Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 123 of 425
Found at i:36474295 original size:14 final size:13
Alignment explanation
Indices: 36474275--36474306 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
36474265 AATATTTAAC
36474275 TTGTTCTTAATTA
1 TTGTTCTTAATTA
36474288 TGTGTTCTTAATTA
1 T-TGTTCTTAATTA
36474302 TTGTT
1 TTGTT
36474307 TTGATATCCC
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:36475443 original size:41 final size:42
Alignment explanation
Indices: 36475361--36475470 Score: 150
Period size: 41 Copynumber: 2.6 Consensus size: 42
36475351 CGTCTGTCTC
* ** * *
36475361 AAAACATATACTCATTAACTACAAACCTGTATATACCTGACA
1 AAAACATATACACATTAACTACAAACCAATATACACATGACA
*
36475403 AAAACATATACACATTAACTACATACCAAT-TACACATGACA
1 AAAACATATACACATTAACTACAAACCAATATACACATGACA
*
36475444 AAAACATATACACATCAACTACAAACC
1 AAAACATATACACATTAACTACAAACC
36475471 TTTCTCATGT
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 34 0.57
42 26 0.43
ACGTcount: A:0.50, C:0.25, G:0.03, T:0.22
Consensus pattern (42 bp):
AAAACATATACACATTAACTACAAACCAATATACACATGACA
Found at i:36475487 original size:41 final size:41
Alignment explanation
Indices: 36475355--36475487 Score: 112
Period size: 41 Copynumber: 3.2 Consensus size: 41
36475345 CACGGTCGTC
* * *
36475355 TGTCTC-AAAACATATACTCATTAACTACAAACCTGTAT-A
1 TGTCTCAAAAACATATACACATTAACTACAAACCTTTCTCA
** * * *
36475394 TACCTGACAAAAACATATACACATTAACTACATACCAATTACACA
1 TGTCT--CAAAAACATATACACATTAACTACAAACC--TTTCTCA
* *
36475439 TG--ACAAAAACATATACACATCAACTACAAACCTTTCTCA
1 TGTCTCAAAAACATATACACATTAACTACAAACCTTTCTCA
36475478 TGTCTCAAAA
1 TGTCTCAAAA
36475488 CATGATCAAA
Statistics
Matches: 71, Mismatches: 15, Indels: 14
0.71 0.15 0.14
Matches are distributed among these distances:
39 10 0.14
41 33 0.46
42 25 0.35
44 1 0.01
45 2 0.03
ACGTcount: A:0.45, C:0.26, G:0.04, T:0.26
Consensus pattern (41 bp):
TGTCTCAAAAACATATACACATTAACTACAAACCTTTCTCA
Found at i:36479534 original size:40 final size:40
Alignment explanation
Indices: 36479479--36479659 Score: 276
Period size: 40 Copynumber: 4.5 Consensus size: 40
36479469 TATTCGGATG
* *
36479479 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
36479519 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
**
36479559 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
36479599 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
36479639 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
36479660 ATACTTGGGT
Statistics
Matches: 130, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 13 0.10
40 115 0.88
41 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:36487174 original size:40 final size:40
Alignment explanation
Indices: 36487129--36487296 Score: 198
Period size: 40 Copynumber: 4.2 Consensus size: 40
36487119 CGGAATACAA
*
36487129 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
* * *
36487169 CCGGATATAACGACTCGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
* **
36487209 CCGGATATAACAACTTGCACGAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
* * *
36487249 CCGGATA-AAGTCACTA-GCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAA-CCAC-ACGCACGAA-TGCCTTCGGGTATTAGC
36487289 CCGGATAT
1 CCGGATAT
36487297 CATTCAATTG
Statistics
Matches: 112, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
39 4 0.04
40 108 0.96
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
Found at i:36487269 original size:80 final size:80
Alignment explanation
Indices: 36487129--36487296 Score: 232
Period size: 80 Copynumber: 2.1 Consensus size: 80
36487119 CGGAATACAA
* * *
36487129 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTCGCACAAATG
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATATAACGACTAGCACAAATG
*
36487194 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAAC
** *
36487209 CCGGATATAACAACTTGCACGAATGCCTTCGGGTATTAGCCCGGATA-AA-GTCACTAGCACAAT
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATATAACG--ACTAGCACAAA
*
36487272 TGCCTTCGGGTCTTAAC
64 TGCCTTCGGGTATTAAC
36487289 CCGGATAT
1 CCGGATAT
36487297 CATTCAATTG
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
78 1 0.01
79 2 0.03
80 75 0.96
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (80 bp):
CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATATAACGACTAGCACAAATG
CCTTCGGGTATTAAC
Found at i:36495186 original size:40 final size:40
Alignment explanation
Indices: 36495141--36495308 Score: 198
Period size: 40 Copynumber: 4.2 Consensus size: 40
36495131 CGGAATACAA
*
36495141 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
* * *
36495181 CCGGATATAACGACTCGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
* **
36495221 CCGGATATAACAACTTGCACGAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
* * *
36495261 CCGGATA-AAGTCACTA-GCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAA-CCAC-ACGCACGAA-TGCCTTCGGGTATTAGC
36495301 CCGGATAT
1 CCGGATAT
36495309 CATTCAATTG
Statistics
Matches: 112, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
39 4 0.04
40 108 0.96
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
Found at i:36495281 original size:80 final size:80
Alignment explanation
Indices: 36495141--36495308 Score: 232
Period size: 80 Copynumber: 2.1 Consensus size: 80
36495131 CGGAATACAA
* * *
36495141 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTCGCACAAATG
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATATAACGACTAGCACAAATG
*
36495206 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAAC
** *
36495221 CCGGATATAACAACTTGCACGAATGCCTTCGGGTATTAGCCCGGATA-AA-GTCACTAGCACAAT
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATATAACG--ACTAGCACAAA
*
36495284 TGCCTTCGGGTCTTAAC
64 TGCCTTCGGGTATTAAC
36495301 CCGGATAT
1 CCGGATAT
36495309 CATTCAATTG
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
78 1 0.01
79 2 0.03
80 75 0.96
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (80 bp):
CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATATAACGACTAGCACAAATG
CCTTCGGGTATTAAC
Found at i:36502863 original size:14 final size:14
Alignment explanation
Indices: 36502844--36502871 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
36502834 AATTATACAA
36502844 TGTGTGTATTAAAT
1 TGTGTGTATTAAAT
36502858 TGTGTGTATTAAAT
1 TGTGTGTATTAAAT
36502872 AAGTTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (14 bp):
TGTGTGTATTAAAT
Found at i:36507365 original size:39 final size:40
Alignment explanation
Indices: 36507241--36507368 Score: 129
Period size: 40 Copynumber: 3.2 Consensus size: 40
36507231 ACTCGCTCAG
* ** *
36507241 ATGCCTTCGGGAC-GAAGCCCGG-TTATAGCGACTTGCACGA
1 ATGCCTTCGGGACTTAA-CCCGGATT-TAGTAACTCGCACGA
* *
36507281 ATGCCTTCGGGACTTAACCCGGGTTTAGTAACTTGCAC-A
1 ATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACGA
* * *
36507320 AAGCCTTCGGGA-TTAGCCCGGATTTATTAACTCGCACGA
1 ATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACGA
36507359 ATGCCTTCGG
1 ATGCCTTCGG
36507369 ATCCTAGTCC
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
38 21 0.28
39 22 0.29
40 29 0.38
41 4 0.05
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.25
Consensus pattern (40 bp):
ATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACGA
Found at i:36507405 original size:40 final size:37
Alignment explanation
Indices: 36507256--36507420 Score: 132
Period size: 40 Copynumber: 4.2 Consensus size: 37
36507246 TTCGGGACGA
* ** *
36507256 AGCCCGGTTATAGCGACTTGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAGTAACTTGCAC-AAAGCCTTC-GGA-TT
* * *
36507296 AACCCGGGTTTAGTAACTTGCACAAAGCCTTCGGGATT
1 AGCCCGGATATAGTAACTTGCACAAAGCCTTC-GGATT
* * * *
36507334 AGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCT
1 AGCCCGGATATAGTAACTTGCAC-AAAGCCTTCGGAT--T
* *
36507374 AGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGACTT
1 AGCCCGGATATAGTAACTT-GCACAAAGCCTTCGGA-TT
36507413 AGCCCGGA
1 AGCCCGGA
36507421 CATCATTCGA
Statistics
Matches: 102, Mismatches: 18, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
38 25 0.25
39 28 0.27
40 44 0.43
41 5 0.05
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (37 bp):
AGCCCGGATATAGTAACTTGCACAAAGCCTTCGGATT
Found at i:36507406 original size:79 final size:78
Alignment explanation
Indices: 36507275--36507420 Score: 197
Period size: 78 Copynumber: 1.9 Consensus size: 78
36507265 ATAGCGACTT
* * *
36507275 GCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTAACTTGCACAAAGCCTTCGGGA-TTAGCCC
1 GCACGAATGCCTTCGGGACCTAACCCGGATATAGTAACTTGCACAAAGCCTTC-GGACTTAGCCC
36507339 GGATTTATTAACTC
65 GGATTTATTAACTC
** *
36507353 GCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGACTTAGCC
1 GCACGAATGCCTTCGGGA-CCTAACCCGGATATAGTAACTT-GCACAAAGCCTTCGGACTTAGCC
36507417 CGGA
64 CGGA
36507421 CATCATTCGA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
77 3 0.05
78 33 0.56
79 23 0.39
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (78 bp):
GCACGAATGCCTTCGGGACCTAACCCGGATATAGTAACTTGCACAAAGCCTTCGGACTTAGCCCG
GATTTATTAACTC
Found at i:36511969 original size:39 final size:39
Alignment explanation
Indices: 36511891--36512014 Score: 212
Period size: 39 Copynumber: 3.2 Consensus size: 39
36511881 TATGGTAACC
* *
36511891 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
36511931 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
36511970 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
36512009 CGCACA
1 CGCACA
36512015 TTCATACACA
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
39 64 0.79
40 17 0.21
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.22
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:36517275 original size:40 final size:40
Alignment explanation
Indices: 36517217--36517370 Score: 213
Period size: 39 Copynumber: 3.9 Consensus size: 40
36517207 TGTTCAAACA
* * * * * *
36517217 CCTTCGGGACATAGCCCGGTTATGATAACCCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATTG
*
36517257 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATTG
*
36517297 CCTTC-GGTCTTAGCCCGGATATCACAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATTG
*
36517336 CCTTCGGG-CTTAGCCCGGATATCACAATTCGCACA
1 CCTTCGGGACTTAGCCCGGATATCACAACTCGCACA
36517371 TTCATACACA
Statistics
Matches: 103, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
39 63 0.61
40 40 0.39
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATTG
Found at i:36520104 original size:40 final size:40
Alignment explanation
Indices: 36520049--36520127 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
36520039 GGATGATAAC
*
36520049 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCTATATT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATT
36520089 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
36520128 CCTTTGTGCG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATT
Found at i:36520135 original size:21 final size:21
Alignment explanation
Indices: 36520109--36520150 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
36520099 CCCGAAGGCA
36520109 TTTGTGCGAGTTACTATATCC
1 TTTGTGCGAGTTACTATATCC
36520130 TTTGTGCGAGTTACTATATCC
1 TTTGTGCGAGTTACTATATCC
36520151 GGGCTAAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (21 bp):
TTTGTGCGAGTTACTATATCC
Found at i:36520164 original size:61 final size:61
Alignment explanation
Indices: 36520069--36520187 Score: 211
Period size: 61 Copynumber: 2.0 Consensus size: 61
36520059 CCCGAAGGCA
* * *
36520069 TTTGTGCGAGTTGCTATATTCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 TTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTTACTATATCC
36520130 TTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTTACTATA
1 TTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTTACTATA
36520188 ACCGGGCTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (61 bp):
TTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTTACTATATCC
Found at i:36521945 original size:29 final size:29
Alignment explanation
Indices: 36521913--36522075 Score: 272
Period size: 29 Copynumber: 5.6 Consensus size: 29
36521903 GCTTGGAAGG
36521913 TATGGCACTAAGTGTGCGAACTTAAATTA
1 TATGGCACTAAGTGTGCGAACTTAAATTA
*
36521942 TATGGCACTAAGTGTCCGAACTTAAATTA
1 TATGGCACTAAGTGTGCGAACTTAAATTA
36521971 TATGGCACTAAGTGTGCGAACTTAAATTA
1 TATGGCACTAAGTGTGCGAACTTAAATTA
*
36522000 TATGGCACTAAGTGTGCAAACTTAAATTA
1 TATGGCACTAAGTGTGCGAACTTAAATTA
* * *
36522029 TATGGCACTATGTGTGCGAGCTTAAATCA
1 TATGGCACTAAGTGTGCGAACTTAAATTA
*
36522058 CATGGCACTAAGTGTGCG
1 TATGGCACTAAGTGTGCG
36522076 TGATCGAGTA
Statistics
Matches: 125, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 125 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (29 bp):
TATGGCACTAAGTGTGCGAACTTAAATTA
Found at i:36530066 original size:29 final size:29
Alignment explanation
Indices: 36530034--36530167 Score: 223
Period size: 29 Copynumber: 4.6 Consensus size: 29
36530024 GCTTGGAAGG
36530034 TATGGCACTAAGTGTGCGAACTTAAATTA
1 TATGGCACTAAGTGTGCGAACTTAAATTA
36530063 TATGGCACTAAGTGTGCGAACTTAAATTA
1 TATGGCACTAAGTGTGCGAACTTAAATTA
*
36530092 TATGGCACTAAGTGTGCAAACTTAAATTA
1 TATGGCACTAAGTGTGCGAACTTAAATTA
* * *
36530121 TATGGCACTATGTGTGCGAGCTTAAATCA
1 TATGGCACTAAGTGTGCGAACTTAAATTA
*
36530150 CATGGCACTAAGTGTGCG
1 TATGGCACTAAGTGTGCG
36530168 TGATCGAGTA
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 98 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (29 bp):
TATGGCACTAAGTGTGCGAACTTAAATTA
Found at i:36534914 original size:23 final size:23
Alignment explanation
Indices: 36534873--36534916 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
36534863 AACCCCTAAT
36534873 ATGCATAATTGAATGATTTATGA
1 ATGCATAATTGAATGATTTATGA
*
36534896 ATGCATGA-TGAATGCATTTAT
1 ATGCATAATTGAATG-ATTTAT
36534917 TATTAGCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (23 bp):
ATGCATAATTGAATGATTTATGA
Found at i:36544342 original size:40 final size:40
Alignment explanation
Indices: 36544215--36544344 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
36544205 ATGCTGGAAA
* *
36544215 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
36544255 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
36544295 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
36544335 TTATATCCGG
1 TTATATCCGG
36544345 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:36544343 original size:80 final size:80
Alignment explanation
Indices: 36544177--36544344 Score: 198
Period size: 80 Copynumber: 2.1 Consensus size: 80
36544167 CAATTGAATG
* * *
36544177 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGACATTCATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCA
36544242 ATTGTGCTAGTGGCT
66 ATTGTGCTAGTGGCT
* * * ** *
36544257 ACATCCGGGCTAAGACCCGAAGGCATTCGTGC-GAGTCATTCTATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGACATTCATGCTG-GAAATTATATCCGGGCTAAGACCCGAAGGC
*
36544321 -ATTCGTGC-ACGTGGTT
65 AATT-GTGCTA-GTGGCT
36544337 ATATCCGG
1 ATATCCGG
36544345 TTGTATTCCG
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
79 5 0.07
80 69 0.93
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGACATTCATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCA
ATTGTGCTAGTGGCT
Found at i:36550654 original size:29 final size:29
Alignment explanation
Indices: 36550620--36550695 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
36550610 TACTCGATTT
* * *
36550620 CGCACACTTAGTGCCATGCGATTTAAGCC
1 CGCACACTTAGTGCCATACCATTCAAGCC
** * * *
36550649 CGCACACACAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATACCATTCAAGCC
36550678 CGCACACTTAGTGCCATA
1 CGCACACTTAGTGCCATA
36550696 TATTTCCAGC
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.25, C:0.36, G:0.18, T:0.21
Consensus pattern (29 bp):
CGCACACTTAGTGCCATACCATTCAAGCC
Found at i:36550712 original size:58 final size:57
Alignment explanation
Indices: 36550619--36550749 Score: 133
Period size: 58 Copynumber: 2.3 Consensus size: 57
36550609 ATACTCGATT
* * *
36550619 TCGCACACTTAGTGCCATGCGATTTAAGCCCGCACACACAGTGCCATACCCTTCGAGC-
1 TCGCACACTTAGTGCCATGAGATTTAAGCACGCACAC-CAGTGCCATA-CCTTCCAGCA
* * * * **
36550677 TCGCACACTTAGTGCCAT-ATATTTCCAGCATGCACACTAGTGCCATATTTTCCAGCA
1 TCGCACACTTAGTGCCATGAGATTT-AAGCACGCACACCAGTGCCATACCTTCCAGCA
36550734 T-GCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
36550750 ATCTCGTCAC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
56 21 0.34
57 14 0.23
58 27 0.44
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (57 bp):
TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACCAGTGCCATACCTTCCAGCA
Found at i:36550735 original size:27 final size:29
Alignment explanation
Indices: 36550679--36550749 Score: 128
Period size: 28 Copynumber: 2.5 Consensus size: 29
36550669 CTTCGAGCTC
36550679 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
36550708 GCACAC-TAGTGCCATAT-TTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
36550735 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
36550750 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 16 0.39
28 19 0.46
29 6 0.15
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:36559298 original size:46 final size:46
Alignment explanation
Indices: 36559198--36559367 Score: 164
Period size: 46 Copynumber: 3.7 Consensus size: 46
36559188 TTGTGTGCTG
* * * * * *
36559198 GTGTAAGACCATGTATGGGACATGGCATC-GGCATTGAGACGAGGGCTA
1 GTGTAAGA-CATGTCTGGGACAT-GCATCAGCCA-CGAGATGAGAGCCA
*
36559246 GTGTAAGACATGTTTGGGACATGCATCAGCCAC-AGTATGAGAGCCA
1 GTGTAAGACATGTCTGGGACATGCATCAGCCACGAG-ATGAGAGCCA
* * **
36559292 GTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTTAGCCA
1 GTGTAAGACATGTCTGGGACATGCATCAGCCACGAGATGAGAGCCA
* * *
36559338 ATGTCAGACATGTCTGGGACATGCGTCAGC
1 GTGTAAGACATGTCTGGGACATGCATCAGC
36559368 ACGGTTACAT
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
45 2 0.02
46 76 0.73
47 18 0.17
48 8 0.08
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.22
Consensus pattern (46 bp):
GTGTAAGACATGTCTGGGACATGCATCAGCCACGAGATGAGAGCCA
Found at i:36562291 original size:29 final size:29
Alignment explanation
Indices: 36562258--36562330 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
36562248 GTGACGAGAT
36562258 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
* *
36562287 TGGCACTGAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
36562316 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
36562331 GAGCTCGAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.29, C:0.15, G:0.30, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAAAATA
Found at i:36562346 original size:29 final size:29
Alignment explanation
Indices: 36562314--36562390 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 29
36562304 GCTGGAAATA
* *
36562314 TATGGCACTAAGTGTGCGAGCTCGAAGGG
1 TATGGCACTAAGTGTGCGAGCTCAAAGCG
** * * *
36562343 TATGGCACTGTGTGTGCGGGCTTAAATCG
1 TATGGCACTAAGTGTGCGAGCTCAAAGCG
*
36562372 CATGGCACTAAGTGTGCGA
1 TATGGCACTAAGTGTGCGA
36562391 AATCGAGTAT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.22, C:0.18, G:0.35, T:0.25
Consensus pattern (29 bp):
TATGGCACTAAGTGTGCGAGCTCAAAGCG
Found at i:36562347 original size:58 final size:59
Alignment explanation
Indices: 36562258--36562390 Score: 146
Period size: 58 Copynumber: 2.3 Consensus size: 59
36562248 GTGACGAGAT
* * *
36562258 TGGCACTAAGTGTGC-ATGCTGGAAAAATATGGCACTGAGTGTGCATGCTGGAAAT-ATA
1 TGGCACTAAGTGTGCGATGCTCGAAAAATATGGCACTGAGTGTGCAGGCT-GAAATCACA
*** * * * *
36562316 TGGCACTAAGTGTGCGA-GCTCGAAGGGTATGGCACTGTGTGTGCGGGCTTAAATCGCA
1 TGGCACTAAGTGTGCGATGCTCGAAAAATATGGCACTGAGTGTGCAGGCTGAAATCACA
36562374 TGGCACTAAGTGTGCGA
1 TGGCACTAAGTGTGCGA
36562391 AATCGAGTAT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
57 4 0.06
58 58 0.92
59 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.25
Consensus pattern (59 bp):
TGGCACTAAGTGTGCGATGCTCGAAAAATATGGCACTGAGTGTGCAGGCTGAAATCACA
Found at i:36565180 original size:20 final size:18
Alignment explanation
Indices: 36565155--36565191 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
36565145 ATTGCTAAGT
36565155 TGTAAAATGAGTTGTAAATG
1 TGTAAAAT-AGTTG-AAATG
36565175 TGTAAAATAGTTGAAAT
1 TGTAAAATAGTTGAAAT
36565192 TATGAGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (18 bp):
TGTAAAATAGTTGAAATG
Found at i:36572953 original size:11 final size:11
Alignment explanation
Indices: 36572930--36572963 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
36572920 TGTATATTAA
36572930 TTTTACATATTT
1 TTTTACAT-TTT
*
36572942 TTTTATATTTT
1 TTTTACATTTT
36572953 TTTTACATTTT
1 TTTTACATTTT
36572964 AATGAATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTACATTTT
Found at i:36574470 original size:16 final size:16
Alignment explanation
Indices: 36574451--36574482 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
36574441 ATATTAATTT
*
36574451 TATTTAATTTTAAAAA
1 TATTTAATATTAAAAA
36574467 TATTTAATATTAAAAA
1 TATTTAATATTAAAAA
36574483 ATACAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTTAATATTAAAAA
Found at i:36574484 original size:17 final size:16
Alignment explanation
Indices: 36574451--36574485 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
36574441 ATATTAATTT
*
36574451 TATTTAATTTTAAAAA
1 TATTTAATTTAAAAAA
36574467 TATTTAATATTAAAAAA
1 TATTTAAT-TTAAAAAA
36574484 TA
1 TA
36574486 CAAAAGAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATTTAATTTAAAAAA
Found at i:36575133 original size:3 final size:3
Alignment explanation
Indices: 36575120--36575170 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
36575110 GATTATTAAC
* *
36575120 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
36575168 ATT
1 ATT
36575171 TTGTTAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:36577247 original size:19 final size:19
Alignment explanation
Indices: 36577208--36577244 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
36577198 TAGTACAACC
*
36577208 ATTTAATTTGTCTTGAGTT
1 ATTTAATTTATCTTGAGTT
36577227 ATTTAATTTATCTT-AGTT
1 ATTTAATTTATCTTGAGTT
36577245 TATACAGCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.24, C:0.05, G:0.11, T:0.59
Consensus pattern (19 bp):
ATTTAATTTATCTTGAGTT
Found at i:36580190 original size:2 final size:2
Alignment explanation
Indices: 36580183--36580229 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
36580173 TGAAAGTCGA
*
36580183 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36580225 -T AT AT
1 AT AT AT
36580230 TTTGAAAGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:36581335 original size:38 final size:38
Alignment explanation
Indices: 36581279--36581358 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 38
36581269 GATGTGTATT
* * *
36581279 CGGGTTAAATCCCGCAGGCTTTGTGCTGGTATTATATC
1 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
*
36581317 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATT
1 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
36581355 CGGG
1 CGGG
36581359 CCTTCGTGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (38 bp):
CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
Found at i:36581405 original size:43 final size:43
Alignment explanation
Indices: 36581330--36581474 Score: 206
Period size: 43 Copynumber: 3.4 Consensus size: 43
36581320 GATAAATCCC
* * *
36581330 GCAGGCCTAGTGCTGGT-AT-TATATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
36581371 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
36581414 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTTGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
36581457 GCA-GCATAATGCCGGTGA
1 GCAGGCTTAGTGCCGGTGA
36581475 AATGATATGT
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
41 15 0.16
42 14 0.15
43 65 0.69
ACGTcount: A:0.14, C:0.23, G:0.33, T:0.30
Consensus pattern (43 bp):
GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
Found at i:36584560 original size:6 final size:6
Alignment explanation
Indices: 36584543--36584614 Score: 67
Period size: 6 Copynumber: 11.7 Consensus size: 6
36584533 ACAATCTGTG
* * *
36584543 GAAAAA GCAAAA GAAAAA GAACAA GAAAAA -AATAAT GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAA-AAA GAAAAA GAAAAA
36584591 G-AAAA GAAAATTGA GAAAAA GAAA
1 GAAAAA GAAAA---A GAAAAA GAAA
36584615 TGAAAAAGTG
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
5 7 0.13
6 39 0.72
7 2 0.04
9 6 0.11
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.06
Consensus pattern (6 bp):
GAAAAA
Found at i:36584610 original size:21 final size:21
Alignment explanation
Indices: 36584584--36584630 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
36584574 ATAATGAAAA
*
36584584 AGAAAAAGAAAAG-AAAATTG
1 AGAAAAAGAAAAGAAAAAGTG
*
36584604 AGAAAAAGAAATGAAAAAGTG
1 AGAAAAAGAAAAGAAAAAGTG
36584625 AGAAAA
1 AGAAAA
36584631 GTGAGGCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.70, C:0.00, G:0.21, T:0.09
Consensus pattern (21 bp):
AGAAAAAGAAAAGAAAAAGTG
Found at i:36584610 original size:36 final size:37
Alignment explanation
Indices: 36584543--36584622 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 37
36584533 ACAATCTGTG
* *
36584543 GAAAAAGCAAAAGAAAAAGAACAAGAAAAAAA-TAAT
1 GAAAAAGAAAAAGAAAAAGAACAAGAAAAAAAGAAAT
*
36584579 GAAAAAGAAAAAG-AAAAGAA-AATTGAGAAAAAGAAAT
1 GAAAAAGAAAAAGAAAAAGAACAA--GAAAAAAAGAAAT
36584616 GAAAAAG
1 GAAAAAG
36584623 TGAGAAAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
34 2 0.05
35 7 0.18
36 19 0.50
37 10 0.26
ACGTcount: A:0.74, C:0.03, G:0.17, T:0.06
Consensus pattern (37 bp):
GAAAAAGAAAAAGAAAAAGAACAAGAAAAAAAGAAAT
Found at i:36584631 original size:20 final size:19
Alignment explanation
Indices: 36584576--36584631 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
36584566 AGAAAAAAAT
36584576 AATGAAAAA-GA-AAAAGA
1 AATGAAAAATGAGAAAAGA
* *
36584593 AAAGAAAATTGAGAAAAAGA
1 AATGAAAAATGAG-AAAAGA
36584613 AATGAAAAAGTGAGAAAAG
1 AATGAAAAA-TGAGAAAAG
36584632 TGAGGCAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 7 0.23
18 2 0.06
20 18 0.58
21 4 0.13
ACGTcount: A:0.70, C:0.00, G:0.21, T:0.09
Consensus pattern (19 bp):
AATGAAAAATGAGAAAAGA
Found at i:36587805 original size:19 final size:19
Alignment explanation
Indices: 36587766--36587802 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
36587756 TAGTACAACC
*
36587766 ATTTAATTTGTCTTGAGTT
1 ATTTAATTTGTATTGAGTT
36587785 ATTTAATTTGTATT-AGTT
1 ATTTAATTTGTATTGAGTT
36587803 TATACAGCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.24, C:0.03, G:0.14, T:0.59
Consensus pattern (19 bp):
ATTTAATTTGTATTGAGTT
Found at i:36587816 original size:46 final size:45
Alignment explanation
Indices: 36587676--36587830 Score: 109
Period size: 46 Copynumber: 3.4 Consensus size: 45
36587666 GTTTAAGTAA
* * * * * *
36587676 TTAACATGTCTTGAGTTTATTTAATATGTCTAAGTATATAC-GATAA
1 TTAATATGTCTTGAG-TTATTTAATTTGT-TTAGTTTATACAGCTAT
* * * * * *
36587722 TTAATATGTCTTAAGATAATTAATTTGTTCTA-ATTAGTACAACCAT
1 TTAATATGTCTTGAGTTATTTAATTTGTT-TAGTTTA-TACAGCTAT
*
36587768 TTAATTTGTCTTGAGTTATTTAATTTGTATTAGTTTATACAGCTAT
1 TTAATATGTCTTGAGTTATTTAATTTGT-TTAGTTTATACAGCTAT
*
36587814 TTAA-AGTGTCTTAAGTT
1 TTAATA-TGTCTTGAGTT
36587831 TAGATAACTT
Statistics
Matches: 82, Mismatches: 21, Indels: 12
0.71 0.18 0.10
Matches are distributed among these distances:
44 3 0.04
45 14 0.17
46 61 0.74
47 4 0.05
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.47
Consensus pattern (45 bp):
TTAATATGTCTTGAGTTATTTAATTTGTTTAGTTTATACAGCTAT
Found at i:36593905 original size:7 final size:7
Alignment explanation
Indices: 36593893--36593918 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
36593883 AGAAACAAAA
36593893 GATGATT
1 GATGATT
36593900 GATGATT
1 GATGATT
36593907 GATGATT
1 GATGATT
36593914 GATGA
1 GATGA
36593919 AAAGAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (7 bp):
GATGATT
Found at i:36597889 original size:20 final size:20
Alignment explanation
Indices: 36597864--36597901 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
36597854 GTCACATATA
36597864 TCATGAACTCAGACCACAAC
1 TCATGAACTCAGACCACAAC
* *
36597884 TCATGAGCTCAGATCACA
1 TCATGAACTCAGACCACA
36597902 TAATTCTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.32, G:0.13, T:0.18
Consensus pattern (20 bp):
TCATGAACTCAGACCACAAC
Found at i:36608945 original size:24 final size:24
Alignment explanation
Indices: 36608913--36608966 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
36608903 TAAGAGTAGG
36608913 ATCTATGTCTGCATCTATATATGA
1 ATCTATGTCTGCATCTATATATGA
* * *
36608937 ATCTATGTCTGCATTTGTATCTGA
1 ATCTATGTCTGCATCTATATATGA
36608961 ATCTAT
1 ATCTAT
36608967 ATAAGCATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (24 bp):
ATCTATGTCTGCATCTATATATGA
Found at i:36612358 original size:48 final size:46
Alignment explanation
Indices: 36612296--36612418 Score: 147
Period size: 46 Copynumber: 2.6 Consensus size: 46
36612286 AAGCTGACGC
* * * *
36612296 CATGTCCCAAACATGTCTTACACTAGCTCGTATATCTCGAGGCTAATG
1 CATGTCCCAGACATGTCTTACACTAGCTC-T-CATCTCAAGGCCAATG
* * * *
36612344 CATGTCCCAGACATGTCTTAAACTAGCACTCGTCTCAATGCCAATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAAGGCCAATG
*
36612390 CATGTCCCAGACATGTCTTACACTGGCTC
1 CATGTCCCAGACATGTCTTACACTAGCTC
36612419 ACATACCACC
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 37 0.58
47 1 0.02
48 26 0.41
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAAGGCCAATG
Found at i:36620883 original size:21 final size:22
Alignment explanation
Indices: 36620850--36620893 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
36620840 ATAAGATAAT
*
36620850 AAACATATTTAA-TAATACATGA
1 AAACATATGTAATTAATA-ATGA
36620872 AAACATA-GTAATTAATAATGA
1 AAACATATGTAATTAATAATGA
36620893 A
1 A
36620894 TTTTGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (22 bp):
AAACATATGTAATTAATAATGA
Found at i:36621104 original size:26 final size:27
Alignment explanation
Indices: 36621074--36621128 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
36621064 TAATAATGTG
*
36621074 AAATAATAT-AT--TGTTAAAATATA-
1 AAATAATATAATAATGTAAAAATATAT
36621097 AAATAATATAATAATGTAAAAATATAT
1 AAATAATATAATAATGTAAAAATATAT
36621124 AAATA
1 AAATA
36621129 TTATGTGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 9 0.33
24 2 0.07
26 11 0.41
27 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (27 bp):
AAATAATATAATAATGTAAAAATATAT
Found at i:36621108 original size:41 final size:41
Alignment explanation
Indices: 36621046--36621123 Score: 115
Period size: 43 Copynumber: 1.9 Consensus size: 41
36621036 TATACATGAA
*
36621046 AAAATATATAATAGATAATAATAATGTGAAATAATATATTGTT
1 AAAATATAAAATAGATAATAATAATGT-AAA-AATATATTGTT
36621089 AAAATATAAAATA-AT-ATAATAATGTAAAAATATAT
1 AAAATATAAAATAGATAATAATAATGTAAAAATATAT
36621124 AAATATTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
39 7 0.21
40 3 0.09
41 10 0.29
42 2 0.06
43 12 0.35
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (41 bp):
AAAATATAAAATAGATAATAATAATGTAAAAATATATTGTT
Found at i:36621225 original size:5 final size:5
Alignment explanation
Indices: 36621215--36621282 Score: 52
Period size: 5 Copynumber: 13.4 Consensus size: 5
36621205 AAATATGAAG
* *
36621215 TAATA TAATA TAATA AAATA TAAGTA -AATAA TAATA TAAAA T-ATA TAATACA
1 TAATA TAATA TAATA TAATA TAA-TA TAAT-A TAATA TAATA TAATA TAAT--A
*
36621267 TAAAA TAATA T-ATA TA
1 TAATA TAATA TAATA TA
36621283 CAATTTAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
4 8 0.16
5 33 0.66
6 5 0.10
7 4 0.08
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (5 bp):
TAATA
Found at i:36621246 original size:28 final size:25
Alignment explanation
Indices: 36621219--36621278 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
36621209 ATGAAGTAAT
36621219 ATAATATAATAAAATATAAGTAAAT-A
1 ATAATATAA-AAAATATAA-TAAATAA
* *
36621245 ATAATATAAAATATATAATACATAAA
1 ATAATATAAAAAATATAATAAAT-AA
36621271 ATAATATA
1 ATAATATA
36621279 TATACAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 4 0.13
25 8 0.27
26 18 0.60
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (25 bp):
ATAATATAAAAAATATAATAAATAA
Found at i:36621248 original size:89 final size:90
Alignment explanation
Indices: 36621046--36621250 Score: 215
Period size: 89 Copynumber: 2.2 Consensus size: 90
36621036 TATACATGAA
*
36621046 AAAATATATAATAGATAATAATAATGTGAAATAATATATTGTTAAAATATAAAATAATATAATAA
1 AAAA-ATATAATAAATAATAATAATGT-AAATAATATATTGTTAAAATATAAAATAATATAATAA
* * *
36621111 TGTAAAAATATATAAATATTATGTGAT
64 TGTAAAAATATATAAATATAATATAAT
* * * *
36621138 AAAAATATAATATAATAAATAATAA-GT-AATGATATA-TGTTAAAATATATATTAATATGATAA
1 AAAAATATAATA-AAT-AATAATAATGTAAATAATATATTGTTAAAATATAAAATAATATAATAA
36621200 TAG-AAAAATATGA-AGTAATATAATATAAT
64 T-GTAAAAATAT-ATA--AATATAATATAAT
36621229 -AAAATATAAGTAAATAATAATA
1 AAAAATATAA-TAAATAATAATA
36621251 TAAAATATAT
Statistics
Matches: 98, Mismatches: 8, Indels: 17
0.80 0.07 0.14
Matches are distributed among these distances:
89 40 0.41
90 22 0.22
91 20 0.20
92 8 0.08
93 8 0.08
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (90 bp):
AAAAATATAATAAATAATAATAATGTAAATAATATATTGTTAAAATATAAAATAATATAATAATG
TAAAAATATATAAATATAATATAAT
Found at i:36621269 original size:16 final size:18
Alignment explanation
Indices: 36621250--36621284 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
36621240 AAATAATAAT
36621250 ATAAAAT-ATATA-ATAC
1 ATAAAATAATATATATAC
36621266 ATAAAATAATATATATAC
1 ATAAAATAATATATATAC
36621284 A
1 A
36621285 ATTTAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 5 0.29
18 5 0.29
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAAATAATATATATAC
Found at i:36621269 original size:21 final size:20
Alignment explanation
Indices: 36621219--36621282 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
36621209 ATGAAGTAAT
*
36621219 ATAATATAATAAAATATAAGTAA
1 ATAATAAAATAAAATAT-A-T-A
*
36621242 ATAATAATATAAAATATATA
1 ATAATAAAATAAAATATATA
*
36621262 ATACATAAAATAATATATATA
1 ATA-ATAAAATAAAATATATA
36621283 CAATTTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.11
21 16 0.44
22 1 0.03
23 15 0.42
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
ATAATAAAATAAAATATATA
Found at i:36621273 original size:23 final size:26
Alignment explanation
Indices: 36621140--36621262 Score: 84
Period size: 25 Copynumber: 4.9 Consensus size: 26
36621130 TATGTGATAA
36621140 AAAT-ATAATATAAT-AAATAATAAGT
1 AAATAATAATATAATAAAAT-ATAAGT
* ** *
36621165 -AATGAT-ATATGTTAAAATATATATT
1 AAATAATAATATAATAAAATATA-AGT
* *
36621190 AATATGATAATA-GA-AAAATATGAAGT
1 AA-ATAATAATATAATAAAATAT-AAGT
36621216 -AAT-ATAATATAATAAAATATAAGT
1 AAATAATAATATAATAAAATATAAGT
*
36621240 AAATAATAATATAA-AATATATAA
1 AAATAATAATATAATAAAATATAA
36621263 TACATAAAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 22
0.73 0.06 0.20
Matches are distributed among these distances:
23 6 0.08
24 18 0.22
25 27 0.34
26 19 0.24
27 7 0.09
28 3 0.04
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (26 bp):
AAATAATAATATAATAAAATATAAGT
Found at i:36624713 original size:18 final size:19
Alignment explanation
Indices: 36624686--36624743 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
36624676 ATGAAAATAG
*
36624686 AATGGGAAATGGAAT-TGA
1 AATGGGAAATGAAATGTGA
*
36624704 AATGGTAAATGAAATGTGA
1 AATGGGAAATGAAATGTGA
*
36624723 AATTGTGG-AATGAATTGTGA
1 AA-TG-GGAAATGAAATGTGA
36624743 A
1 A
36624744 CCTTGATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 13 0.39
19 5 0.15
20 14 0.42
21 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.28
Consensus pattern (19 bp):
AATGGGAAATGAAATGTGA
Found at i:36630779 original size:87 final size:87
Alignment explanation
Indices: 36630670--36630845 Score: 343
Period size: 87 Copynumber: 2.0 Consensus size: 87
36630660 ACTTTGTACA
36630670 TATCATCTTTGCACATGCAACATATTTCTTATGTTTTACTCATTCATTGAATACTCAAAATTCAT
1 TATCATCTTTGCACATGCAACATATTTCTTATGTTTTACTCATTCATTGAATACTCAAAATTCAT
36630735 CACTATTTAAATTACTTACTGG
66 CACTATTTAAATTACTTACTGG
*
36630757 TATCATCTTTGCGCATGCAACATATTTCTTATGTTTTACTCATTCATTGAATACTCAAAATTCAT
1 TATCATCTTTGCACATGCAACATATTTCTTATGTTTTACTCATTCATTGAATACTCAAAATTCAT
36630822 CACTATTTAAATTACTTACTGG
66 CACTATTTAAATTACTTACTGG
36630844 TA
1 TA
36630846 CTGTTCACAT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (87 bp):
TATCATCTTTGCACATGCAACATATTTCTTATGTTTTACTCATTCATTGAATACTCAAAATTCAT
CACTATTTAAATTACTTACTGG
Found at i:36640744 original size:51 final size:52
Alignment explanation
Indices: 36640679--36640776 Score: 171
Period size: 51 Copynumber: 1.9 Consensus size: 52
36640669 ACATAAAATC
*
36640679 AAATATATAACATCACATATGTACATATCTATATGGCCAAATATACAAGATA
1 AAATATATAACATCACATATGTACATACCTATATGGCCAAATATACAAGATA
*
36640731 AAATATA-AACATCACATATGTACATACCTATATGGCCGAATATACA
1 AAATATATAACATCACATATGTACATACCTATATGGCCAAATATACA
36640777 TGGTCATTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 37 0.84
52 7 0.16
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (52 bp):
AAATATATAACATCACATATGTACATACCTATATGGCCAAATATACAAGATA
Found at i:36647282 original size:40 final size:40
Alignment explanation
Indices: 36647189--36647446 Score: 337
Period size: 40 Copynumber: 6.5 Consensus size: 40
36647179 AAGCCAAGTA
* * *
36647189 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
36647227 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
36647267 CCTTCGGGACTTAGCCCGGATATAGTAACTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
36647307 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * * *
36647347 CCTTCGGGACTTAGCCTGGATGTAATAACTCGCGCAGATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
36647387 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCA-AAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACT--CGCACAAATG
36647428 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
36647447 TTATCATCCA
Statistics
Matches: 194, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
38 12 0.06
39 17 0.09
40 139 0.72
41 23 0.12
42 3 0.02
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:36659118 original size:29 final size:29
Alignment explanation
Indices: 36659086--36659189 Score: 91
Period size: 29 Copynumber: 3.5 Consensus size: 29
36659076 CTTTGTGGTT
36659086 GAATCTGTTATATGTGAGCCTTAGTGGCA
1 GAATCTGTTATATGTGAGCCTTAGTGGCA
* * **
36659115 GAATCTATTATATGTGGAAGCCTTTGTGGTT
1 GAATCTGTTATATGT-G-AGCCTTAGTGGCA
** * *
36659146 GTCTTTGTTATATGTGAGCCCTAGTGGCA
1 GAATCTGTTATATGTGAGCCTTAGTGGCA
* * *
36659175 AAACCTGTCATATGT
1 GAATCTGTTATATGT
36659190 TAAAGCCTTT
Statistics
Matches: 55, Mismatches: 18, Indels: 4
0.71 0.23 0.05
Matches are distributed among these distances:
29 32 0.58
30 2 0.04
31 21 0.38
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.38
Consensus pattern (29 bp):
GAATCTGTTATATGTGAGCCTTAGTGGCA
Found at i:36659171 original size:60 final size:60
Alignment explanation
Indices: 36659074--36659201 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 60
36659064 TTAAAGTGAT
* * * * *
36659074 GCCTTTGTGGTTGAATCTGTTATATGTGAGCCTTAGTGGCAGAATCTATTATATGTGGAA
1 GCCTTTGTGGTTGAATCTGTTATATGTGAGCCCTAGTGGCAAAACCTATCATATGTGAAA
** * * *
36659134 GCCTTTGTGGTTGTCTTTGTTATATGTGAGCCCTAGTGGCAAAACCTGTCATATGTTAAA
1 GCCTTTGTGGTTGAATCTGTTATATGTGAGCCCTAGTGGCAAAACCTATCATATGTGAAA
36659194 GCCTTTGT
1 GCCTTTGT
36659202 AGCGAAATCG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.39
Consensus pattern (60 bp):
GCCTTTGTGGTTGAATCTGTTATATGTGAGCCCTAGTGGCAAAACCTATCATATGTGAAA
Found at i:36661295 original size:15 final size:16
Alignment explanation
Indices: 36661260--36661292 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
36661250 GAATGCTTAG
36661260 AACAACCACTATGCAA
1 AACAACCACTATGCAA
36661276 AACAACCACTATGCAA
1 AACAACCACTATGCAA
36661292 A
1 A
36661293 CAAGTCATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.30, G:0.06, T:0.12
Consensus pattern (16 bp):
AACAACCACTATGCAA
Found at i:36665345 original size:22 final size:23
Alignment explanation
Indices: 36665302--36665345 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
36665292 GTACGTTTAG
**
36665302 TTGTATTTTAGGATTTTCCATTA
1 TTGTATTTTAGGAAATTCCATTA
*
36665325 TTGT-TTTTAGGAAATTGCATT
1 TTGTATTTTAGGAAATTCCATT
36665346 GAAAGGCTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.23, C:0.07, G:0.16, T:0.55
Consensus pattern (23 bp):
TTGTATTTTAGGAAATTCCATTA
Found at i:36673720 original size:24 final size:24
Alignment explanation
Indices: 36673693--36673746 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
36673683 GTACTCACAC
*
36673693 ATTAATTAATTAA-ATAAAACTTCA
1 ATTAAATAA-TAATATAAAACTTCA
*
36673717 ATTAAATAATAATATTAAACTTCA
1 ATTAAATAATAATATAAAACTTCA
*
36673741 CTTAAA
1 ATTAAA
36673747 ACAAGAGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 3 0.12
24 23 0.88
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (24 bp):
ATTAAATAATAATATAAAACTTCA
Found at i:36674668 original size:19 final size:19
Alignment explanation
Indices: 36674637--36674693 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
36674627 TATTTATTTA
*
36674637 AATATTAAATTATTGTTA-T
1 AATATT-AATTATTATTATT
36674656 AATTATTAATTATTATTATT
1 AA-TATTAATTATTATTATT
36674676 AATATTATATTA-TATTAT
1 AATATTA-ATTATTATTAT
36674694 GAAATAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 23 0.68
20 11 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
AATATTAATTATTATTATT
Found at i:36674673 original size:13 final size:13
Alignment explanation
Indices: 36674652--36674693 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
36674642 TAAATTATTG
*
36674652 TTATAATTATTAA
1 TTATTATTATTAA
36674665 TTATTATTATTAA
1 TTATTATTATTAA
36674678 -TATTA-TATTATA
1 TTATTATTATTA-A
36674690 TTAT
1 TTAT
36674694 GAAATAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 5 0.19
12 6 0.23
13 15 0.58
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATTATTATTAA
Found at i:36675072 original size:20 final size:19
Alignment explanation
Indices: 36675047--36675085 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
36675037 GCAGGGGAAG
*
36675047 GAAAGAAAGAAAGGAGAAAA
1 GAAAGAAAAAAAGGA-AAAA
36675067 GAAAGAAAAAAAGGAAAAA
1 GAAAGAAAAAAAGGAAAAA
36675086 TTAAGGATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (19 bp):
GAAAGAAAAAAAGGAAAAA
Found at i:36676314 original size:16 final size:17
Alignment explanation
Indices: 36676290--36676323 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
36676280 GTATTGATAT
*
36676290 TTGAGTTGAAT-GAGAA
1 TTGAATTGAATGGAGAA
36676306 TTGAATTGAATGGAGAA
1 TTGAATTGAATGGAGAA
36676323 T
1 T
36676324 GTGTATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.32
Consensus pattern (17 bp):
TTGAATTGAATGGAGAA
Found at i:36676656 original size:30 final size:31
Alignment explanation
Indices: 36676632--36676690 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
36676622 GTAAATACTC
36676632 AAAATTTG-AGGGATTAA-AGTGTAAATATGA
1 AAAATTTGAAGGG-TTAATAGTGTAAATATGA
*
36676662 AAAATTTGAAGGGTTAATAGTGAAAATAT
1 AAAATTTGAAGGGTTAATAGTGTAAATAT
36676691 TTTAAGTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.47, C:0.00, G:0.22, T:0.31
Consensus pattern (31 bp):
AAAATTTGAAGGGTTAATAGTGTAAATATGA
Found at i:36676976 original size:11 final size:11
Alignment explanation
Indices: 36676960--36676984 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
36676950 ATATGATATT
36676960 TTATTATTTTA
1 TTATTATTTTA
36676971 TTATTATTTTA
1 TTATTATTTTA
36676982 TTA
1 TTA
36676985 GTATATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:36677037 original size:31 final size:31
Alignment explanation
Indices: 36676999--36677061 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
36676989 ATATAAAGAA
36676999 AGAAAGATGAGGAAAATTCTCATCCATGTCC
1 AGAAAGATGAGGAAAATTCTCATCCATGTCC
* *
36677030 AGAAAGATGGGGAAAATTCTCATCCATTTCC
1 AGAAAGATGAGGAAAATTCTCATCCATGTCC
36677061 A
1 A
36677062 TGCATTCACG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (31 bp):
AGAAAGATGAGGAAAATTCTCATCCATGTCC
Found at i:36679134 original size:23 final size:22
Alignment explanation
Indices: 36679108--36679194 Score: 79
Period size: 21 Copynumber: 4.0 Consensus size: 22
36679098 GCTTTACTGA
*
36679108 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTCATGTGTCGTA-T
* * *
36679131 TCAGGCACCTCGTGTGCCGTA-
1 TCAGGCACTTCATGTGTCGTAT
* *
36679152 TCAAGCACTTCGTGTGTCGTAT
1 TCAGGCACTTCATGTGTCGTAT
* *
36679174 T-AGGCACTTTATGTGTTGTAT
1 TCAGGCACTTCATGTGTCGTAT
36679195 ACTGATCAGG
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
21 34 0.65
22 1 0.02
23 17 0.33
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (22 bp):
TCAGGCACTTCATGTGTCGTAT
Found at i:36680763 original size:20 final size:20
Alignment explanation
Indices: 36680734--36680783 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
36680724 AATAGGGGTC
36680734 ACACGCCCGTGTGGCTTGGG
1 ACACGCCCGTGTGGCTTGGG
*
36680754 ACACGTCCGTGTGGCTTGGG
1 ACACGCCCGTGTGGCTTGGG
*
36680774 ACATGCCCGT
1 ACACGCCCGT
36680784 ATGGGCAGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.12, C:0.30, G:0.36, T:0.22
Consensus pattern (20 bp):
ACACGCCCGTGTGGCTTGGG
Found at i:36686214 original size:39 final size:40
Alignment explanation
Indices: 36686107--36686329 Score: 276
Period size: 40 Copynumber: 5.6 Consensus size: 40
36686097 CGGATGATAA
* * *
36686107 CCGGGCTAAGTCCCG-AGAGCATTTGAGCTAG-TGGCTA-ATT
1 CCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGCT-ACTATA-T
*
36686147 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
* *
36686187 CCGGGCTAAGT-CCGAAGGCGTTTGTGCGAGCTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
* *
36686226 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
* * * *
36686265 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACCATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
36686305 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
36686330 AGCTAGTGGC
Statistics
Matches: 166, Mismatches: 12, Indels: 10
0.88 0.06 0.05
Matches are distributed among these distances:
39 72 0.43
40 90 0.54
41 4 0.02
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
Found at i:36686328 original size:79 final size:79
Alignment explanation
Indices: 36686147--36686329 Score: 269
Period size: 79 Copynumber: 2.3 Consensus size: 79
36686137 GTGGCTAATT
* *
36686147 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGTCCGAAGGCGTTTGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCGAAGGCATTTGT
* ** *
36686212 GCGAGCTATTATAT
66 GCAAGCTACCATAA
* *
36686226 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA-CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGT-CCGAAGGCATTTG
*
36686290 TGCAAGTTACCATAA
65 TGCAAGCTACCATAA
36686305 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
36686330 AGCTAGTGGC
Statistics
Matches: 94, Mismatches: 9, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
78 11 0.12
79 83 0.88
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCGAAGGCATTTGT
GCAAGCTACCATAA
Found at i:36686351 original size:79 final size:79
Alignment explanation
Indices: 36686147--36686362 Score: 267
Period size: 79 Copynumber: 2.7 Consensus size: 79
36686137 GTGGCTAATT
* *
36686147 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGT-CCGAAGGCGTTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATATCCGGGCTAAGTCCCGAAGGCATTTG
* ** *
36686211 TGCGAGCTATTATAT
65 TGCAAGCTACCATAA
*
36686226 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA-CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATATCCGGGCTAAGTCCCGAAGGCATTTG
*
36686290 TGCAAGTTACCATAA
65 TGCAAGCTACCATAA
* * * **
36686305 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-ACTATATCCGGGCTAAGTCCCGAAGG
36686363 TACTTGGTTT
Statistics
Matches: 119, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
78 12 0.10
79 105 0.88
80 2 0.02
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
GCAAGCTACCATAA
Found at i:36686362 original size:39 final size:39
Alignment explanation
Indices: 36686107--36686362 Score: 270
Period size: 40 Copynumber: 6.5 Consensus size: 39
36686097 CGGATGATAA
* * *
36686107 CCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTA-ATT
1 CCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGT-ACTATA-T
*
36686147 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
* *
36686187 CCGGGCTAAGT-CCGAAGGCGTTTGTGCGAGCTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
*
36686226 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
* * *
36686265 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACCATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
* * *
36686305 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-ACTATAT
**
36686345 CC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
36686363 TACTTGGTTT
Statistics
Matches: 191, Mismatches: 19, Indels: 13
0.86 0.09 0.06
Matches are distributed among these distances:
39 87 0.46
40 100 0.52
41 4 0.02
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAT
Found at i:36694282 original size:40 final size:39
Alignment explanation
Indices: 36694227--36694450 Score: 217
Period size: 40 Copynumber: 5.6 Consensus size: 39
36694217 CGGATGATAA
* *
36694227 CCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTAATT
1 CCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGT-GCTAATT
* *
36694267 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGCTAAT-T
*
36694307 CCGGGCTAAGTCCCGAAGGCGTTTGTGCGA--GCTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGCTA--AT-T
** * *
36694347 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGCTAATT
* *
36694386 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGT--TACCATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGCTA--AT-T
36694426 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
36694451 AGCTAGTGGC
Statistics
Matches: 159, Mismatches: 14, Indels: 22
0.82 0.07 0.11
Matches are distributed among these distances:
37 3 0.02
39 35 0.22
40 117 0.74
41 3 0.02
42 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGCTAATT
Found at i:36694430 original size:79 final size:80
Alignment explanation
Indices: 36694267--36694450 Score: 280
Period size: 79 Copynumber: 2.3 Consensus size: 80
36694257 GTGGCTAATT
* *
36694267 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCGTTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
* ** *
36694332 TGCGAGCTATTATAT
66 TGCAAGCTACCATAA
* *
36694347 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA-CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
*
36694411 TGCAAGTTACCATAA
66 TGCAAGCTACCATAA
36694426 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
36694451 AGCTAGTGGC
Statistics
Matches: 95, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
79 59 0.62
80 36 0.38
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.24
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
TGCAAGCTACCATAA
Found at i:36694465 original size:119 final size:120
Alignment explanation
Indices: 36694227--36694483 Score: 306
Period size: 119 Copynumber: 2.2 Consensus size: 120
36694217 CGGATGATAA
* * *
36694227 CCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTAATTCCGGGCTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAG-GCATTTGAGCGAGTGGATAATACCGGGCTAAGTCCCGAAGGCATTC
* * * * * *
36694291 GTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGCTATTATAT
65 GTGCAAGCTACCATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGCTACTATAT
* * * *
36694347 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-TATTATACCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGGATAATACCGGGCTAAGTCCCGAAGGCATTCG
* * *
36694411 TGCAAGTTACCATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAG-TGGCTATAT
66 TGCAAGCTACCATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGCT-ACTATAT
**
36694466 CC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
36694484 TACTTGGTTT
Statistics
Matches: 117, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
118 15 0.13
119 73 0.62
120 27 0.23
121 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (120 bp):
CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGGATAATACCGGGCTAAGTCCCGAAGGCATTCG
TGCAAGCTACCATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGCTACTATAT
Found at i:36694472 original size:79 final size:79
Alignment explanation
Indices: 36694267--36694483 Score: 276
Period size: 79 Copynumber: 2.7 Consensus size: 79
36694257 GTGGCTAATT
* *
36694267 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCGTTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATATCCGGGCTAAGTCCCGAAGGCATTTG
* ** *
36694332 TGCGAGCTATTATAT
65 TGCAAGCTACCATAA
*
36694347 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA-CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATATCCGGGCTAAGTCCCGAAGGCATTTG
*
36694411 TGCAAGTTACCATAA
65 TGCAAGCTACCATAA
* * * **
36694426 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-ACTATATCCGGGCTAAGTCCCGAAGG
36694484 TACTTGGTTT
Statistics
Matches: 120, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
78 1 0.01
79 81 0.68
80 38 0.32
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
GCAAGCTACCATAA
Found at i:36696818 original size:46 final size:45
Alignment explanation
Indices: 36696751--36696922 Score: 215
Period size: 46 Copynumber: 3.7 Consensus size: 45
36696741 AACCCGCCCC
*
36696751 TAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-GGCATTCGCATCCA
* *
36696797 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG-ATGC-CTAGTTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGC-A--TCCA
* *
36696843 TTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGG-CATTCGCATCCA
36696890 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
36696923 ATGCTCAACC
Statistics
Matches: 108, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 4 0.04
46 61 0.56
47 31 0.29
48 2 0.02
49 4 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCATCCA
Found at i:36696868 original size:93 final size:93
Alignment explanation
Indices: 36696756--36696926 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
36696746 GCCCCTAAGT
36696756 GAACTCGGACTCAACTCAACGAGCTCAGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
36696820 ACGAGTTCGGATGCCTAGTTACATTTCAC
65 ACGAGTTCGGATGCCTAGTTACATTTCAC
*
36696849 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
36696914 CGAGTTCGGATGC
66 CGAGTTCGGATGC
36696927 TCAACCATCC
Statistics
Matches: 76, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:36702508 original size:22 final size:22
Alignment explanation
Indices: 36702482--36702526 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
36702472 CCAACACTTA
36702482 GAAAATTTTTCACTAAAATAGG
1 GAAAATTTTTCACTAAAATAGG
36702504 GAAAATTTTTCACTAAAATAGG
1 GAAAATTTTTCACTAAAATAGG
36702526 G
1 G
36702527 GTCACACGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (22 bp):
GAAAATTTTTCACTAAAATAGG
Found at i:36704943 original size:15 final size:15
Alignment explanation
Indices: 36704923--36704957 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
36704913 GTCATGAATT
36704923 TTTGCAAGTTTTGTC
1 TTTGCAAGTTTTGTC
36704938 TTTGCAAGTTTTGTC
1 TTTGCAAGTTTTGTC
36704953 TTTGC
1 TTTGC
36704958 TAGTGGGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.54
Consensus pattern (15 bp):
TTTGCAAGTTTTGTC
Found at i:36708746 original size:29 final size:28
Alignment explanation
Indices: 36708712--36708814 Score: 136
Period size: 29 Copynumber: 3.6 Consensus size: 28
36708702 TAATCGATCA
*
36708712 CGCACACTTAGTGCCATGTGATTTAAGCT
1 CGCACACTTAGTGCCAT-TAATTTAAGCT
*
36708741 CGCACACATAGTGCCATATAATTTAAGCT
1 CGCACACTTAGTGCCAT-TAATTTAAGCT
36708770 CGCACACTTAGTGCCA-TACATTTCAAGCT
1 CGCACACTTAGTGCCATTA-ATTT-AAGCT
*
36708799 TGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
36708815 ATCTCGTCAC
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
27 2 0.03
28 4 0.06
29 61 0.91
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCCATTAATTTAAGCT
Found at i:36710727 original size:27 final size:28
Alignment explanation
Indices: 36710686--36710759 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 28
36710676 ACACACCATA
* * *
36710686 AAAATGAAGCCTTTGTGG-CAATTTATG
1 AAAATGAAGCATTTGTGGTAAATCTATG
*
36710713 AAAATGAAGTATTTGTGGTAAATCTATG
1 AAAATGAAGCATTTGTGGTAAATCTATG
* *
36710741 AAAAAGAAAGCCTTTGTGG
1 AAAATG-AAGCATTTGTGG
36710760 CGATCTATCA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 16 0.42
28 12 0.32
29 10 0.26
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (28 bp):
AAAATGAAGCATTTGTGGTAAATCTATG
Found at i:36710765 original size:28 final size:28
Alignment explanation
Indices: 36710692--36710776 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 28
36710682 CATAAAAATG
* *
36710692 AAGCCTTTGTGGCAATTTATGAAAATG-
1 AAGCCTTTGTGGCAATCTATGAAAAAGA
** *
36710719 AAGTATTTGTGGTAAATCTATGAAAAAGA
1 AAGCCTTTGTGG-CAATCTATGAAAAAGA
* * *
36710748 AAGCCTTTGTGGCGATCTATCATAAAGA
1 AAGCCTTTGTGGCAATCTATGAAAAAGA
36710776 A
1 A
36710777 GTGTTTGTGA
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
27 10 0.22
28 25 0.56
29 10 0.22
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.31
Consensus pattern (28 bp):
AAGCCTTTGTGGCAATCTATGAAAAAGA
Found at i:36715011 original size:17 final size:17
Alignment explanation
Indices: 36714981--36715037 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
36714971 TATTTTATCT
*
36714981 AATAT-TTATTAATTAA
1 AATATATTATAAATTAA
*
36714997 AATATATTATAAATTTA
1 AATATATTATAAATTAA
* * *
36715014 TATGTATGATAAATTTAA
1 AATATATTATAAA-TTAA
36715032 AATATA
1 AATATA
36715038 ACTAATTTTA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
16 5 0.16
17 19 0.61
18 7 0.23
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (17 bp):
AATATATTATAAATTAA
Found at i:36716321 original size:21 final size:20
Alignment explanation
Indices: 36716300--36716337 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
36716290 TTAAGAAAAT
36716300 TTGCTAAAGTATCGATACAA
1 TTGCTAAAGTATCGATACAA
* *
36716320 TTGCTTAGGTATCGATAC
1 TTGCTAAAGTATCGATAC
36716338 CTCAGAGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (20 bp):
TTGCTAAAGTATCGATACAA
Found at i:36722860 original size:40 final size:39
Alignment explanation
Indices: 36722805--36722972 Score: 187
Period size: 40 Copynumber: 4.2 Consensus size: 39
36722795 CAATTGAATG
* * *
36722805 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTG-TT
36722845 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAG-TGTT
* * * *
36722885 ATATCCGGGCTAATATCCGAAGGCATTTGTGCGAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGT-GTT
**
36722925 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGT-GTT
36722965 ATATCCGG
1 ATATCCGG
36722973 TTGTATTTTG
Statistics
Matches: 111, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
39 6 0.05
40 101 0.91
41 4 0.04
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGTT
Found at i:36722938 original size:80 final size:80
Alignment explanation
Indices: 36722805--36722972 Score: 239
Period size: 80 Copynumber: 2.1 Consensus size: 80
36722795 CAATTGAATG
* *
36722805 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGACTATATCCGGGCTAAGACCCGAAGGCA
*
36722870 TTCGTGCAAGTTGTT
66 TTCGTGCAAGTGGTT
* * * *
36722885 ATATCCGGGCTAATATCCGAAGGCATTTGTGCGAGTCG-TTATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGT-GACTATATCCGGGCTAAGACCCGAAGGC
**
36722949 ATTCGTGCGTGTGGTT
65 ATTCGTGCAAGTGGTT
36722965 ATATCCGG
1 ATATCCGG
36722973 TTGTATTTTG
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
80 77 0.99
81 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGACTATATCCGGGCTAAGACCCGAAGGCA
TTCGTGCAAGTGGTT
Found at i:36731044 original size:40 final size:39
Alignment explanation
Indices: 36730989--36731156 Score: 187
Period size: 40 Copynumber: 4.2 Consensus size: 39
36730979 CAATTGAATG
* * *
36730989 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTG-TT
36731029 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAG-TGTT
* * * *
36731069 ATATCCGGGCTAATATCCGAAGGCATTTGTGCGAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGT-GTT
**
36731109 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGT-GTT
36731149 ATATCCGG
1 ATATCCGG
36731157 TTGTATTCCG
Statistics
Matches: 111, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
39 6 0.05
40 101 0.91
41 4 0.04
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGTT
Found at i:36731122 original size:80 final size:80
Alignment explanation
Indices: 36730989--36731156 Score: 239
Period size: 80 Copynumber: 2.1 Consensus size: 80
36730979 CAATTGAATG
* *
36730989 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGACTATATCCGGGCTAAGACCCGAAGGCA
*
36731054 TTCGTGCAAGTTGTT
66 TTCGTGCAAGTGGTT
* * * *
36731069 ATATCCGGGCTAATATCCGAAGGCATTTGTGCGAGTCG-TTATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGT-GACTATATCCGGGCTAAGACCCGAAGGC
**
36731133 ATTCGTGCGTGTGGTT
65 ATTCGTGCAAGTGGTT
36731149 ATATCCGG
1 ATATCCGG
36731157 TTGTATTCCG
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
80 77 0.99
81 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGACTATATCCGGGCTAAGACCCGAAGGCA
TTCGTGCAAGTGGTT
Found at i:36737035 original size:37 final size:37
Alignment explanation
Indices: 36736977--36737084 Score: 198
Period size: 37 Copynumber: 2.9 Consensus size: 37
36736967 GCTCAGACGA
* *
36736977 AATCTCCACACGAAGTTATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
36737014 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
36737051 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
36737085 ATATATTTCC
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
Found at i:36737356 original size:48 final size:48
Alignment explanation
Indices: 36737230--36737462 Score: 378
Period size: 48 Copynumber: 4.8 Consensus size: 48
36737220 GCACATCGCC
*
36737230 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
* * *
36737280 TATATATTTCACATT-GACCATTCAGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
*
36737328 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATTTCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
36737376 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATTTCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
36737424 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
36737463 TGCATGTTCA
Statistics
Matches: 173, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
48 130 0.75
49 2 0.01
50 41 0.24
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.36
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:36737525 original size:47 final size:47
Alignment explanation
Indices: 36737337--36737531 Score: 119
Period size: 48 Copynumber: 4.1 Consensus size: 47
36737327 ATACATATTT
* * * * * *
36737337 CACATTAGCCATTCGGCTTTACCACATATACATTTCTCATACATATT--T
1 CACATTAGCCATTCGGCCTTACCACATAT--A-TACACATTCACATTCAC
* * * * * *
36737385 CACATTAGCCATTCGGCTTTACCACATATACATTTCTCATACATATT--T
1 CACATTAGCCATTCGGCCTTACCACATAT--A-TACACATTCACATTCAC
* * ** *
36737433 CACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCAC
1 CACATTAGCCATTCGGCCTTACCACATATATACACATTCACATTCAC
* * * *
36737480 CACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCAT
1 CACATTAGCCATTCGGCCTTACCACATATATACACATTCACATTCAC
36737527 CACAT
1 CACAT
36737532 AAAATCCTAA
Statistics
Matches: 130, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
45 9 0.07
46 1 0.01
47 43 0.33
48 77 0.59
ACGTcount: A:0.29, C:0.28, G:0.08, T:0.35
Consensus pattern (47 bp):
CACATTAGCCATTCGGCCTTACCACATATATACACATTCACATTCAC
Found at i:36741883 original size:15 final size:15
Alignment explanation
Indices: 36741863--36741894 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
36741853 CATTTCACTA
*
36741863 TTATGTCTTTTATAT
1 TTATGTCTTTCATAT
36741878 TTATGTCTTTCATAT
1 TTATGTCTTTCATAT
36741893 TT
1 TT
36741895 TACATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.09, G:0.06, T:0.66
Consensus pattern (15 bp):
TTATGTCTTTCATAT
Found at i:36755407 original size:39 final size:39
Alignment explanation
Indices: 36755338--36755412 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
36755328 TGTACCTTAT
* *
36755338 AAAAAATTAATACATTCAATTATTTCTTTTCTTTTTCCA
1 AAAAAATTAATAAATTCAATTATTTCTTTTCCTTTTCCA
* *
36755377 AAAAAATTATTAAATTTATATTATTT-TTTTCCTTTT
1 AAAAAATTAATAAATTCA-ATTATTTCTTTTCCTTTT
36755413 ACTAATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 24 0.77
40 7 0.23
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (39 bp):
AAAAAATTAATAAATTCAATTATTTCTTTTCCTTTTCCA
Found at i:36755775 original size:14 final size:14
Alignment explanation
Indices: 36755756--36755786 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
36755746 TGCTACCATT
36755756 TTACTATTATGTTG
1 TTACTATTATGTTG
*
36755770 TTACTATTTTGTTG
1 TTACTATTATGTTG
36755784 TTA
1 TTA
36755787 ATGTTTGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (14 bp):
TTACTATTATGTTG
Found at i:36755855 original size:30 final size:30
Alignment explanation
Indices: 36755820--36755878 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
36755810 TATTTTATTG
36755820 TTAATTTTGTTATTATTTTAAAGACATTTA
1 TTAATTTTGTTATTATTTTAAAGACATTTA
*
36755850 TTAATTTTGTTATTATTTTAGAGACATTT
1 TTAATTTTGTTATTATTTTAAAGACATTT
36755879 TCTTGTTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGACATTTA
Found at i:36755983 original size:18 final size:18
Alignment explanation
Indices: 36755962--36756001 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
36755952 GAAATATTTA
*
36755962 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
36755980 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
36755998 TTTT
1 TTTT
36756002 AAATTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:36758909 original size:21 final size:21
Alignment explanation
Indices: 36758885--36758954 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
36758875 CATATACATC
36758885 ATGAACTCAGACCATAACTCA
1 ATGAACTCAGACCATAACTCA
* *
36758906 ATGAATTCAGGTGCCACATATA-TC-
1 ATGAACTCA---GAC-CATA-ACTCA
*
36758930 ATGAACTCAGACCACAACTCA
1 ATGAACTCAGACCATAACTCA
36758951 ATGA
1 ATGA
36758955 GTTAAAATGA
Statistics
Matches: 37, Mismatches: 5, Indels: 14
0.66 0.09 0.25
Matches are distributed among these distances:
19 1 0.03
20 5 0.14
21 14 0.38
24 10 0.27
25 6 0.16
26 1 0.03
ACGTcount: A:0.40, C:0.26, G:0.13, T:0.21
Consensus pattern (21 bp):
ATGAACTCAGACCATAACTCA
Found at i:36760091 original size:3 final size:3
Alignment explanation
Indices: 36760078--36760108 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
36760068 TCATTAAATG
36760078 AGA ATGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA
36760109 GAATGTTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:36761674 original size:46 final size:46
Alignment explanation
Indices: 36761528--36761746 Score: 180
Period size: 46 Copynumber: 4.7 Consensus size: 46
36761518 TCACTTGTGT
* * * *
36761528 GAGCTAGTGTAAGACATGCCTGGGACATGCATCAGCCA-C-ATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATC-GGCATCGA-GACGA
* *
36761574 GAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCATTGAGACGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCGAGACGA
* * ** *
36761622 GTGCTAGTGTAAGACATGTTTGGGACATGTTTCGGCCTCGAGACGTA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACG-A
* * * *
36761669 -AGCTAGTGTAAGACATGTCTGAGACATGCATCGGTTAT-GAGATGT
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGG-CATCGAGACGA
*
36761714 G-TC-AGTGTAAGACCATGTCTGGGACATGGCATC
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATC
36761747 AGTACAGATA
Statistics
Matches: 140, Mismatches: 24, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
44 9 0.06
45 14 0.10
46 66 0.47
47 29 0.21
48 21 0.15
49 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACGA
Found at i:36764780 original size:43 final size:43
Alignment explanation
Indices: 36764625--36764867 Score: 256
Period size: 43 Copynumber: 5.7 Consensus size: 43
36764615 GTTTATGAAA
* * ** * *
36764625 AAAAATGCCACTAAAGGTCATGATCTTTAACGGCGCTTTTCCC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCC
** * *
36764668 AAAAGTGCCGCTAAAGAACATGACTTTTAGTGGCG-TTTTCCC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCC
*
36764710 AAAAACGCCGCTAAATAACATGACCTTTAGCGGCGCTTTTCCC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCC
** * * ** *
36764753 AAAAATACCGTTAGAGGTCATGGCCTTTAGCGGCGCTTTTCCC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCC
* **
36764796 ACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCTT
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCC
* *
36764839 ACAAACGCCACTAAA-AATCATGACCTTTA
1 AAAAACGCCGCTAAAGAA-CATGACCTTTA
36764868 AAAAAATTAT
Statistics
Matches: 166, Mismatches: 32, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
42 39 0.23
43 127 0.77
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCC
Found at i:36764817 original size:86 final size:85
Alignment explanation
Indices: 36764625--36764836 Score: 262
Period size: 85 Copynumber: 2.5 Consensus size: 85
36764615 GTTTATGAAA
* * ** * * * *
36764625 AAAAATGCCACTAAAGGTCATGATCTTTAACGGCGCTTTTCCCAAAAGTGCCGCTAAAGAACATG
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAAAAATACCGCTAAAGAACATG
* *
36764690 ACTTTTAGTGGCGTTTTCCC
66 ACCTTTAGCGGCGTTTTCCC
* * * **
36764710 AAAAACGCCGCTAAATAACATGACCTTTAGCGGCGCTTTTCCCAAAAATACCGTTAGAGGTCATG
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAAAAATACCGCTAAAGAACATG
*
36764775 GCCTTTAGCGGCGCTTTTCCC
66 ACCTTTAGCGGCG-TTTTCCC
*
36764796 ACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTC
36764837 TTACAAACGC
Statistics
Matches: 108, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
85 62 0.57
86 46 0.43
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (85 bp):
AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAAAAATACCGCTAAAGAACATG
ACCTTTAGCGGCGTTTTCCC
Found at i:36767871 original size:40 final size:40
Alignment explanation
Indices: 36767788--36768043 Score: 297
Period size: 40 Copynumber: 6.5 Consensus size: 40
36767778 ACCCAAGTAT
* ** * *
36767788 CTTCGGGATTTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
36767826 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
36767866 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
36767906 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * * *
36767946 CTTC-GGATGTTAGTCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCACTAGCACAAATGC
*
36767986 CTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAAGGC
1 CTTCGGGACTTAGCCCGGATA-TAGTCACTAGCACAAATGC
*
36768026 CTTCGGGACCTAGCCCGG
1 CTTCGGGACTTAGCCCGG
36768044 TTATCATCCG
Statistics
Matches: 185, Mismatches: 26, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
38 11 0.06
39 19 0.10
40 152 0.82
41 3 0.02
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:36767999 original size:120 final size:119
Alignment explanation
Indices: 36767788--36768043 Score: 338
Period size: 120 Copynumber: 2.2 Consensus size: 119
36767778 ACCCAAGTAT
* * *
36767788 CTTCGGGAT-TTAG-CCGGATATAACCACTCGCACAAGGCCTTCGGGTCTTAGCCCGGATATGGT
1 CTTCGGG-TCTTAGCCCGGATATAACAACTCGCACAAGGCCTTCGGATCTTAGCCCGGATATAGT
* * * *
36767851 CACTAGCATAAATGCCTTCGGGACTTAGCCCGG-ATATAGTCGCTAGCACAAATGC
65 AACTAGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTCACTAGCACAAAGGC
* * * *
36767906 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGATGTTAGTCCGGATATAGT
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCAC-AAGGCCTTCGGATCTTAGCCCGGATATAGT
*
36767971 AACTTGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTCACTAGCACAAAGGC
65 AACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTCACTAGCACAAAGGC
* *
36768026 CTTCGGGACCTAGCCCGG
1 CTTCGGGTCTTAGCCCGG
36768044 TTATCATCCG
Statistics
Matches: 120, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
117 1 0.01
118 11 0.09
119 18 0.15
120 88 0.73
121 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (119 bp):
CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAGGCCTTCGGATCTTAGCCCGGATATAGTA
ACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTCACTAGCACAAAGGC
Found at i:36769029 original size:32 final size:32
Alignment explanation
Indices: 36768993--36769060 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
36768983 ATGAAACAAC
36768993 AACCATCACCCTTATTAATTTCCATAGCCGAA
1 AACCATCACCCTTATTAATTTCCATAGCCGAA
36769025 AACCATCACCCTTATTAATTTCCATAGCCGAA
1 AACCATCACCCTTATTAATTTCCATAGCCGAA
36769057 AACC
1 AACC
36769061 TTACTCATTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.35, C:0.32, G:0.06, T:0.26
Consensus pattern (32 bp):
AACCATCACCCTTATTAATTTCCATAGCCGAA
Found at i:36769998 original size:27 final size:27
Alignment explanation
Indices: 36769968--36770021 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
36769958 GAAAATATGA
36769968 TTGAAAACTTATTTTGTGCAAGTACAG
1 TTGAAAACTTATTTTGTGCAAGTACAG
*
36769995 TTGAAATCTTATTTTGTGCAAGTACAG
1 TTGAAAACTTATTTTGTGCAAGTACAG
36770022 CACTAGAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (27 bp):
TTGAAAACTTATTTTGTGCAAGTACAG
Found at i:36770851 original size:89 final size:89
Alignment explanation
Indices: 36770700--36770900 Score: 339
Period size: 89 Copynumber: 2.3 Consensus size: 89
36770690 GTAAAGTCCA
* * * *
36770700 AAAGATAGACTGGGGGCAAATTAAGAAACAAATACTAACATTCAGAAGCATTGAACCAAGTCGTA
1 AAAGACAGATTGGGGGCAAATTTAGAAACAAAGACTAACATTCAGAAGCATTGAACCAAGTCGTA
36770765 TCGCAACAAATGAATCAAGGTTCC
66 TCGCAACAAATGAATCAAGGTTCC
36770789 AAAGACAGATTGGGGGCAAATTTAGAAACAAAGACTAACATTCAGAAGCATTGAACCAAGTCGTA
1 AAAGACAGATTGGGGGCAAATTTAGAAACAAAGACTAACATTCAGAAGCATTGAACCAAGTCGTA
* *
36770854 TGGCAACAATTGAATCAAGGTTCC
66 TCGCAACAAATGAATCAAGGTTCC
*
36770878 AAAGACAGATTGAGGGCAAATTT
1 AAAGACAGATTGGGGGCAAATTT
36770901 TATAACAGAC
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 105 1.00
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (89 bp):
AAAGACAGATTGGGGGCAAATTTAGAAACAAAGACTAACATTCAGAAGCATTGAACCAAGTCGTA
TCGCAACAAATGAATCAAGGTTCC
Found at i:36772326 original size:7 final size:7
Alignment explanation
Indices: 36772314--36772458 Score: 123
Period size: 7 Copynumber: 20.4 Consensus size: 7
36772304 CCCCAACCCT
36772314 TAAACCA
1 TAAACCA
36772321 TAAACCA
1 TAAACCA
36772328 TAAACCA
1 TAAACCA
36772335 TAAACCA
1 TAAACCA
36772342 TAAACCA
1 TAAACCA
36772349 TAAACCA
1 TAAACCA
36772356 TAAACCA
1 TAAACCA
* *
36772363 TAATCCC
1 TAAACCA
36772370 TAAACCCA
1 TAAA-CCA
**
36772378 TAGTCCA
1 TAAACCA
*
36772385 TAAACCT
1 TAAACCA
36772392 TAAA--A
1 TAAACCA
*
36772397 TAGTAACTCC
1 TA--AAC-CA
*
36772407 TAAACCT
1 TAAACCA
*
36772414 TAAACCC
1 TAAACCA
36772421 TAAACCA
1 TAAACCA
**
36772428 TATGCCA
1 TAAACCA
*
36772435 TAAACCT
1 TAAACCA
*
36772442 TAAACCC
1 TAAACCA
*
36772449 TAAACTA
1 TAAACCA
36772456 TAA
1 TAA
36772459 TGTAATTAAT
Statistics
Matches: 110, Mismatches: 22, Indels: 12
0.76 0.15 0.08
Matches are distributed among these distances:
5 2 0.02
7 99 0.90
8 7 0.06
10 2 0.02
ACGTcount: A:0.48, C:0.29, G:0.02, T:0.21
Consensus pattern (7 bp):
TAAACCA
Found at i:36772921 original size:40 final size:38
Alignment explanation
Indices: 36772877--36773017 Score: 153
Period size: 40 Copynumber: 3.6 Consensus size: 38
36772867 ATTTTTTTGT
36772877 GGCGTTTTTCAAAAGGTGCCGCTAATAGTCGACCTATAGC
1 GGCGTTTTTCAAAA-G-GCCGCTAATAGTCGACCTATAGC
*
36772917 GGCGTTTTTCAAAAAGCACCGCTAATAGTCGACCTATAGC
1 GGCGTTTTTC-AAAAG-GCCGCTAATAGTCGACCTATAGC
* * * *
36772957 AGCATTTTTCAAAA-G-CACTAAT-GCTCGATCTATAGC
1 GGCGTTTTTCAAAAGGCCGCTAATAG-TCGACCTATAGC
*
36772993 GGCGTTTTTCAAAAAGCACGCTAAT
1 GGCGTTTTTCAAAAGGC-CGCTAAT
36773018 GCCACTAAAG
Statistics
Matches: 86, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
35 1 0.01
36 29 0.34
37 1 0.01
39 10 0.12
40 41 0.48
41 4 0.05
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (38 bp):
GGCGTTTTTCAAAAGGCCGCTAATAGTCGACCTATAGC
Found at i:36773172 original size:40 final size:40
Alignment explanation
Indices: 36773054--36773184 Score: 156
Period size: 40 Copynumber: 3.3 Consensus size: 40
36773044 ATTTTTTTGT
*
36773054 GGCGTTTTTAAAAAAGCGCCGCTAAATACTCGATCTATAGC
1 GGCGTTTTTTAAAAAGCGCCGCT-AATACTCGATCTATAGC
* * * * * *
36773095 GGCGCTTTTTGAAAA-TGCCACTAATGCTCGATTTATAGC
1 GGCGTTTTTTAAAAAGCGCCGCTAATACTCGATCTATAGC
* * *
36773134 GGCATTTTTTAAAAAGCGCCGCTAATTCTTGATCTATAGC
1 GGCGTTTTTTAAAAAGCGCCGCTAATACTCGATCTATAGC
36773174 GGCGTTTTTTA
1 GGCGTTTTTTA
36773185 TCCAAAAGCC
Statistics
Matches: 73, Mismatches: 16, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
39 27 0.37
40 34 0.47
41 12 0.16
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (40 bp):
GGCGTTTTTTAAAAAGCGCCGCTAATACTCGATCTATAGC
Found at i:36775773 original size:13 final size:13
Alignment explanation
Indices: 36775725--36775767 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
36775715 TTAAATAATC
* *
36775725 TAAAATTTTATTA
1 TAAAATATTACTA
36775738 CTAAAATA-TACTA
1 -TAAAATATTACTA
36775751 TAAAATATTACTA
1 TAAAATATTACTA
36775764 TAAA
1 TAAA
36775768 GAATTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 7 0.27
13 13 0.50
14 6 0.23
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAAATATTACTA
Found at i:36777623 original size:3 final size:3
Alignment explanation
Indices: 36777615--36777655 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
36777605 CTTTGCCTTA
36777615 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
36777656 AGCTAGCTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:36778452 original size:13 final size:13
Alignment explanation
Indices: 36778436--36778460 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36778426 TTACTTTTAT
36778436 TTTTAAAAAATTA
1 TTTTAAAAAATTA
36778449 TTTTAAAAAATT
1 TTTTAAAAAATT
36778461 TTAACCAAAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTAAAAAATTA
Done.