAGCCTCGGGTCACATGCCGAGGTATTTTCAAATTCTGTTTTTAATTTCTGTTTTCCAAAAATCA
131 GAGCCTCAGG--ACACGCTGAGGTATTTTCAATTTCTG---------T-TGTCTT-CAAAAATCA
*
28689479 ACTCATATTTCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAAAATT-TGTTT
183 ACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTC-AAATTCTGTTT
* *
28689543 TTCAAATTCTTTTTTT
247 TT-AATTTCTGTTTTT
28689559 AATTTCTGTT
Statistics
Matches: 876, Mismatches: 61, Indels: 64
0.88 0.06 0.06
Matches are distributed among these distances:
342 151 0.17
343 66 0.08
344 262 0.30
345 16 0.02
346 23 0.03
349 1 0.00
350 1 0.00
353 1 0.00
355 2 0.00
357 110 0.13
358 91 0.10
359 11 0.01
360 78 0.09
361 63 0.07
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (343 bp):
TTTTTAATTTCTTTTTTTCAAAAAAACAACGCATATTGTGAGAGGTGAGTTGAGCCTCGGGACAC
GCTGAGGTATTTCTTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
GAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCTTCAAAAATCAACTCATATTGCGA
GAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAAATTCTGTTTTTAATTTCTGTTTT
TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACATGCCGAGGTATTTTCAA
AATTGTTTTTCAAATCTG
Found at i:28688935 original size:13 final size:14
Alignment explanation
Indices: 28688913--28688961 Score: 66
Period size: 13 Copynumber: 3.6 Consensus size: 14
28688903 TGCCGAGGTA
28688913 TTTTCAAAATT-TGT
1 TTTTC-AAATTCTGT
28688927 TTTTCAAATTCTGT
1 TTTTCAAATTCTGT
*
28688941 TTTT-AATTTCTGT
1 TTTTCAAATTCTGT
28688954 TTTTCAAA
1 TTTTCAAA
28688962 AAAACAACGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 17 0.55
14 14 0.45
ACGTcount: A:0.24, C:0.10, G:0.06, T:0.59
Consensus pattern (14 bp):
TTTTCAAATTCTGT
Found at i:28689005 original size:101 final size:100
Alignment explanation
Indices: 28688826--28689016 Score: 258
Period size: 101 Copynumber: 1.9 Consensus size: 100
28688816 TGCCGAGGTA
* * **
28688826 TTTTCAAATTCTGTTTTTAATTTATATTTTTCAAAAACCAACTCATATTGCGAGGGTGAGTTGAG
1 TTTTCAAATTCTGTTTTTAATTTATATTTTTCAAAAAACAACGCATATTGCGAAAGTGAGTTGAG
* *
28688891 CCTTGGGTCACATGCCGAGGTATTTTCAAAATTTGT
66 CCTCGGG-CACATGCCAAGGTATTTTCAAAATTTGT
* * *
28688927 TTTTCAAATTCTGTTTTTAATTTCTGTTTTTCAAAAAAACAACGCATATTGTGAAAAGTGAGTTG
1 TTTTCAAATTCTGTTTTTAATTTATATTTTTC-AAAAAACAACGCATATTGCG-AAAGTGAGTTG
*
28688992 AGCCTCGGG-ACATGCTAAGGTATTT
64 AGCCTCGGGCACATGCCAAGGTATTT
28689017 CTTTTCAATT
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
101 44 0.56
102 17 0.22
103 17 0.22
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (100 bp):
TTTTCAAATTCTGTTTTTAATTTATATTTTTCAAAAAACAACGCATATTGCGAAAGTGAGTTGAG
CCTCGGGCACATGCCAAGGTATTTTCAAAATTTGT
Found at i:28689075 original size:79 final size:80
Alignment explanation
Indices: 28688940--28689529 Score: 448
Period size: 88 Copynumber: 7.0 Consensus size: 80
28688930 TCAAATTCTG
* * * * *
28688940 TTTTTAATTTCTGTTTTTCAAAAAAA-CAACGCATATTGTGAAAAGTGAGTTGAGCCTCGGGACA
1 TTTTTAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACA
*
28689004 TGCTAAGGTATTTC-
66 TGCTGAGGTATTTCA
* * *
28689018 TTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAACA
1 TTTTTAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACA
*
28689083 CGCTGAGGTATTTTCAA
66 TGCTGAGGTA-TTTC-A
28689100 TTTCTGTTTTTTCAATTTCTG-TTCTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 -------TTTTT-AATTTCTGCTT-TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
*
28689162 CTCGGGTCACATGCTGAGGTATTTTTAAA
57 CTCGGG--ACATGCTGAGGTA--TTT-CA
* * *** *
28689191 TTCTGTT--TTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTG
1 TT-T-TTAATTT--CTGCT-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
*
28689254 GGTCACATGCCGAGGTATTTTCAAA
61 GG--ACATGCTGAGGTA-TTTC--A
* * * *
28689279 TTCTGTTTTTAATTTCT-ATTTAGCAAAAAAA-CAACGCATATTGTGAGAGGTGAGTTGAGCCTC
1 -----TTTTTAATTTCTGCTTT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
*
28689342 GGGACACGCTGAGGTATTTC-
60 GGGACATGCTGAGGTATTTCA
*
28689362 TTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTTAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG--A
*
28689427 CATGCCGAGGTATTTTCAAA
64 CATGCTGAGGTA-TTTC--A
* *
28689447 TTCTGTTTTTAATTTCTG-TTTTC-CAAAAATCAACTCATATTTCGAGAGGTGAGTTGAGCCTCG
1 -----TTTTTAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
*
28689510 GGTCACATGCCGAGGTATTT
61 GG--ACATGCTGAGGTATTT
28689530 TCAAAATTTG
Statistics
Matches: 422, Mismatches: 42, Indels: 87
0.77 0.08 0.16
Matches are distributed among these distances:
78 43 0.10
79 76 0.18
80 4 0.01
81 11 0.03
82 4 0.01
83 3 0.01
84 2 0.00
85 2 0.00
86 9 0.02
87 19 0.05
88 149 0.35
89 45 0.11
90 41 0.10
91 8 0.02
92 1 0.00
93 5 0.01
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (80 bp):
TTTTTAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACA
TGCTGAGGTATTTCA
Found at i:28689113 original size:15 final size:15
Alignment explanation
Indices: 28689093--28689122 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28689083 CGCTGAGGTA
28689093 TTTTCAATTTCTGTT
1 TTTTCAATTTCTGTT
28689108 TTTTCAATTTCTGTT
1 TTTTCAATTTCTGTT
28689123 CTTCAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (15 bp):
TTTTCAATTTCTGTT
Found at i:28689127 original size:14 final size:15
Alignment explanation
Indices: 28689095--28689128 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28689085 CTGAGGTATT
*
28689095 TTCAATTTCTGTTTT
1 TTCAATTTCTGTTTC
28689110 TTCAATTTCTG-TTC
1 TTCAATTTCTGTTTC
28689124 TTCAA
1 TTCAA
28689129 AAATCAACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.59
Consensus pattern (15 bp):
TTCAATTTCTGTTTC
Found at i:28689201 original size:13 final size:13
Alignment explanation
Indices: 28689183--28689213 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28689173 TGCTGAGGTA
28689183 TTTTTAAATTCTG
1 TTTTTAAATTCTG
*
28689196 TTTTTAATTTCTG
1 TTTTTAAATTCTG
28689209 TTTTT
1 TTTTT
28689214 CAAAAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.71
Consensus pattern (13 bp):
TTTTTAAATTCTG
Found at i:28689205 original size:88 final size:87
Alignment explanation
Indices: 28689018--28689544 Score: 659
Period size: 88 Copynumber: 6.1 Consensus size: 87
28689008 AAGGTATTTC
* * *
28689018 TTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AG-AA
1 TTTTTAATTTCTG-TTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
* * *
28689081 CACGCTGAGGTATTTTCAATTTCTG
63 CATGCCGAGGTATTTTCAAATTCTG
28689106 TTTTTTCAATTTCTGTTCTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 -TTTTT-AATTTCTGTT-TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
* *
28689171 CATGCTGAGGTATTTTTAAATTCTG
63 CATGCCGAGGTATTTTCAAATTCTG
*
28689196 TTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACA
1 TTTTTAATTTCTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA
28689261 TGCCGAGGTATTTTCAAATTCTG
65 TGCCGAGGTATTTTCAAATTCTG
* * * * *
28689284 TTTTTAATTTCTATTTAGCAAAAAAACAACGCATATTGTGAGAGGTGAGTTGAGCCTCGGG--AC
1 TTTTTAATTTCTGTTT-TC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* *
28689347 ACGCTGAGGTA---T----TTC--
64 ATGCCGAGGTATTTTCAAATTCTG
* *
28689362 TTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTTAATTTCTG-TTTT--CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
28689427 CATGCCGAGGTATTTTCAAATTCTG
63 CATGCCGAGGTATTTTCAAATTCTG
*
28689452 TTTTTAATTTCTGTTTTCCAAAAATCAACTCATATTTCGAGAGGTGAGTTGAGCCTCGGGTCACA
1 TTTTTAATTTCTGTTTT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA
28689517 TGCCGAGGTATTTTCAAAATT-TG
65 TGCCGAGGTATTTTC-AAATTCTG
28689540 TTTTT
1 TTTTT
28689545 CAAATTCTTT
Statistics
Matches: 386, Mismatches: 30, Indels: 45
0.84 0.07 0.10
Matches are distributed among these distances:
78 11 0.03
79 41 0.11
80 3 0.01
81 11 0.03
84 2 0.01
87 14 0.04
88 198 0.51
89 60 0.16
90 46 0.12
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (87 bp):
TTTTTAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACAT
GCCGAGGTATTTTCAAATTCTG
Found at i:28689392 original size:256 final size:260
Alignment explanation
Indices: 28689035--28689713 Score: 806
Period size: 256 Copynumber: 2.5 Consensus size: 260
28689025 TTTCTGCTTT
* * * *
28689035 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAACACGCTGAGGTATTTTCAA
1 TCAAAAAAA-CAACGCATATTGTGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGG-----T--A
28689100 TTTCTGTTTTTTCAATTTCTGTTCTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
58 TTTC---TTTTTCAATTTCTGTTCTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
* * *
28689165 GGGTCACATGCTGAGGTATTTTTAAATTCTGTTTTTAATTTCTGTTTTTCAAAAATCAACTCATA
120 GGGTCACATGCCGAGGTATTTTCAAATTCTGTTTTTAATTTCTGTTTTCCAAAAATCAACTCATA
*
28689230 TTGCGAGAGGTGAGTTGAGCCTTGGGTCACATGCCGAGGTATTTTC-AAATTCTGTTTTT-AA-T
185 TTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAAAATT-TGTTTTTAAATT
28689292 TTCT-ATTT-AG
249 TTCTAATTTCAG
28689302 -CAAAAAAACAACGCATATTGTGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTC-TTT
1 TCAAAAAAACAACGCATATTGTGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTCTTTT
28689365 TCAATTTCTGCTT-TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA
66 TCAATTTCTG-TTCTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA
*
28689429 TGCCGAGGTATTTTCAAATTCTGTTTTTAATTTCTGTTTTCCAAAAATCAACTCATATTTCGAGA
128 TGCCGAGGTATTTTCAAATTCTGTTTTTAATTTCTGTTTTCCAAAAATCAACTCATATTGCGAGA
*
28689494 GGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAAAATTTGTTTTTCAAATTCTTTTTTT
193 GGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAAAATTTGTTTTT-AAA----TTTTCT
*
28689559 AATTTCTG
253 AATTTCAG
*
28689567 TTTTTC-AAAAAACAACGCATATTGTGAGAGGTGAGTTGAGCCTCAGTGACACGCTGAGGTATTT
1 ----TCAAAAAAACAACGCATATTGTGAGAGGTGAGTTGAGCCTC-GGGACACGCTGAGG-----
* * *
28689631 TCAATTTCTGTTTTTTCAA-TTCATG-T-TTCAACAATCAACTCATATTGTGAGAAGTGAGTTGA
56 T--ATTTC---TTTTTCAATTTC-TGTTCTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
*
28689693 GCCTCGGGTCACAGGCCGAGG
115 GCCTCGGGTCACATGCCGAGG
28689714 ATAAAGATTG
Statistics
Matches: 365, Mismatches: 16, Indels: 52
0.84 0.04 0.12
Matches are distributed among these distances:
254 16 0.04
255 2 0.01
256 151 0.41
257 5 0.01
258 7 0.02
260 1 0.00
263 4 0.01
264 4 0.01
265 43 0.12
266 8 0.02
269 38 0.10
270 14 0.04
275 1 0.00
277 55 0.15
279 4 0.01
280 3 0.01
281 9 0.02
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (260 bp):
TCAAAAAAACAACGCATATTGTGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTCTTTT
TCAATTTCTGTTCTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGC
CGAGGTATTTTCAAATTCTGTTTTTAATTTCTGTTTTCCAAAAATCAACTCATATTGCGAGAGGT
GAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAAAATTTGTTTTTAAATTTTCTAATTTCAG
Found at i:28689557 original size:14 final size:14
Alignment explanation
Indices: 28689527--28689575 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
28689517 TGCCGAGGTA
28689527 TTTTCAAAATT-TGT
1 TTTTC-AAATTCTGT
28689541 TTTTCAAATTCT-T
1 TTTTCAAATTCTGT
* *
28689554 TTTTTAATTTCTGT
1 TTTTCAAATTCTGT
28689568 TTTTCAAA
1 TTTTCAAA
28689576 AAACAACGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 16 0.55
14 13 0.45
ACGTcount: A:0.24, C:0.10, G:0.04, T:0.61
Consensus pattern (14 bp):
TTTTCAAATTCTGT
Found at i:28689639 original size:344 final size:332
Alignment explanation
Indices: 28688940--28689639 Score: 890
Period size: 344 Copynumber: 2.0 Consensus size: 332
28688930 TCAAATTCTG
* **
28688940 TTTTT-AATTTCTGTTTTTCAAAAAAACAACGCATATTGTGAAAAGTGAGTTGAGCCTCGGGACA
1 TTTTTCAATTTCTATTTAGCAAAAAAACAACGCATATTGTGAAAAGTGAGTTGAGCCTCGGGACA
*
28689004 TGCTAAGGTATTTCTTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGT
66 CGCTAAGGTATTTCTTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGT
* *
28689069 TGAGCCTCAGAACACGCTGAGGTATTTTCAATTTCTGTTTTTTCAATTTCTGTTCTTCAAAAATC
131 TGAGCCTCAGAACACGCCGAGGTATTTTCAAATTCTGTTTTTTCAATTTCTGTTCTTCAAAAATC
*
28689134 AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGTATTTTTAAATTCTGTTT
196 AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTAAATTCTGTTT
* * ** *
28689199 TTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACATGC
261 TTAATTTCTGTTTTTCAAAAAACAACGCATATTGCGAGAGGTGAGTTGAGCCTTCAGTCACACGC
28689264 CGAGGTA
326 CGAGGTA
* *
28689271 TTTTCAAATTCTGTTTTTAATTTCTATTTAGCAAAAAAACAACGCATATTGTGAGAGGTGAGTTG
1 -TTT----TTC-------AATTTCTATTTAGCAAAAAAACAACGCATATTGTGAAAAGTGAGTTG
*
28689336 AGCCTCGGGACACGCTGAGGTATTTCTTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTG
54 AGCCTCGGGACACGCTAAGGTATTTCTTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTG
* * *
28689401 CGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAAATTCTG-TTTTT-AATTTCT
119 CGAGAGGTGAGTTGAGCCTC-AG-AACACGCCGAGGTATTTTCAAATTCTGTTTTTTCAATTTCT
*
28689464 GTT-TTCCAAAAATCAACTCATATTTCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTAT
182 GTTCTT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGG---
* *
28689528 TTTCAAAATTTGTTTTTCAAATTCTTTTTTTAATTTCTGTTTTTCAAAAAACAACGCATATTGTG
243 --T----A----TTTTT-AAATTCTGTTTTTAATTTCTGTTTTTCAAAAAACAACGCATATTGCG
* *
28689593 AGAGGTGAGTTGAGCC-TCAGTGACACGCTGAGGTA
297 AGAGGTGAGTTGAGCCTTCAGTCACACGCCGAGGTA
28689628 -TTTTCAATTTCT
1 TTTTTCAATTTCT
28689640 GTTTTTTCAA
Statistics
Matches: 316, Mismatches: 23, Indels: 46
0.82 0.06 0.12
Matches are distributed among these distances:
332 3 0.01
336 2 0.01
343 2 0.01
344 195 0.62
345 6 0.02
346 23 0.07
349 1 0.00
351 3 0.01
353 1 0.00
355 2 0.01
357 19 0.06
358 59 0.19
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (332 bp):
TTTTTCAATTTCTATTTAGCAAAAAAACAACGCATATTGTGAAAAGTGAGTTGAGCCTCGGGACA
CGCTAAGGTATTTCTTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGT
TGAGCCTCAGAACACGCCGAGGTATTTTCAAATTCTGTTTTTTCAATTTCTGTTCTTCAAAAATC
AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTAAATTCTGTTT
TTAATTTCTGTTTTTCAAAAAACAACGCATATTGCGAGAGGTGAGTTGAGCCTTCAGTCACACGC
CGAGGTA
Found at i:28689649 original size:102 final size:102
Alignment explanation
Indices: 28689439--28689634 Score: 297
Period size: 102 Copynumber: 1.9 Consensus size: 102
28689429 TGCCGAGGTA
* *
28689439 TTTTCAAATTCTGTTTTTAATTTCTGTTTTCCAAAAATCAACTCATATTTCGAGAGGTGAGTTGA
1 TTTTCAAATTCTGTTTTTAATTTCTGTTTTCCAAAAAACAACGCATATTTCGAGAGGTGAGTTGA
* *
28689504 GCCTCGGGTCACATGCCGAGGTATTTTCAAAATTTGT
66 GCCTCGAGTCACACGCCGAGGTATTTTCAAAATTTGT
* *
28689541 TTTTCAAATTCTTTTTTTAATTTCTGTTTTTCAAAAAACAACGCATATTGT-GAGAGGTGAGTTG
1 TTTTCAAATTCTGTTTTTAATTTCTGTTTTCCAAAAAACAACGCATATT-TCGAGAGGTGAGTTG
* *
28689605 AGCCTC-AGTGACACGCTGAGGTATTTTCAA
65 AGCCTCGAGTCACACGCCGAGGTATTTTCAA
28689635 TTTCTGTTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
101 20 0.24
102 64 0.75
103 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.40
Consensus pattern (102 bp):
TTTTCAAATTCTGTTTTTAATTTCTGTTTTCCAAAAAACAACGCATATTTCGAGAGGTGAGTTGA
GCCTCGAGTCACACGCCGAGGTATTTTCAAAATTTGT
Found at i:28689690 original size:189 final size:192
Alignment explanation
Indices: 28689362--28689713 Score: 511
Period size: 189 Copynumber: 1.8 Consensus size: 192
28689352 GAGGTATTTC
* *
28689362 TTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGCTTTTCAAAAAAATCAACGCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCA
*
28689427 CATGCCGAGGTATTTTCAAATTCTGTTTTTAATTTCTGTTTTCCAAAAATCAACTCATATTTCGA
66 CACGCCGAGGTATTTTCAAATTCTGTTTTTAATTTCTGTTTTCCAAAAATCAACTCATATTTCGA
* *
28689492 GAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAAAATTTGTTTTTCAAATTCTT
131 GAAGTGAGTTGAGCCTCGGGTCACAGGCCGAGGTATTTTCAAAATTTGTTTTTCAAATTCTT
* * * *
28689554 TTTTTAATTTCTGTTTTTC-AAAAAA-CAACGCATATTGTGAGAGGTGAGTTGAGCCTC-AGTGA
1 TTTTCAATTTCTGCTTTTCAAAAAAATCAACGCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCA
* * *
28689616 CACGCTGAGGTATTTTCAATTTCTGTTTTTTCAA-TTCATG-TTT-CAACAATCAACTCATATTG
66 CACGCCGAGGTATTTTCAAATTCTG-TTTTT-AATTTC-TGTTTTCCAAAAATCAACTCATATT-
28689678 T-GAGAAGTGAGTTGAGCCTCGGGTCACAGGCCGAGG
127 TCGAGAAGTGAGTTGAGCCTCGGGTCACAGGCCGAGG
28689714 ATAAAGATTG
Statistics
Matches: 144, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
189 75 0.52
190 42 0.29
191 10 0.07
192 17 0.12
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (192 bp):
TTTTCAATTTCTGCTTTTCAAAAAAATCAACGCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCA
CACGCCGAGGTATTTTCAAATTCTGTTTTTAATTTCTGTTTTCCAAAAATCAACTCATATTTCGA
GAAGTGAGTTGAGCCTCGGGTCACAGGCCGAGGTATTTTCAAAATTTGTTTTTCAAATTCTT
Found at i:28689801 original size:21 final size:21
Alignment explanation
Indices: 28689754--28689804 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
28689744 TTTTGCCTCC
**
28689754 TTGAAGTTGTAGTGGAGCTGA
1 TTGAAGTTGTAGTGGAGCACA
*
28689775 TCGAAGTT-TCAGTGGAGCACA
1 TTGAAGTTGT-AGTGGAGCACA
28689796 TTGAAGTTG
1 TTGAAGTTG
28689805 CAGATCTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.25, C:0.10, G:0.33, T:0.31
Consensus pattern (21 bp):
TTGAAGTTGTAGTGGAGCACA
Found at i:28691366 original size:3 final size:3
Alignment explanation
Indices: 28691358--28691406 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
28691348 TCCTTTTTGT
* *
28691358 TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA GTA TATA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
28691403 TTA T
1 TTA T
28691407 ATATGTATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:28691403 original size:18 final size:19
Alignment explanation
Indices: 28691359--28691418 Score: 70
Period size: 18 Copynumber: 3.2 Consensus size: 19
28691349 CCTTTTTGTT
*
28691359 TATTATTATTATTATTAT-
1 TATTATTATTATTAGTATA
*
28691377 TGTTATTATTATTAGTATA
1 TATTATTATTATTAGTATA
28691396 TATT-TTATTATATATGTATA
1 TATTATTATTAT-TA-GTATA
28691416 TAT
1 TAT
28691419 CTTTAATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 23 0.64
19 5 0.14
20 8 0.22
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
TATTATTATTATTAGTATA
Found at i:28691538 original size:25 final size:27
Alignment explanation
Indices: 28691501--28691562 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
28691491 TATGTAAATA
28691501 TTTTAATACTATGTTAT-GA-ATATATT
1 TTTTAATA-TATGTTATAGACATATATT
* *
28691527 TTTTTATATATGTTATATACATATATT
1 TTTTAATATATGTTATAGACATATATT
28691554 TTTTAATAT
1 TTTTAATAT
28691563 TATATTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.26
26 8 0.26
27 15 0.48
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (27 bp):
TTTTAATATATGTTATAGACATATATT
Found at i:28691566 original size:15 final size:16
Alignment explanation
Indices: 28691548--28691581 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
28691538 GTTATATACA
28691548 TATATTTTTTA-ATAT
1 TATATTTTTTATATAT
28691563 TATATTTTTTATATAT
1 TATATTTTTTATATAT
28691579 TAT
1 TAT
28691582 TATGTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATATTTTTTATATAT
Found at i:28691595 original size:24 final size:24
Alignment explanation
Indices: 28691484--28691650 Score: 101
Period size: 24 Copynumber: 7.3 Consensus size: 24
28691474 TTCTAATAGG
* *
28691484 TATA-TATTATGTAAATATTTTAA
1 TATATTATTATGTATATATTTTTA
* * *
28691507 TACTA-TGTTATGAATATATTTTTT
1 TA-TATTATTATGTATATATTTTTA
* * *
28691531 TATATATGTTATATACATATATTTT-
1 TATAT-TATTATGTATATAT-TTTTA
28691556 T-TA--A-TAT-TATAT-TTTTTA
1 TATATTATTATGTATATATTTTTA
28691574 TATATTATTATGTATATA-TTTTA
1 TATATTATTATGTATATATTTTTA
*
28691597 -ATATCATTA-GTTATATATTTTTA
1 TATATTATTATG-TATATATTTTTA
*
28691620 TACTATT-TTATGTATATATTTCTA
1 TA-TATTATTATGTATATATTTTTA
28691644 -ATATTAT
1 TATATTAT
28691651 ATATTGAATA
Statistics
Matches: 114, Mismatches: 13, Indels: 34
0.71 0.08 0.21
Matches are distributed among these distances:
17 4 0.04
18 2 0.02
19 6 0.05
20 3 0.03
21 2 0.02
22 21 0.18
23 21 0.18
24 35 0.31
25 16 0.14
26 4 0.04
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (24 bp):
TATATTATTATGTATATATTTTTA
Found at i:28691605 original size:22 final size:22
Alignment explanation
Indices: 28691484--28691640 Score: 92
Period size: 23 Copynumber: 6.9 Consensus size: 22
28691474 TTCTAATAGG
*
28691484 TATATATTATGTAAATATTTTAA
1 TATATATTATGTATATATTTT-A
* *
28691507 TACTATGTTATGAATATATTTTTTTA
1 TA-TATATTATG--TATA-TATTTTA
* * *
28691533 TATATGTTATATACATATATTT-
1 TATATATTATGTATATAT-TTTA
* *
28691555 T-T-TAATAT-TATATTTTTTA
1 TATATATTATGTATATATTTTA
28691574 TATATTATTATGTATATATTTTA
1 TATA-TATTATGTATATATTTTA
28691597 -ATATCATTA-GTTATATATTTTTA
1 TATAT-ATTATG-TATATA-TTTTA
*
28691620 TACTATTTTATGTATATATTT
1 TA-TATATTATGTATATATTT
28691641 CTAATATTAT
Statistics
Matches: 105, Mismatches: 13, Indels: 32
0.70 0.09 0.21
Matches are distributed among these distances:
18 3 0.03
19 6 0.06
20 5 0.05
21 3 0.03
22 21 0.20
23 26 0.25
24 18 0.17
25 12 0.11
26 6 0.06
27 5 0.05
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (22 bp):
TATATATTATGTATATATTTTA
Found at i:28691648 original size:22 final size:23
Alignment explanation
Indices: 28691575--28691687 Score: 92
Period size: 22 Copynumber: 4.8 Consensus size: 23
28691565 TATTTTTTAT
28691575 ATATTATTATGTATATATTT-TA
1 ATATTATTATGTATATATTTCTA
* *
28691597 ATATCATTA-GTTATATATTTTTA
1 ATATTATTATG-TATATATTTCTA
28691620 TACTATT-TTATGTATATATTTCTA
1 -A-TATTATTATGTATATATTTCTA
28691644 ATATTATATAT-TGA-ATATTTCTA
1 ATATTAT-TATGT-ATATATTTCTA
*
28691667 ATACCATTATTATTTATATAT
1 AT---ATTATTATGTATATAT
28691688 ATACGTACGT
Statistics
Matches: 75, Mismatches: 3, Indels: 22
0.75 0.03 0.22
Matches are distributed among these distances:
21 1 0.01
22 21 0.28
23 16 0.21
24 19 0.25
25 8 0.11
26 10 0.13
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.56
Consensus pattern (23 bp):
ATATTATTATGTATATATTTCTA
Found at i:28691775 original size:22 final size:22
Alignment explanation
Indices: 28691750--28691847 Score: 78
Period size: 22 Copynumber: 4.3 Consensus size: 22
28691740 ATTTCTAATG
*
28691750 TATATATA-TATCGTATATGTTT
1 TATATATATTAT-GTATATATTT
*
28691772 TATAAATATTATGTATATATTT
1 TATATATATTATGTATATATTT
28691794 TA-ATATTATTA-GTTATATATTTT
1 TATATA-TATTATG-TATATA-TTT
*
28691817 TTTATACTATTTCATGTATATATTT
1 TATATA-TA-TT-ATGTATATATTT
28691842 T-TATAT
1 TATATAT
28691848 TATCCTTATT
Statistics
Matches: 63, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.05
22 29 0.46
23 8 0.13
24 9 0.14
25 6 0.10
26 7 0.11
27 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (22 bp):
TATATATATTATGTATATATTT
Found at i:28692005 original size:24 final size:24
Alignment explanation
Indices: 28691971--28692036 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
28691961 TTCTAATATG
* *
28691971 TATATACTATGTAAATATTTTA-A
1 TATATATTATGTATATATTTTATA
*
28691994 TACTATATTATGTATACATTTTATA
1 TA-TATATTATGTATATATTTTATA
*
28692019 TATATATTACGTATATAT
1 TATATATTATGTATATAT
28692037 GCCTTTTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
23 2 0.06
24 31 0.86
25 3 0.08
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.50
Consensus pattern (24 bp):
TATATATTATGTATATATTTTATA
Found at i:28692094 original size:45 final size:45
Alignment explanation
Indices: 28692045--28692148 Score: 108
Period size: 45 Copynumber: 2.3 Consensus size: 45
28692035 ATGCCTTTTA
28692045 ATATTGTATTTTTATA-TATC-ATATATATATTTCGAATACTATATT
1 ATATTGTATTTTTATATTATCTATATATATATTT--AATACTATATT
* *
28692090 ATATT-T-TTTTACATATTATCTTATGTATATATTTAATACTATATT
1 ATATTGTATTTT-TATATTATC-TATATATATATTTAATACTATATT
*
28692135 ATGTATGTATTTTT
1 ATAT-TGTATTTTT
28692149 TAACGCCATA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
43 4 0.08
44 4 0.08
45 23 0.48
46 1 0.02
47 12 0.25
48 4 0.08
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.57
Consensus pattern (45 bp):
ATATTGTATTTTTATATTATCTATATATATATTTAATACTATATT
Found at i:28692185 original size:20 final size:21
Alignment explanation
Indices: 28692160--28692203 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
28692150 AACGCCATAT
*
28692160 TATGTACATA-TTTTTAATAC
1 TATGTACATACTTTGTAATAC
*
28692180 TATGTATATACTTTGTAATAC
1 TATGTACATACTTTGTAATAC
28692201 TAT
1 TAT
28692204 TATTATGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.50
Consensus pattern (21 bp):
TATGTACATACTTTGTAATAC
Found at i:28702749 original size:6 final size:6
Alignment explanation
Indices: 28702716--28702800 Score: 100
Period size: 6 Copynumber: 14.0 Consensus size: 6
28702706 ATAGAAAAAC
* *
28702716 AATATA AAT-AA AATAAAA TAAGAAA AATAAA AATAAA AATAAA AATAAA
1 AATAAA AATAAA AAT-AAA -AATAAA AATAAA AATAAA AATAAA AATAAA
* * *
28702765 AATAAA GATAAA AATAAA AATAAA CATAAA GATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
28702801 TGGACTTAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
5 4 0.06
6 58 0.84
7 5 0.07
8 2 0.03
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:28704422 original size:7 final size:7
Alignment explanation
Indices: 28704386--28704435 Score: 57
Period size: 7 Copynumber: 7.0 Consensus size: 7
28704376 AGTAATAGAG
*
28704386 AAATAGT
1 AAATAAT
*
28704393 AACATAAG
1 AA-ATAAT
28704401 AAATAAAT
1 AAAT-AAT
28704409 AAA-AAT
1 AAATAAT
28704415 AAATAAT
1 AAATAAT
28704422 AAATAAT
1 AAATAAT
28704429 AAATAAT
1 AAATAAT
28704436 GCTAATAAGG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
6 6 0.16
7 21 0.57
8 10 0.27
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (7 bp):
AAATAAT
Found at i:28705482 original size:93 final size:94
Alignment explanation
Indices: 28705323--28705533 Score: 361
Period size: 93 Copynumber: 2.3 Consensus size: 94
28705313 TTAAACAACT
* **
28705323 TAGGACACGCCTGTGTGTCCAGGCCGTGTGGGGTACATGGCTATATCACATGACCGTGGAACCTA
1 TAGGACACGCCCGTGTGTCCAGGCCGTGTGGGGTACATGGCTATATCACACAACCGTGGAACCTA
*
28705388 TTATCGTG-CCATGTTAAGTCACACGGCC
66 TTATCGCGCCCATGTTAAGTCACACGGCC
* *
28705416 TAGGACATGGCCGTGTGTCCAGGCCGTGTGGGGTACATGGCTATATCACACAACCGTGGAACCTA
1 TAGGACACGCCCGTGTGTCCAGGCCGTGTGGGGTACATGGCTATATCACACAACCGTGGAACCTA
28705481 TTATCGCGCCCATGTTAAGTCACACGGCC
66 TTATCGCGCCCATGTTAAGTCACACGGCC
28705510 TAGGACACGCCCGTGTGTCCAGGC
1 TAGGACACGCCCGTGTGTCCAGGC
28705534 TGTATGGGTC
Statistics
Matches: 109, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
93 67 0.61
94 42 0.39
ACGTcount: A:0.21, C:0.27, G:0.28, T:0.23
Consensus pattern (94 bp):
TAGGACACGCCCGTGTGTCCAGGCCGTGTGGGGTACATGGCTATATCACACAACCGTGGAACCTA
TTATCGCGCCCATGTTAAGTCACACGGCC
Found at i:28717396 original size:28 final size:29
Alignment explanation
Indices: 28717363--28717417 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
28717353 ATCCGAAATA
*
28717363 CTGATA-TCATGGCCCGAAGCCAAATCAG
1 CTGATATTCATGGCCCAAAGCCAAATCAG
28717391 CTGATATTCATGGCCCAAAGCCAAATC
1 CTGATATTCATGGCCCAAAGCCAAATC
28717418 GGTATAACTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (29 bp):
CTGATATTCATGGCCCAAAGCCAAATCAG
Found at i:28718450 original size:30 final size:29
Alignment explanation
Indices: 28718393--28718450 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
28718383 CCTTTTTACT
* * *
28718393 TTTCCCTCAAAACTTTTCCTCCTTCCCAC
1 TTTCCCCCAAAACTTTTACTCCCTCCCAC
28718422 TTTCCCCCAAAACTTTTACTCCCCTCCCA
1 TTTCCCCCAAAACTTTTACT-CCCTCCCA
28718451 TCCCAACCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.19, C:0.47, G:0.00, T:0.34
Consensus pattern (29 bp):
TTTCCCCCAAAACTTTTACTCCCTCCCAC
Found at i:28718822 original size:30 final size:29
Alignment explanation
Indices: 28718765--28718822 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
28718755 CCTTTTTACT
* * *
28718765 TTTCCCTCAAAACTTTTCCTCCTTCCCAC
1 TTTCCCCCAAAACTTTTACTCCCTCCCAC
28718794 TTTCCCCCAAAACTTTTACTCCCCTCCCA
1 TTTCCCCCAAAACTTTTACT-CCCTCCCA
28718823 TCCCAACCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.19, C:0.47, G:0.00, T:0.34
Consensus pattern (29 bp):
TTTCCCCCAAAACTTTTACTCCCTCCCAC
Found at i:28719036 original size:372 final size:372
Alignment explanation
Indices: 28718351--28719102 Score: 1495
Period size: 372 Copynumber: 2.0 Consensus size: 372
28718341 ATCAACCAAT
28718351 AATATTTTACATTTTTACCCCAAATTCCCAAACCTTTTTACTTTTCCCTCAAAACTTTTCCTCCT
1 AATATTTTACATTTTTACCCCAAATTCCCAAACCTTTTTACTTTTCCCTCAAAACTTTTCCTCCT
28718416 TCCCACTTTCCCCCAAAACTTTTACTCCCCTCCCATCCCAACCCCCCAATTTACCCAAAATCAAT
66 TCCCACTTTCCCCCAAAACTTTTACTCCCCTCCCATCCCAACCCCCCAATTTACCCAAAATCAAT
28718481 TTCCTACCAAAATTTTACTCTCCCATTTACTTTTTCTCAAAATTTTACTCCTAAAACCCTCAAAA
131 TTCCTACCAAAATTTTACTCTCCCATTTACTTTTTCTCAAAATTTTACTCCTAAAACCCTCAAAA
28718546 CTTTTTATTTTCCCCCAAAAAATTTTACTCCCTCTCACTTTCCCCCTAAAACTTTTACTCCTTTC
196 CTTTTTATTTTCCCCCAAAAAATTTTACTCCCTCTCACTTTCCCCCTAAAACTTTTACTCCTTTC
28718611 CCATCCCACCTCCCATTTACCCCAAACCTACCCCCTCCCCCAATTTTTTTTAATATTTTCCCTCC
261 CCATCCCACCTCCCATTTACCCCAAACCTACCCCCTCCCCCAATTTTTTTTAATATTTTCCCTCC
28718676 AAAATTTTACTTCCCCTATTTACTTTCCCTCAAACTTTTATTCCCCC
326 AAAATTTTACTTCCCCTATTTACTTTCCCTCAAACTTTTATTCCCCC
28718723 AATATTTTACATTTTTACCCCAAATTCCCAAACCTTTTTACTTTTCCCTCAAAACTTTTCCTCCT
1 AATATTTTACATTTTTACCCCAAATTCCCAAACCTTTTTACTTTTCCCTCAAAACTTTTCCTCCT
28718788 TCCCACTTTCCCCCAAAACTTTTACTCCCCTCCCATCCCAACCCCCCAATTTACCCAAAATCAAT
66 TCCCACTTTCCCCCAAAACTTTTACTCCCCTCCCATCCCAACCCCCCAATTTACCCAAAATCAAT
28718853 TTCCTACCAAAATTTTACTCTCCCATTTACTTTTTCTCAAAATTTTACTCCTAAAACCCTCAAAA
131 TTCCTACCAAAATTTTACTCTCCCATTTACTTTTTCTCAAAATTTTACTCCTAAAACCCTCAAAA
28718918 CTTTTTATTTTCCCCCAAAAAATTTTACTCCCTCTCACTTTCCCCCTAAAACTTTTACTCCTTTC
196 CTTTTTATTTTCCCCCAAAAAATTTTACTCCCTCTCACTTTCCCCCTAAAACTTTTACTCCTTTC
28718983 CCATCCCACCTCCCATTTACCCCAAACCTACCCCCTCCCCCAATTTTTTTTAATATTTTCCCTCC
261 CCATCCCACCTCCCATTTACCCCAAACCTACCCCCTCCCCCAATTTTTTTTAATATTTTCCCTCC
28719048 AAAATTTTACTTCCCCTATTTACTTTCCCTCAAACTTTTATTCCCCC
326 AAAATTTTACTTCCCCTATTTACTTTCCCTCAAACTTTTATTCCCCC
*
28719095 AATTTTTT
1 AATATTTT
28719103 TATTTTTCCC
Statistics
Matches: 379, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
372 379 1.00
ACGTcount: A:0.25, C:0.37, G:0.00, T:0.38
Consensus pattern (372 bp):
AATATTTTACATTTTTACCCCAAATTCCCAAACCTTTTTACTTTTCCCTCAAAACTTTTCCTCCT
TCCCACTTTCCCCCAAAACTTTTACTCCCCTCCCATCCCAACCCCCCAATTTACCCAAAATCAAT
TTCCTACCAAAATTTTACTCTCCCATTTACTTTTTCTCAAAATTTTACTCCTAAAACCCTCAAAA
CTTTTTATTTTCCCCCAAAAAATTTTACTCCCTCTCACTTTCCCCCTAAAACTTTTACTCCTTTC
CCATCCCACCTCCCATTTACCCCAAACCTACCCCCTCCCCCAATTTTTTTTAATATTTTCCCTCC
AAAATTTTACTTCCCCTATTTACTTTCCCTCAAACTTTTATTCCCCC
Found at i:28719688 original size:5 final size:5
Alignment explanation
Indices: 28719678--28719704 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
28719668 AAAAAATTTC
28719678 ATTCG ATTCG ATTCG ATTCG ATTCG AT
1 ATTCG ATTCG ATTCG ATTCG ATTCG AT
28719705 CAAATGCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (5 bp):
ATTCG
Found at i:28719933 original size:13 final size:14
Alignment explanation
Indices: 28719907--28719935 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
28719897 AGTTACTAGT
28719907 TTACTAAGTTAACC
1 TTACTAAGTTAACC
28719921 TTACTAA-TTAACC
1 TTACTAAGTTAACC
28719934 TT
1 TT
28719936 TAAATCAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.41
Consensus pattern (14 bp):
TTACTAAGTTAACC
Found at i:28721747 original size:10 final size:10
Alignment explanation
Indices: 28721708--28721751 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
28721698 TGAAAATAAG
28721708 AAAATATATT
1 AAAATATATT
*
28721718 -TAATATATT
1 AAAATATATT
**
28721727 TTAATATATT
1 AAAATATATT
28721737 AAAATATATT
1 AAAATATATT
28721747 AAAAT
1 AAAAT
28721752 TTTGGAACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
AAAATATATT
Found at i:28721797 original size:8 final size:8
Alignment explanation
Indices: 28721784--28721808 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28721774 TAATTTTAAG
28721784 AAAATTTA
1 AAAATTTA
28721792 AAAATTTA
1 AAAATTTA
28721800 AAAATTTA
1 AAAATTTA
28721808 A
1 A
28721809 TATATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAAATTTA
Found at i:28722662 original size:22 final size:22
Alignment explanation
Indices: 28722634--28722678 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
28722624 CTTTCTCTTC
*
28722634 TAGGGTTATGGTTTTTAATTTT
1 TAGGGTTAGGGTTTTTAATTTT
28722656 TAGGGTTAGGGTTTTTAATTTT
1 TAGGGTTAGGGTTTTTAATTTT
28722678 T
1 T
28722679 TTAATGGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.24, T:0.58
Consensus pattern (22 bp):
TAGGGTTAGGGTTTTTAATTTT
Found at i:28724354 original size:19 final size:19
Alignment explanation
Indices: 28724332--28724368 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28724322 ACTACATTCA
*
28724332 CCCACCGTAATTAAATTTT
1 CCCACCGTAATGAAATTTT
28724351 CCCACCGTAATGAAATTT
1 CCCACCGTAATGAAATTT
28724369 GTTATTAACT
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:0.32, C:0.27, G:0.08, T:0.32
Consensus pattern (19 bp):
CCCACCGTAATGAAATTTT
Found at i:28724955 original size:21 final size:20
Alignment explanation
Indices: 28724913--28724956 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
28724903 CGGGGTGGGA
*
28724913 TGGAAGGAAAGTAAAAGCTT
1 TGGAAGGAAAGTAAAAGATT
*
28724933 TGGAGGGAAAGTAAAAAGATT
1 TGGAAGGAAAGT-AAAAGATT
28724954 TGG
1 TGG
28724957 GGGTTTGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.43, C:0.02, G:0.34, T:0.20
Consensus pattern (20 bp):
TGGAAGGAAAGTAAAAGATT
Found at i:28726949 original size:33 final size:33
Alignment explanation
Indices: 28726912--28726976 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
28726902 GTGAATTTTT
*
28726912 CCTGAAACTAGACTCATTTGCCCATCTACATAA
1 CCTGAAACTAGACTCATTTGCCCATCCACATAA
*
28726945 CCTGAAACTAGACTCATTTTCCCATCCACATA
1 CCTGAAACTAGACTCATTTGCCCATCCACATA
28726977 TTTTTTTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.32, C:0.32, G:0.08, T:0.28
Consensus pattern (33 bp):
CCTGAAACTAGACTCATTTGCCCATCCACATAA
Found at i:28734414 original size:63 final size:63
Alignment explanation
Indices: 28734315--28734437 Score: 219
Period size: 63 Copynumber: 2.0 Consensus size: 63
28734305 ACAAGCTGCT
*
28734315 ACTCTGCGTACTAGTCGCTTTAAAAATCATATCTTGAGTTCTGAAACTCAAAATCCAGTTGCC
1 ACTCTGCATACTAGTCGCTTTAAAAATCATATCTTGAGTTCTGAAACTCAAAATCCAGTTGCC
* *
28734378 ACTCTGCATACTAGTCGCTTTAAAAATCATATCTTGATTTCTGAAACTCGAAATCCAGTT
1 ACTCTGCATACTAGTCGCTTTAAAAATCATATCTTGAGTTCTGAAACTCAAAATCCAGTT
28734438 CCGTGAATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (63 bp):
ACTCTGCATACTAGTCGCTTTAAAAATCATATCTTGAGTTCTGAAACTCAAAATCCAGTTGCC
Found at i:28740959 original size:39 final size:39
Alignment explanation
Indices: 28740869--28741032 Score: 154
Period size: 40 Copynumber: 4.1 Consensus size: 39
28740859 CGGAATTTAA
** * *
28740869 CCGGATATAGCT-ACTCGTTCAAATGCCTTCAGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTC-GGGCTTAGC
*
28740909 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGCTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGC
* * *
28740948 CCGGA-ATTAGTATCTCGCACAAATGCCTTCGGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGG-GCTTAGC
* * *
28740988 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGC
28741028 CCGGA
1 CCGGA
28741033 CATCATTCAA
Statistics
Matches: 103, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
38 1 0.01
39 36 0.35
40 57 0.55
41 9 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (39 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGC
Found at i:28749154 original size:58 final size:58
Alignment explanation
Indices: 28749064--28749179 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
28749054 ATCCCCTGTG
*
28749064 TATGAATATACTGGTTGAAGCGTGAAGTAAGTATGATTTTGGGAATATGCGTATATGC
1 TATGAATATACTGGTTGAAGCGTGAAGTAAGTATGATTTTGGGAATATGCATATATGC
28749122 TATGAATATACTGGTTGAAGCGTGAAGTAAGTATGATTTTGGGAATATGCATATATGC
1 TATGAATATACTGGTTGAAGCGTGAAGTAAGTATGATTTTGGGAATATGCATATATGC
28749180 AATTATTCAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (58 bp):
TATGAATATACTGGTTGAAGCGTGAAGTAAGTATGATTTTGGGAATATGCATATATGC
Found at i:28752259 original size:220 final size:220
Alignment explanation
Indices: 28751877--28752309 Score: 866
Period size: 220 Copynumber: 2.0 Consensus size: 220
28751867 TGGCCGAAGG
28751877 CCGGTAGCTCGTTTATCAACTGAGCGAACATTTATTTGTAAGGGCTCGATTAATATTTAACACAT
1 CCGGTAGCTCGTTTATCAACTGAGCGAACATTTATTTGTAAGGGCTCGATTAATATTTAACACAT
28751942 ACGTAACATATCCCCATATTGGGATGTTTTTCGAGTATTCGCTGGAATTTTACAGCAAGCTCATT
66 ACGTAACATATCCCCATATTGGGATGTTTTTCGAGTATTCGCTGGAATTTTACAGCAAGCTCATT
28752007 CATTACCAAATCACGTACCTTCGGGATTTAACCGGATATAGCTCCTCGTTCAAATGCCTTCGGGA
131 CATTACCAAATCACGTACCTTCGGGATTTAACCGGATATAGCTCCTCGTTCAAATGCCTTCGGGA
28752072 CATAGCCCGGTTTTAGTAACTCACA
196 CATAGCCCGGTTTTAGTAACTCACA
28752097 CCGGTAGCTCGTTTATCAACTGAGCGAACATTTATTTGTAAGGGCTCGATTAATATTTAACACAT
1 CCGGTAGCTCGTTTATCAACTGAGCGAACATTTATTTGTAAGGGCTCGATTAATATTTAACACAT
28752162 ACGTAACATATCCCCATATTGGGATGTTTTTCGAGTATTCGCTGGAATTTTACAGCAAGCTCATT
66 ACGTAACATATCCCCATATTGGGATGTTTTTCGAGTATTCGCTGGAATTTTACAGCAAGCTCATT
28752227 CATTACCAAATCACGTACCTTCGGGATTTAACCGGATATAGCTCCTCGTTCAAATGCCTTCGGGA
131 CATTACCAAATCACGTACCTTCGGGATTTAACCGGATATAGCTCCTCGTTCAAATGCCTTCGGGA
28752292 CATAGCCCGGTTTTAGTA
196 CATAGCCCGGTTTTAGTA
28752310 CTCGCACGAA
Statistics
Matches: 213, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
220 213 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (220 bp):
CCGGTAGCTCGTTTATCAACTGAGCGAACATTTATTTGTAAGGGCTCGATTAATATTTAACACAT
ACGTAACATATCCCCATATTGGGATGTTTTTCGAGTATTCGCTGGAATTTTACAGCAAGCTCATT
CATTACCAAATCACGTACCTTCGGGATTTAACCGGATATAGCTCCTCGTTCAAATGCCTTCGGGA
CATAGCCCGGTTTTAGTAACTCACA
Found at i:28752322 original size:39 final size:40
Alignment explanation
Indices: 28752277--28752368 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 40
28752267 GCTCCTCGTT
* *
28752277 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTA-CTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTATCTCGCA
* *
28752316 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTATCTCGCA
*
28752356 CAAAGGCCTTCGG
1 CAAATGCCTTCGG
28752369 ATCTTAGTCC
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 29 0.63
40 17 0.37
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTATCTCGCA
Found at i:28752365 original size:40 final size:39
Alignment explanation
Indices: 28752277--28752421 Score: 159
Period size: 40 Copynumber: 3.7 Consensus size: 39
28752267 GCTCCTCGTT
* *
28752277 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCA
* *
28752316 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCA
* * * * *
28752356 CAAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCA
28752397 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28752422 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
39 32 0.36
40 45 0.51
41 12 0.13
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCA
Found at i:28752430 original size:41 final size:41
Alignment explanation
Indices: 28752353--28752430 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
28752343 TTAGTATCTC
* * *
28752353 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
28752394 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
28752431 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:28758529 original size:13 final size:13
Alignment explanation
Indices: 28758506--28758539 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
28758496 AAACATATTA
28758506 TAAACATTTTGTGT
1 TAAA-ATTTTGTGT
28758520 TAAAATTTTGTGT
1 TAAAATTTTGTGT
28758533 TAGAAAT
1 TA-AAAT
28758540 AATAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (13 bp):
TAAAATTTTGTGT
Found at i:28759702 original size:138 final size:138
Alignment explanation
Indices: 28759454--28759728 Score: 550
Period size: 138 Copynumber: 2.0 Consensus size: 138
28759444 GGTTGACAAG
28759454 TGTCTTGTGTTTGAGTTCTAGTAATGAAAATGAAATATAGATGTGTTATGATTTATTGATATATG
1 TGTCTTGTGTTTGAGTTCTAGTAATGAAAATGAAATATAGATGTGTTATGATTTATTGATATATG
28759519 TGCATGATTATTCGGATCATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTGACTATATCCG
66 TGCATGATTATTCGGATCATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTGACTATATCCG
28759584 GGCTAAGC
131 GGCTAAGC
28759592 TGTCTTGTGTTTGAGTTCTAGTAATGAAAATGAAATATAGATGTGTTATGATTTATTGATATATG
1 TGTCTTGTGTTTGAGTTCTAGTAATGAAAATGAAATATAGATGTGTTATGATTTATTGATATATG
28759657 TGCATGATTATTCGGATCATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTGACTATATCCG
66 TGCATGATTATTCGGATCATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTGACTATATCCG
28759722 GGCTAAG
131 GGCTAAG
28759729 TCCCGAAGGC
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
138 137 1.00
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (138 bp):
TGTCTTGTGTTTGAGTTCTAGTAATGAAAATGAAATATAGATGTGTTATGATTTATTGATATATG
TGCATGATTATTCGGATCATAACCGGACTAAGATCCGAAGGCATTTGTGCTAGTGACTATATCCG
GGCTAAGC
Found at i:28759739 original size:40 final size:40
Alignment explanation
Indices: 28759691--28759856 Score: 210
Period size: 40 Copynumber: 4.2 Consensus size: 40
28759681 GGACTAAGAT
*
28759691 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTC
* * *
28759731 CCGAAGGCATTTGTGCGAGTTACTATATCCGAGCCAAGTC
1 CCGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTC
* * *
28759771 CCGAAGGCATTTGGGCGAGTTACTATATCTGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTC
* * * *
28759811 CCGAAAGCATTTGTGCGAATTG-CTATATCC-GGCAAAATC
1 CCGAAGGCATTTGTGCG-AGTGACTATATCCGGGCTAAGTC
28759850 CCGAAGG
1 CCGAAGG
28759857 TACTTGGGTT
Statistics
Matches: 109, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
39 13 0.12
40 94 0.86
41 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTC
Found at i:28759824 original size:80 final size:79
Alignment explanation
Indices: 28759691--28759856 Score: 242
Period size: 80 Copynumber: 2.1 Consensus size: 79
28759681 GGACTAAGAT
* * * *
28759691 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
1 CCGAAGGCATTTGGGCGAGTGACTATATCCGGGCTAAGTCCCGAAAGCATTTGTGCGAATTACTA
* *
28759756 TATCCGAGCCAAGTC
66 TATCCG-GCAAAATC
* * *
28759771 CCGAAGGCATTTGGGCGAGTTACTATATCTGGGCTAAGTCCCGAAAGCATTTGTGCGAATTGCTA
1 CCGAAGGCATTTGGGCGAGTGACTATATCCGGGCTAAGTCCCGAAAGCATTTGTGCGAATTACTA
28759836 TATCCGGCAAAATC
66 TATCCGGCAAAATC
28759850 CCGAAGG
1 CCGAAGG
28759857 TACTTGGGTT
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
79 13 0.17
80 64 0.83
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGGGCGAGTGACTATATCCGGGCTAAGTCCCGAAAGCATTTGTGCGAATTACTA
TATCCGGCAAAATC
Found at i:28763897 original size:17 final size:18
Alignment explanation
Indices: 28763864--28763898 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28763854 GCTTCACATT
*
28763864 CTAGAATAATAAAATTTG
1 CTAGAAAAATAAAATTTG
28763882 CTAGAAAAAT-AAATTTG
1 CTAGAAAAATAAAATTTG
28763899 TCAACTCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.31
Consensus pattern (18 bp):
CTAGAAAAATAAAATTTG
Found at i:28777517 original size:40 final size:40
Alignment explanation
Indices: 28777433--28777616 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
28777423 TTGAATGCTG
* * * *
28777433 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
**
28777472 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
28777513 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
28777553 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
28777593 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
28777617 GTATGAGTTA
Statistics
Matches: 125, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
39 2 0.02
40 113 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:28777570 original size:80 final size:81
Alignment explanation
Indices: 28777433--28777613 Score: 230
Period size: 80 Copynumber: 2.3 Consensus size: 81
28777423 TTGAATGCTG
* *
28777433 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
28777497 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
28777513 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
28777574 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
28777593 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
28777614 ATTGTATGAG
Statistics
Matches: 90, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
79 4 0.04
80 77 0.86
81 9 0.10
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:28785383 original size:40 final size:39
Alignment explanation
Indices: 28785352--28785561 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
28785342 GGACTAAGAT
* *
28785352 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
28785392 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
28785432 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
28785472 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
28785512 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
28785551 CCGAAGGCATT
1 CCGAAGGCATT
28785562 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:28785515 original size:120 final size:120
Alignment explanation
Indices: 28785299--28785561 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
28785289 TTGAATGCTG
* *
28785299 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
28785363 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
28785419 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
28785482 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
28785538 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
28785562 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:28785581 original size:79 final size:80
Alignment explanation
Indices: 28785300--28785596 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
28785290 TGAATGCTGT
* ** * * * **
28785300 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
28785363 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
28785380 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
28785444 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
28785460 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
28785524 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
28785539 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
28785597 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:28789680 original size:42 final size:42
Alignment explanation
Indices: 28789626--28789745 Score: 129
Period size: 42 Copynumber: 2.8 Consensus size: 42
28789616 TACCGAGATG
*
28789626 TGATATTGTGTAAGACCATGTCTGAGACAT-TGGCATCG-TATA
1 TGATATCGTGTAAGACCATGTCTG-GA-ATATGGCATCGATATA
* * *
28789668 TGATTTCGTGTAAGACCCTGTCTGGAATAGTGGCATCGATATT
1 TGATATCGTGTAAGACCATGTCTGGAATA-TGGCATCGATATA
* *
28789711 TGATATCATGTAAGACCATATCTAGG-ATATGGCAT
1 TGATATCGTGTAAGACCATGTCT-GGAATATGGCAT
28789746 TGTACGAGTT
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
40 2 0.03
41 2 0.03
42 35 0.53
43 25 0.38
44 2 0.03
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.33
Consensus pattern (42 bp):
TGATATCGTGTAAGACCATGTCTGGAATATGGCATCGATATA
Found at i:28797351 original size:41 final size:42
Alignment explanation
Indices: 28797306--28797384 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
28797296 ATGCAGGGGA
* *
28797306 CACACAGTCT-ATCAACATGCCTGTGTG-CAAGCCGTGTGTCT
1 CACACAGTCTGATC-ACACGCCCGTGTGACAAGCCGTGTGTCT
*
28797347 CACACAGTCTGATCACACGCCCGTGTGACATGCCGTGT
1 CACACAGTCTGATCACACGCCCGTGTGACAAGCCGTGT
28797385 AGACTCAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 21 0.64
42 12 0.36
ACGTcount: A:0.22, C:0.32, G:0.23, T:0.24
Consensus pattern (42 bp):
CACACAGTCTGATCACACGCCCGTGTGACAAGCCGTGTGTCT
Found at i:28798187 original size:6 final size:6
Alignment explanation
Indices: 28798135--28798186 Score: 68
Period size: 6 Copynumber: 8.7 Consensus size: 6
28798125 ACACCGTAGT
* * * *
28798135 AGTAAT AGTAAC AGTAAC ATTAAC AGTAAC AGTAAC AGTAAT AGTAGC
1 AGTAAC AGTAAC AGTAAC AGTAAC AGTAAC AGTAAC AGTAAC AGTAAC
28798183 AGTA
1 AGTA
28798187 GTGGTACACA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.23
Consensus pattern (6 bp):
AGTAAC
Found at i:28804177 original size:53 final size:53
Alignment explanation
Indices: 28804116--28804220 Score: 201
Period size: 53 Copynumber: 2.0 Consensus size: 53
28804106 AGTAATTTTG
*
28804116 CTTTGTTTTTATTTGTGTAGTCATTTTGAAATTCTTTTTATTATATTATTTAA
1 CTTTGTTTTCATTTGTGTAGTCATTTTGAAATTCTTTTTATTATATTATTTAA
28804169 CTTTGTTTTCATTTGTGTAGTCATTTTGAAATTCTTTTTATTATATTATTTA
1 CTTTGTTTTCATTTGTGTAGTCATTTTGAAATTCTTTTTATTATATTATTTA
28804221 CACATTTTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.22, C:0.07, G:0.10, T:0.62
Consensus pattern (53 bp):
CTTTGTTTTCATTTGTGTAGTCATTTTGAAATTCTTTTTATTATATTATTTAA
Found at i:28806607 original size:108 final size:108
Alignment explanation
Indices: 28806418--28806633 Score: 432
Period size: 108 Copynumber: 2.0 Consensus size: 108
28806408 AAGGGGATAG
28806418 CTTGGCAGAAGGATATACATCAGAGTTGCAGAACTTCACTCGCATCAATGTAACACAGAATGAGT
1 CTTGGCAGAAGGATATACATCAGAGTTGCAGAACTTCACTCGCATCAATGTAACACAGAATGAGT
28806483 TGCAAGATTGAAAGATATATGGGCTCGTTGGGATAAGGGAACC
66 TGCAAGATTGAAAGATATATGGGCTCGTTGGGATAAGGGAACC
28806526 CTTGGCAGAAGGATATACATCAGAGTTGCAGAACTTCACTCGCATCAATGTAACACAGAATGAGT
1 CTTGGCAGAAGGATATACATCAGAGTTGCAGAACTTCACTCGCATCAATGTAACACAGAATGAGT
28806591 TGCAAGATTGAAAGATATATGGGCTCGTTGGGATAAGGGAACC
66 TGCAAGATTGAAAGATATATGGGCTCGTTGGGATAAGGGAACC
28806634 AAACAGTTGT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (108 bp):
CTTGGCAGAAGGATATACATCAGAGTTGCAGAACTTCACTCGCATCAATGTAACACAGAATGAGT
TGCAAGATTGAAAGATATATGGGCTCGTTGGGATAAGGGAACC
Found at i:28808628 original size:19 final size:19
Alignment explanation
Indices: 28808604--28808643 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
28808594 GATTCCTCAT
*
28808604 TTGCATT-CATGCATTTGCA
1 TTGCATTACAT-CATATGCA
28808623 TTGCATTACATCATATGCA
1 TTGCATTACATCATATGCA
28808642 TT
1 TT
28808644 AAAGGCAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.42
Consensus pattern (19 bp):
TTGCATTACATCATATGCA
Found at i:28817294 original size:88 final size:87
Alignment explanation
Indices: 28817202--28817471 Score: 242
Period size: 88 Copynumber: 3.1 Consensus size: 87
28817192 GTAGCAAGAA
*
28817202 AGCAGACTGAAAATCTCAGATTTATCTCCCTAAGTAGTAGCGGAGCAGATCGAAGATGGCGAATC
1 AGCAGACTGAAAATCACAGATTTATCTCCCTAAGTAGTAGCGGAGCAGATCGAAGATGGCGAATC
28817267 TTATCTCCATGTATCGACAATGG
66 TTATCTCCATGTATCG-CAATGG
** ** ** * * * * * *
28817290 AGCAGA-TTTAAGCCACAAGCCTTATCTCCCTGAAGTTGCAGTGGAGCAAGCTC-AATAT-AC-A
1 AGCAGACTGAAAATCAC-AGATTTATCTCCCT-AAGTAGTAGCGGAGC-AGATCGAAGATGGCGA
* ** * **
28817351 AGTCTTATCTCCTTAAAGTTGCGGTGG
63 A-TCTTATCTCCATGTA-TCGCAATGG
* * * *
28817378 AGCAGACTGAAAATCACAGATTTATCTCCCTAAGCAGTAGCAGAGCAGATCGAAGACGGTGAATC
1 AGCAGACTGAAAATCACAGATTTATCTCCCTAAGTAGTAGCGGAGCAGATCGAAGATGGCGAATC
28817443 TTATCTCCATGTATCGGCAATGG
66 TTATCTCCATGTATC-GCAATGG
28817466 AGCAGA
1 AGCAGA
28817472 TTTAAGCCAC
Statistics
Matches: 131, Mismatches: 41, Indels: 20
0.68 0.21 0.10
Matches are distributed among these distances:
86 4 0.03
87 21 0.16
88 76 0.58
89 26 0.20
90 4 0.03
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.24
Consensus pattern (87 bp):
AGCAGACTGAAAATCACAGATTTATCTCCCTAAGTAGTAGCGGAGCAGATCGAAGATGGCGAATC
TTATCTCCATGTATCGCAATGG
Found at i:28817672 original size:180 final size:176
Alignment explanation
Indices: 28817035--28818009 Score: 1054
Period size: 176 Copynumber: 5.5 Consensus size: 176
28817025 ATATTGGTGA
* * *
28817035 AAATTGAAGATCTTATCTCCCTGAAGTTGCAGCGGAGTAGATCGAAGATGGTGAATCTTATCTCT
1 AAATTTAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCGAAGATGGTGAATCTTATCTCC
* *
28817100 ATGTATCGGAAATGGAGCAGATTTTA-CCACC-AGCCTTATCTCTCTGAGGTAGCAAGAGAGCAG
66 ATGTATCGGCAATGGAGCAGATTTAAGCC-CCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAG
* * *
28817163 GTTGAAGAATTAAGTCTTATCTTTCTGAGGTAGCAAGAAAGCAGACTG
130 GTTGAAGAA-TGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTG
* * * * *
28817211 AAAATCTCAGAT-TTATCTCCCT-AAGTAGTAGCGGAGCAGATCGAAGATGGCGAATCTTATCTC
1 -AAATTTAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCGAAGATGGTGAATCTTATCTC
* * * * * *
28817274 CATGTATCGACAATGGAGCAGATTTAAGCCACAAGCCTTATCTCCCTGAAGTTGC-AGTGGAGCA
65 CATGTATCGGCAATGGAGCAGATTTAAGCCCCAAGCCTTATCTCTCTGAGGTAGCAAG-AGAGCA
* * * * ** * * * * *
28817338 AGCTCAATATACAAGTCTTATC-TCCTTAAAGTTGC-GGTGGAGCAGACTG
129 GGTTGAAGA-ATGAGTCTTATCTTCC-TGAGGTAGCAAG-GAAGCAGACTG
* * ** * * *
28817387 AAAATCACAGAT-TTATCTCCCT-AAGCAGTAGCAGAGCAGATCGAAGACGGTGAATCTTATCTC
1 AAATTTA-AGATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCGAAGATGGTGAATCTTATCTC
* * *
28817450 CATGTATCGGCAATGGAGCAGATTTAAGCCACAAGTCTTATCTCTCTGAGATAGCAAGAGAGCAG
65 CATGTATCGGCAATGGAGCAGATTTAAGCCCCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAG
28817515 GTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTG
130 GTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTG
* * **
28817562 AGAATTTAAGATTTTATCTCCCTGAAGTTGCAGCAGAGCAGATCATCGAAGATGGCAAATCTTAT
1 A-AATTTAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCAG---ATCGAAGATGGTGAATCTTAT
* * * *
28817627 CTCCATGTATCGGCAATGGAGCAGACTGAAGCCCCAAGCCTTATCTCTCTAAGGTAGGAAGAGAG
62 CTCCATGTATCGGCAATGGAGCAGATTTAAGCCCCAAGCCTTATCTCTCTGAGGTAGCAAGAGAG
* * * * *
28817692 CAAGTTAAAGATTGAGTCTTATCTTCCTGAGGTAGCAAGGAAGTAGACTA
127 CAGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTG
* * * *
28817742 AAGATTGAAGATCTTATCTCCCTGAAGTTGTAGTGGAGTAGATCGAAGATGGTGAATCTTATCTC
1 AA-ATTTAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCGAAGATGGTGAATCTTATCTC
* * * * ** * *
28817807 CATGTATCAGCAATGGAACAGATTTTAGCTACTTA-CCTTATCTCTTTGAGGTAGTAAGAGAGCA
65 CATGTATCGGCAATGGAGCAGATTTAAGC-CCCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCA
* * * * *
28817871 GGTTGAAGAATGAGTCTTATCTTTCTGAGATAGCAAGAAATCAGATTG
129 GGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTG
* * * * * *
28817919 AAGA-TTAAGATCTTGTCTCCCTGAAGTTGCAACGGAGTAGGTCGAAAATGGTAAATCTTATCTC
1 AA-ATTTAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCGAAGATGGTGAATCTTATCTC
28817983 CATGTATCGGCAATGGAGCAGATTTAA
65 CATGTATCGGCAATGGAGCAGATTTAA
28818010 CCCATCAACC
Statistics
Matches: 666, Mismatches: 114, Indels: 37
0.82 0.14 0.05
Matches are distributed among these distances:
175 100 0.15
176 270 0.41
177 139 0.21
178 2 0.00
179 1 0.00
180 154 0.23
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.27
Consensus pattern (176 bp):
AAATTTAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCGAAGATGGTGAATCTTATCTCC
ATGTATCGGCAATGGAGCAGATTTAAGCCCCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGG
TTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTG
Found at i:28825150 original size:16 final size:16
Alignment explanation
Indices: 28825129--28825160 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28825119 AAAACCCTAA
28825129 TTTTTCCTTTTCTTTT
1 TTTTTCCTTTTCTTTT
28825145 TTTTTCCTTTTCTTTT
1 TTTTTCCTTTTCTTTT
28825161 CTTTCTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTCCTTTTCTTTT
Found at i:28825171 original size:21 final size:21
Alignment explanation
Indices: 28825130--28825177 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
28825120 AAACCCTAAT
* *
28825130 TTTTCCTTTTCTTTTTTTTTCC
1 TTTT-CTTTTCTTTCTATTTCC
*
28825152 TTTTCTTTTCTTTCTATTTCG
1 TTTTCTTTTCTTTCTATTTCC
28825173 TTTTC
1 TTTTC
28825178 ATTCTCTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTTCTTTTCTTTCTATTTCC
Found at i:28834194 original size:28 final size:28
Alignment explanation
Indices: 28834162--28834227 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
28834152 GCAGTTCATG
* *
28834162 ATAGGGGTTCGCCATATGTGAGTTTGCC
1 ATAGGGGTTCGCCATAGGTGAGTTCGCC
*
28834190 ATAGGGGTTCGCCATAGGTGAGTTCGTC
1 ATAGGGGTTCGCCATAGGTGAGTTCGCC
*
28834218 ATAAGGGTTC
1 ATAGGGGTTC
28834228 ATCAATGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (28 bp):
ATAGGGGTTCGCCATAGGTGAGTTCGCC
Found at i:28834205 original size:13 final size:13
Alignment explanation
Indices: 28834162--28834227 Score: 60
Period size: 15 Copynumber: 4.8 Consensus size: 13
28834152 GCAGTTCATG
28834162 ATAGGGGTTCGCC
1 ATAGGGGTTCGCC
* *
28834175 ATATGTGAGTTTGCC
1 ATA-G-GGGTTCGCC
28834190 ATAGGGGTTCGCC
1 ATAGGGGTTCGCC
*
28834203 ATAGGTGAGTTCGTC
1 ATAGG-G-GTTCGCC
*
28834218 ATAAGGGTTC
1 ATAGGGGTTC
28834228 ATCAATGATA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
13 19 0.44
14 4 0.09
15 20 0.47
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (13 bp):
ATAGGGGTTCGCC
Found at i:28835706 original size:42 final size:42
Alignment explanation
Indices: 28835647--28835743 Score: 149
Period size: 42 Copynumber: 2.3 Consensus size: 42
28835637 CTGAGACTAT
*
28835647 GTGTAAGACCATATCTGGGATATGGCATCAATGTGAAACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCAATCTGAAACTTC
* * * *
28835689 GTGTAAAACCATATCTGGGATATGGCATCGATCTGATATTTC
1 GTGTAAGACCATATCTGGGATATGGCATCAATCTGAAACTTC
28835731 GTGTAAGACCATA
1 GTGTAAGACCATA
28835744 GTTGGGCTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (42 bp):
GTGTAAGACCATATCTGGGATATGGCATCAATCTGAAACTTC
Found at i:28843037 original size:16 final size:16
Alignment explanation
Indices: 28843013--28843043 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28843003 GTAATAATAT
*
28843013 ATTTTATTTACTTATG
1 ATTTAATTTACTTATG
28843029 ATTTAATTTACTTAT
1 ATTTAATTTACTTAT
28843044 TTATCCATAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.61
Consensus pattern (16 bp):
ATTTAATTTACTTATG
Found at i:28847204 original size:12 final size:12
Alignment explanation
Indices: 28847187--28847214 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28847177 CTAATAAATG
28847187 AATTAAAAGCCA
1 AATTAAAAGCCA
28847199 AATTAAAAGCCA
1 AATTAAAAGCCA
28847211 AATT
1 AATT
28847215 TTGTCCATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.21
Consensus pattern (12 bp):
AATTAAAAGCCA
Found at i:28848205 original size:15 final size:16
Alignment explanation
Indices: 28848185--28848218 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
28848175 TGTACAAAAA
28848185 AACTCA-TACGTGATG
1 AACTCATTACGTGATG
*
28848200 AACTCATTATGTGATG
1 AACTCATTACGTGATG
28848216 AAC
1 AAC
28848219 CCTCAGTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (16 bp):
AACTCATTACGTGATG
Found at i:28849338 original size:14 final size:13
Alignment explanation
Indices: 28849318--28849349 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
28849308 AATATTTGAC
28849318 TTGTTCTTAATTA
1 TTGTTCTTAATTA
28849331 TGTGTTCTTAATTA
1 T-TGTTCTTAATTA
28849345 TTGTT
1 TTGTT
28849350 TTGATATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (13 bp):
TTGTTCTTAATTA
Found at i:28857978 original size:33 final size:33
Alignment explanation
Indices: 28857937--28858004 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
28857927 CCCCTGGACC
*
28857937 TTTTTTGTTGTATTATGATGAAAGAAGCCTGAT
1 TTTTTTGTTGTATTATGATGAAAGAAGCCTAAT
28857970 TTTTTTGTTGTATTATGATGAAAGAAGCCTAAT
1 TTTTTTGTTGTATTATGATGAAAGAAGCCTAAT
28858003 TT
1 TT
28858005 AGGTTTGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.47
Consensus pattern (33 bp):
TTTTTTGTTGTATTATGATGAAAGAAGCCTAAT
Done.