Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015366.1 Kokia drynarioides strain JFW-HI SEQ_130413, whole genome shotgun sequence
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: 628308
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 91 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1384 original size:39 final size:39
Alignment explanation
Indices: 1335--1433 Score: 171
Period size: 39 Copynumber: 2.5 Consensus size: 39
1325 TTAAATAGGG
1335 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
*
1374 TTTTAATGTGTCTTATTTTGATACATATTTAATAGTTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
* *
1413 TTTTAAGGTGTCTAAGTTTGA
1 TTTTAATGTGTCTTAGTTTGA
1434 GACAAATTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.54
Consensus pattern (39 bp):
TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
Found at i:1515 original size:32 final size:32
Alignment explanation
Indices: 1479--1541 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
1469 AGCCAAAATT
* *
1479 AATTAGCTGATTAATGTGCTTCAGGTACATGC
1 AATTAGCTGATTAATATACTTCAGGTACATGC
*
1511 AATTAGCTGATTAATATATTTCAGGTACATG
1 AATTAGCTGATTAATATACTTCAGGTACATG
1542 TATGGATGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.37
Consensus pattern (32 bp):
AATTAGCTGATTAATATACTTCAGGTACATGC
Found at i:4834 original size:22 final size:23
Alignment explanation
Indices: 4777--4834 Score: 57
Period size: 25 Copynumber: 2.5 Consensus size: 23
4767 TTACAGTCGA
*
4777 TGTCGCAACATAGATAGTGTCTT
1 TGTCGCAACATAGATAGAGTCTT
*
4800 TAGGTCGCGACATA-ATAGAGTGC-T
1 T--GTCGCAACATAGATAGAGT-CTT
4824 TGTCGCAACAT
1 TGTCGCAACAT
4835 TCTCCACAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
22 9 0.31
23 1 0.03
24 8 0.28
25 11 0.38
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (23 bp):
TGTCGCAACATAGATAGAGTCTT
Found at i:7294 original size:13 final size:14
Alignment explanation
Indices: 7276--7305 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
7266 GTCAATGCAA
7276 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
7289 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
7303 TCA
1 TCA
7306 ATTTACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:23690 original size:11 final size:12
Alignment explanation
Indices: 23674--23702 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
23664 ATTTCCCACA
23674 AAAAAAGT-GAT
1 AAAAAAGTAGAT
23685 AAAAAAGTAGAT
1 AAAAAAGTAGAT
23697 AAAAAA
1 AAAAAA
23703 AGAAAAATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (12 bp):
AAAAAAGTAGAT
Found at i:23690 original size:12 final size:13
Alignment explanation
Indices: 23673--23704 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
23663 TATTTCCCAC
23673 AAAAAAAGT-GAT
1 AAAAAAAGTAGAT
23685 -AAAAAAGTAGAT
1 AAAAAAAGTAGAT
23697 AAAAAAAG
1 AAAAAAAG
23705 AAAAATACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.44
12 3 0.17
13 7 0.39
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (13 bp):
AAAAAAAGTAGAT
Found at i:25383 original size:24 final size:24
Alignment explanation
Indices: 25356--25411 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 24
25346 GGAGAGTTCT
*
25356 CAAGAGGAAAATGAAAATGAAAAA
1 CAAGAAGAAAATGAAAATGAAAAA
25380 CAAGAAGAAAATGAAAATG-AAAA
1 CAAGAAGAAAATGAAAATGAAAAA
25403 CAAAGAAGA
1 C-AAGAAGA
25412 TACCCATACA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 5 0.17
24 25 0.83
ACGTcount: A:0.68, C:0.05, G:0.20, T:0.07
Consensus pattern (24 bp):
CAAGAAGAAAATGAAAATGAAAAA
Found at i:33686 original size:48 final size:48
Alignment explanation
Indices: 33614--33726 Score: 172
Period size: 48 Copynumber: 2.4 Consensus size: 48
33604 TTAATGTAAG
* * *
33614 GCATTTAACAAAAAAAATAGTTAATAATGCATATTACTAAACAAAGAT
1 GCATTTAACAAAAAAAACACTTAATAATGCAGATTACTAAACAAAGAT
* * *
33662 GCATTTAACAAACAAAACACTTAATGATGCAGATTATTAAACAAAGAT
1 GCATTTAACAAAAAAAACACTTAATAATGCAGATTACTAAACAAAGAT
33710 GCATTTAACAAAAAAAA
1 GCATTTAACAAAAAAAA
33727 AAAACACTTA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.54, C:0.12, G:0.09, T:0.25
Consensus pattern (48 bp):
GCATTTAACAAAAAAAACACTTAATAATGCAGATTACTAAACAAAGAT
Found at i:39120 original size:12 final size:12
Alignment explanation
Indices: 39103--39131 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
39093 CAACAGAAAA
39103 TTTTTTTGAA-T
1 TTTTTTTGAAGT
39114 TTTTTTTGAAGT
1 TTTTTTTGAAGT
39126 TTTTTT
1 TTTTTT
39132 CAAATCGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (12 bp):
TTTTTTTGAAGT
Found at i:41194 original size:26 final size:26
Alignment explanation
Indices: 41165--41215 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
41155 TTTTGGGCGC
* *
41165 AATTATGGACACGTTCATGTAGCGAA
1 AATTACGGACACGTTCATGCAGCGAA
* *
41191 AATTCCGGACATGTTCATGCAGCGA
1 AATTACGGACACGTTCATGCAGCGA
41216 CATTCTTGGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (26 bp):
AATTACGGACACGTTCATGCAGCGAA
Found at i:41260 original size:37 final size:36
Alignment explanation
Indices: 41207--41338 Score: 124
Period size: 37 Copynumber: 3.6 Consensus size: 36
41197 GGACATGTTC
*
41207 ATGCAGCGACATTCTTGGGTGCAATTGAAGAATACTT
1 ATGCAGCGACAGTCTTGGGTGCAATTGAAGAATA-TT
* *
41244 ATGCAGCGATAGTCTTGGATGCAATTGAAGAATATTT
1 ATGCAGCGACAGTCTTGGGTGCAATTGAAGAATA-TT
* **
41281 CTGCAAG-GACAGTCTTGGGTGC-ATTCCAGAAATATT
1 ATGC-AGCGACAGTCTTGGGTGCAATTGAAG-AATATT
* * *
41317 CATGCAGCAATAGTTTTGGGTG
1 -ATGCAGCGACAGTCTTGGGTG
41339 TAATCTGGAA
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
36 9 0.12
37 67 0.86
38 2 0.03
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (36 bp):
ATGCAGCGACAGTCTTGGGTGCAATTGAAGAATATT
Found at i:42857 original size:7 final size:7
Alignment explanation
Indices: 42834--42871 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
42824 ATACAATTTC
42834 TTTTATT
1 TTTTATT
*
42841 TTAATATT
1 TT-TTATT
42849 TTTTATT
1 TTTTATT
42856 TTTTATT
1 TTTTATT
42863 TTTTATT
1 TTTTATT
42870 TT
1 TT
42872 ACTTACATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 22 0.79
8 6 0.21
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTATT
Found at i:47344 original size:15 final size:16
Alignment explanation
Indices: 47324--47375 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
47314 TCAACAACTC
47324 TTCTCTC-TTTTTTTT
1 TTCTCTCATTTTTTTT
** *
47339 TTCTCTCAAGTTCTTT
1 TTCTCTCATTTTTTTT
47355 TTCTCTCATTTCTTTTT
1 TTCTCTCATTT-TTTTT
47372 TTCT
1 TTCT
47376 TCTCTCTATT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 7 0.24
16 14 0.48
17 8 0.28
ACGTcount: A:0.06, C:0.23, G:0.02, T:0.69
Consensus pattern (16 bp):
TTCTCTCATTTTTTTT
Found at i:47355 original size:20 final size:19
Alignment explanation
Indices: 47352--47396 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 19
47342 TCTCAAGTTC
47352 TTTTTCTCTCATTTCTTTT
1 TTTTTCTCTCATTTCTTTT
47371 TTTCTTCTCTCTATTTCTTTT
1 TTT-TTCTCTC-ATTTCTTTT
47392 TTTTT
1 TTTTT
47397 TGGCTCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.12
20 9 0.38
21 12 0.50
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTCTCTCATTTCTTTT
Found at i:50114 original size:50 final size:50
Alignment explanation
Indices: 49987--50128 Score: 153
Period size: 50 Copynumber: 2.8 Consensus size: 50
49977 AAATAATGGA
* *
49987 TTACTAAATGCATGAC-TTGATTTAATGATGCAAACTTTAACTAACATGGAAG
1 TTACTTAATGCATGTCATT-ATTT-ATGATGCAAA-TTTAACTAACATGGAAG
* ** * * *
50039 TTACATAATGCATGAT-AGGACTTATGATGCATATTTAACTAACATGTAAG
1 TTACTTAATGCATG-TCATTATTTATGATGCAAATTTAACTAACATGGAAG
*
50089 TTACTTAATGCATGTCATTATTTATGATGCAAACTTAACT
1 TTACTTAATGCATGTCATTATTTATGATGCAAATTTAACT
50129 GATCATGAGA
Statistics
Matches: 73, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
49 1 0.01
50 48 0.66
51 9 0.12
52 15 0.21
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (50 bp):
TTACTTAATGCATGTCATTATTTATGATGCAAATTTAACTAACATGGAAG
Found at i:50241 original size:33 final size:34
Alignment explanation
Indices: 50177--50241 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 34
50167 ACTTTATTAA
* *
50177 ATGTAGATCACATAATGCATGTCATATTTAAAAG
1 ATGTAGATCACATAATGCATGACATAATTAAAAG
*
50211 ATGTAGATTA-ATAATGCA-GAACATAATTAAA
1 ATGTAGATCACATAATGCATG-ACATAATTAAA
50242 TCACAATCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 1 0.04
33 17 0.63
34 9 0.33
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (34 bp):
ATGTAGATCACATAATGCATGACATAATTAAAAG
Found at i:50368 original size:17 final size:17
Alignment explanation
Indices: 50337--50369 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
50327 CAAGCACTTA
50337 TTAAACTAAAATAAAAC
1 TTAAACTAAAATAAAAC
50354 TTAAA-TAAAATTAAAA
1 TTAAACTAAAA-TAAAA
50370 AGTCCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAACTAAAATAAAAC
Found at i:51097 original size:21 final size:22
Alignment explanation
Indices: 51067--51107 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
51057 CTTCCTGCTA
*
51067 TGTCATGACA-CGACTCCTATG
1 TGTCACGACATCGACTCCTATG
51088 TGTCACGACATCGACTCCTA
1 TGTCACGACATCGACTCCTA
51108 AATGCTGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (22 bp):
TGTCACGACATCGACTCCTATG
Found at i:51300 original size:39 final size:39
Alignment explanation
Indices: 51253--51331 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
51243 ACACACTTTT
51253 TCCCTTAGATTAATTTCTTATTGTAATTTAGGTTTTTAG
1 TCCCTTAGATTAATTTCTTATTGTAATTTAGGTTTTTAG
51292 TCCCTTAGATTAATTTCTTATTGTAATTTAGGTTTTTAG
1 TCCCTTAGATTAATTTCTTATTGTAATTTAGGTTTTTAG
51331 T
1 T
51332 TGTTTTCTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.54
Consensus pattern (39 bp):
TCCCTTAGATTAATTTCTTATTGTAATTTAGGTTTTTAG
Found at i:58756 original size:32 final size:32
Alignment explanation
Indices: 58720--58780 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
58710 CATCCGTGCT
* *
58720 TGTACCTGAAATATATTAATCAGCTAATTGCA
1 TGTACCTGAAACACATTAATCAGCTAATTGCA
58752 TGTACCTGAAACACATTAATCAGCTAATT
1 TGTACCTGAAACACATTAATCAGCTAATT
58781 AATTTCAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (32 bp):
TGTACCTGAAACACATTAATCAGCTAATTGCA
Found at i:62014 original size:13 final size:14
Alignment explanation
Indices: 61980--62018 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
61970 TATCTCTTTT
*
61980 TCTTCCTTTTCATC
1 TCTTTCTTTTCATC
*
61994 TTTTTCTTTTC-TC
1 TCTTTCTTTTCATC
62007 TCTTTCTTTTCA
1 TCTTTCTTTTCA
62019 CTTTCTTTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.05, C:0.28, G:0.00, T:0.67
Consensus pattern (14 bp):
TCTTTCTTTTCATC
Found at i:62046 original size:29 final size:29
Alignment explanation
Indices: 61998--62054 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 29
61988 TTCATCTTTT
*
61998 TCTTTTCTCTCTTTCTTTTCACTTTCTTTAC
1 TCTTTTCTCTC-TCCTTTTC-CTTTCTTTAC
62029 TCTTTTCTCTC-CCTTTTCCTTTCTTT
1 TCTTTTCTCTCTCCTTTTCCTTTCTTT
62055 TTTTCAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 8 0.32
29 6 0.24
31 11 0.44
ACGTcount: A:0.04, C:0.32, G:0.00, T:0.65
Consensus pattern (29 bp):
TCTTTTCTCTCTCCTTTTCCTTTCTTTAC
Found at i:67228 original size:10 final size:9
Alignment explanation
Indices: 67200--67224 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
67190 ATATGTTGAA
67200 TAAAAAGTG
1 TAAAAAGTG
67209 TAAAAAGTG
1 TAAAAAGTG
67218 TAAAAAG
1 TAAAAAG
67225 GTGTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (9 bp):
TAAAAAGTG
Found at i:68660 original size:33 final size:34
Alignment explanation
Indices: 68623--68691 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
68613 ATGCTAAACT
68623 CTTACC-AATTAACTTTTATTTCCTTATTTAAGA
1 CTTACCAAATTAACTTTTATTTCCTTATTTAAGA
*
68656 CTTACCAAATTAACTTTTATTTCCTTATTTTAGA
1 CTTACCAAATTAACTTTTATTTCCTTATTTAAGA
68690 CT
1 CT
68692 AAGCTGTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 6 0.18
34 28 0.82
ACGTcount: A:0.29, C:0.19, G:0.03, T:0.49
Consensus pattern (34 bp):
CTTACCAAATTAACTTTTATTTCCTTATTTAAGA
Found at i:68971 original size:2 final size:2
Alignment explanation
Indices: 68964--69005 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
68954 AGTACATATG
68964 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
69006 TCATACTTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:73721 original size:24 final size:24
Alignment explanation
Indices: 73687--73736 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
73677 TGTATAGGTA
*
73687 TCTTCTTGTTTTTCATTTTCATTT
1 TCTTCTAGTTTTTCATTTTCATTT
*
73711 TCTTCTAGTTTTTCATTTTCTTTT
1 TCTTCTAGTTTTTCATTTTCATTT
73735 TC
1 TC
73737 CTCTTGAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.08, C:0.18, G:0.04, T:0.70
Consensus pattern (24 bp):
TCTTCTAGTTTTTCATTTTCATTT
Found at i:75256 original size:19 final size:19
Alignment explanation
Indices: 75232--75268 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
75222 CAATCAATCA
75232 GGATGTATTAGAATCAAAT
1 GGATGTATTAGAATCAAAT
75251 GGATGTATTAGAATCAAA
1 GGATGTATTAGAATCAAA
75269 CTAACAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.22, T:0.30
Consensus pattern (19 bp):
GGATGTATTAGAATCAAAT
Found at i:75643 original size:17 final size:18
Alignment explanation
Indices: 75621--75655 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
75611 AATATTTTTT
75621 TATTTTT-ATTTTTCTCA
1 TATTTTTCATTTTTCTCA
*
75638 TATTTTTCTTTTTTCTCA
1 TATTTTTCATTTTTCTCA
75656 GACTTTTTGG
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:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (18 bp):
TATTTTTCATTTTTCTCA
Found at i:78621 original size:20 final size:20
Alignment explanation
Indices: 78596--78641 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
78586 AGAGTCACAC
*
78596 AGTAGATAGGATGTGCAGAA
1 AGTAGATAGGAAGTGCAGAA
78616 AGTAGATAGGAAGTGCAGAA
1 AGTAGATAGGAAGTGCAGAA
*
78636 GGTAGA
1 AGTAGA
78642 GTTGTCAGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.04, G:0.37, T:0.17
Consensus pattern (20 bp):
AGTAGATAGGAAGTGCAGAA
Found at i:79700 original size:27 final size:27
Alignment explanation
Indices: 79670--79760 Score: 87
Period size: 27 Copynumber: 3.4 Consensus size: 27
79660 GCTAATTTGA
79670 TTTTGTTATTTTTAATTTTGTTTCAAT
1 TTTTGTTATTTTTAATTTTGTTTCAAT
* * ** ** *
79697 TTTTGTTAAATTGTTGAGCTAATTT-GA-
1 TTTTGTT--ATTTTTAATTTTGTTTCAAT
79724 TTTTGTTATTTTTAATTTTGTTTCAAT
1 TTTTGTTATTTTTAATTTTGTTTCAAT
79751 TTTTGTTATT
1 TTTTGTTATT
79761 GTAGATTTTT
Statistics
Matches: 46, Mismatches: 14, Indels: 8
0.68 0.21 0.12
Matches are distributed among these distances:
25 10 0.22
26 1 0.02
27 24 0.52
28 1 0.02
29 10 0.22
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (27 bp):
TTTTGTTATTTTTAATTTTGTTTCAAT
Found at i:79710 original size:54 final size:54
Alignment explanation
Indices: 79641--79758 Score: 236
Period size: 54 Copynumber: 2.2 Consensus size: 54
79631 ATTTAGTAAG
79641 ATTTTTGTTAAATTGTTGAGCTAATTTGATTTTGTTATTTTTAATTTTGTTTCA
1 ATTTTTGTTAAATTGTTGAGCTAATTTGATTTTGTTATTTTTAATTTTGTTTCA
79695 ATTTTTGTTAAATTGTTGAGCTAATTTGATTTTGTTATTTTTAATTTTGTTTCA
1 ATTTTTGTTAAATTGTTGAGCTAATTTGATTTTGTTATTTTTAATTTTGTTTCA
79749 ATTTTTGTTA
1 ATTTTTGTTA
79759 TTGTAGATTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.22, C:0.03, G:0.13, T:0.62
Consensus pattern (54 bp):
ATTTTTGTTAAATTGTTGAGCTAATTTGATTTTGTTATTTTTAATTTTGTTTCA
Found at i:86348 original size:24 final size:25
Alignment explanation
Indices: 86321--86372 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
86311 GTAGGTTCTT
*
86321 TTCTTGTTTC-TCTTCTTCCTT-TCC
1 TTCTT-TTTCTTCTTCATCCTTCTCC
*
86345 TTCTTTTTCTTCTTGATCCTTCTCC
1 TTCTTTTTCTTCTTCATCCTTCTCC
86370 TTC
1 TTC
86373 AATTGATCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.17
24 14 0.58
25 6 0.25
ACGTcount: A:0.02, C:0.33, G:0.04, T:0.62
Consensus pattern (25 bp):
TTCTTTTTCTTCTTCATCCTTCTCC
Found at i:102467 original size:6 final size:6
Alignment explanation
Indices: 102456--102494 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
102446 TGATCAAAAT
* * *
102456 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
102495 TATGAATTGT
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:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:102594 original size:34 final size:34
Alignment explanation
Indices: 102556--102620 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
102546 TAGTTGACAT
*
102556 GCCATAGGATTGGAAGAGTTCAAGGATACTTCGA
1 GCCATAGGATTGGAAGAGTTCAAGAATACTTCGA
102590 GCCATAGGATTGGAAGAGTTCAAGAATACTT
1 GCCATAGGATTGGAAGAGTTCAAGAATACTT
102621 TGACCTTGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.25
Consensus pattern (34 bp):
GCCATAGGATTGGAAGAGTTCAAGAATACTTCGA
Found at i:109234 original size:17 final size:17
Alignment explanation
Indices: 109204--109244 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
109194 AAACTAAAAT
109204 GAATGCAATGACAATTAA
1 GAATGCAATGACAA-TAA
109222 -AATGCAA-GAACAATAA
1 GAATGCAATG-ACAATAA
109238 GAATGCA
1 GAATGCA
109245 TGAAAATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.54, C:0.12, G:0.17, T:0.17
Consensus pattern (17 bp):
GAATGCAATGACAATAA
Found at i:121194 original size:30 final size:30
Alignment explanation
Indices: 121160--121252 Score: 186
Period size: 30 Copynumber: 3.1 Consensus size: 30
121150 TTTTTTTAAG
121160 TATGTTTCAATCTTTTTCATAAGTATTCTT
1 TATGTTTCAATCTTTTTCATAAGTATTCTT
121190 TATGTTTCAATCTTTTTCATAAGTATTCTT
1 TATGTTTCAATCTTTTTCATAAGTATTCTT
121220 TATGTTTCAATCTTTTTCATAAGTATTCTT
1 TATGTTTCAATCTTTTTCATAAGTATTCTT
121250 TAT
1 TAT
121253 TAAATGAATG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.24, C:0.13, G:0.06, T:0.57
Consensus pattern (30 bp):
TATGTTTCAATCTTTTTCATAAGTATTCTT
Found at i:128722 original size:24 final size:24
Alignment explanation
Indices: 128686--128731 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
128676 ACATTCATCC
* *
128686 AATTCATGTATTA-GCATTCAAAAG
1 AATTCAAGAATTATGCA-TCAAAAG
128710 AATTCAAGAATTATGCATCAAA
1 AATTCAAGAATTATGCATCAAA
128732 TGAAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (24 bp):
AATTCAAGAATTATGCATCAAAAG
Found at i:138914 original size:20 final size:20
Alignment explanation
Indices: 138893--138991 Score: 119
Period size: 20 Copynumber: 5.0 Consensus size: 20
138883 AAACAAGGGA
* *
138893 ACCAAAGTGCAAATAGGAGA
1 ACCAAAGTGCAAATAGGGGC
* *
138913 ACCAAAGTGAAAACAGGGGC
1 ACCAAAGTGCAAATAGGGGC
138933 ACCAAAGTGCAGAA-AGGGGC
1 ACCAAAGTGCA-AATAGGGGC
* *
138953 ACCAAAGTGTAAAAAGGGGC
1 ACCAAAGTGCAAATAGGGGC
*
138973 ACCAATGTGCAAATAGGGG
1 ACCAAAGTGCAAATAGGGG
138992 ATAGGGGCAC
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.03
20 64 0.94
21 2 0.03
ACGTcount: A:0.43, C:0.17, G:0.30, T:0.09
Consensus pattern (20 bp):
ACCAAAGTGCAAATAGGGGC
Found at i:138991 original size:40 final size:40
Alignment explanation
Indices: 138883--138992 Score: 143
Period size: 40 Copynumber: 2.8 Consensus size: 40
138873 ACAGTTGTAC
* * *
138883 AAACAAGGGAACCAAAGTGCAAATAGGAGAACCAAAGTGA
1 AAACAGGGGCACCAAAGTGCAAATAGGGGAACCAAAGTGA
*
138923 AAACAGGGGCACCAAAGTGCAGAA-AGGGGCACCAAAGTGTA
1 AAACAGGGGCACCAAAGTGCA-AATAGGGGAACCAAAGTG-A
*
138964 AAA-AGGGGCACCAATGTGCAAATAGGGGA
1 AAACAGGGGCACCAAAGTGCAAATAGGGGA
138993 TAGGGGCACC
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
39 2 0.03
40 53 0.87
41 6 0.10
ACGTcount: A:0.45, C:0.16, G:0.30, T:0.08
Consensus pattern (40 bp):
AAACAGGGGCACCAAAGTGCAAATAGGGGAACCAAAGTGA
Found at i:162349 original size:26 final size:26
Alignment explanation
Indices: 162320--162369 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
162310 GTCTTCCAGA
* *
162320 AATTTATCTCATACGAGTCTAGACAC
1 AATTTAGCTCATACGAGCCTAGACAC
* *
162346 AATTTAGCTCTTATGAGCCTAGAC
1 AATTTAGCTCATACGAGCCTAGAC
162370 TGAATAATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (26 bp):
AATTTAGCTCATACGAGCCTAGACAC
Found at i:169432 original size:26 final size:26
Alignment explanation
Indices: 169403--169479 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 26
169393 CTTATGATCG
* *
169403 AGACAGAATAATACCCTTACGGGCTC
1 AGACAGAATAACACCCTTACGAGCTC
* * * *
169429 AGACAAAATAACGCTCTTACGAGCTT
1 AGACAGAATAACACCCTTACGAGCTC
*
169455 AGACAGAATAACGCTCC-TACGAGCT
1 AGACAGAATAACAC-CCTTACGAGCT
169480 ATAATTCAGA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 41 0.98
27 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.19
Consensus pattern (26 bp):
AGACAGAATAACACCCTTACGAGCTC
Found at i:173226 original size:20 final size:20
Alignment explanation
Indices: 173193--173267 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
173183 GAGTACAGTT
* *
173193 GTACAAACAAGGGCACCAAA
1 GTACAAATAGGGGCACCAAA
***
173213 GTACAAATAGGGGCATTGAA
1 GTACAAATAGGGGCACCAAA
**
173233 GTGTAAATAGGGGCACCAAA
1 GTACAAATAGGGGCACCAAA
*
173253 GTGCAAATAGGGGCA
1 GTACAAATAGGGGCA
173268 TATCATCTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.13
Consensus pattern (20 bp):
GTACAAATAGGGGCACCAAA
Found at i:177732 original size:7 final size:7
Alignment explanation
Indices: 177720--177765 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
177710 TGAAGTTCAA
177720 TCTTTTT
1 TCTTTTT
177727 TCTTTTT
1 TCTTTTT
177734 TC-TTTT
1 TCTTTTT
*
177740 T-TTCTT
1 TCTTTTT
177746 TCTTTATT
1 TCTTT-TT
177754 TCTTTTT
1 TCTTTTT
177761 T-TTTT
1 TCTTTT
177766 AACAATTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
6 13 0.38
7 14 0.41
8 7 0.21
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.85
Consensus pattern (7 bp):
TCTTTTT
Found at i:178745 original size:7 final size:7
Alignment explanation
Indices: 178733--178779 Score: 69
Period size: 7 Copynumber: 6.7 Consensus size: 7
178723 AACAATAGAA
178733 ATAAAAC
1 ATAAAAC
178740 ATAAAAC
1 ATAAAAC
*
178747 ATAAATAA
1 ATAAA-AC
178755 ATAAAAC
1 ATAAAAC
178762 ATAAAAC
1 ATAAAAC
178769 ATAAAAC
1 ATAAAAC
178776 -TAAA
1 ATAAA
178780 TGAAATCATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
6 4 0.11
7 27 0.73
8 6 0.16
ACGTcount: A:0.72, C:0.11, G:0.00, T:0.17
Consensus pattern (7 bp):
ATAAAAC
Found at i:178756 original size:22 final size:22
Alignment explanation
Indices: 178731--178773 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
178721 CCAACAATAG
178731 AAATAAAACATAAAACATAAAT
1 AAATAAAACATAAAACATAAAT
178753 AAATAAAACATAAAACATAAA
1 AAATAAAACATAAAACATAAA
178774 ACTAAATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.16
Consensus pattern (22 bp):
AAATAAAACATAAAACATAAAT
Found at i:178760 original size:15 final size:15
Alignment explanation
Indices: 178740--178785 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
178730 GAAATAAAAC
178740 ATAAAACATAAATAA
1 ATAAAACATAAATAA
*
178755 ATAAAACATAAA-AC
1 ATAAAACATAAATAA
178769 ATAAAAC-TAAATGAA
1 ATAAAACATAAAT-AA
178784 AT
1 AT
178786 CATTTTGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 4 0.15
14 8 0.30
15 15 0.56
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.20
Consensus pattern (15 bp):
ATAAAACATAAATAA
Found at i:178826 original size:14 final size:15
Alignment explanation
Indices: 178803--178838 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
178793 GTTAGGGTAG
178803 GAAA-AAAAAA-AAA
1 GAAAGAAAAAATAAA
178816 GAAAGAAAAAATAAA
1 GAAAGAAAAAATAAA
178831 -AAAGAAAA
1 GAAAGAAAA
178839 CTAGCTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.19
14 14 0.67
15 3 0.14
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (15 bp):
GAAAGAAAAAATAAA
Found at i:178831 original size:18 final size:17
Alignment explanation
Indices: 178803--178837 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
178793 GTTAGGGTAG
178803 GAAAAAAAAAAAAGAAA
1 GAAAAAAAAAAAAGAAA
178820 GAAAAAATAAAAAAGAAA
1 GAAAAAA-AAAAAAGAAA
178838 ACTAGCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (17 bp):
GAAAAAAAAAAAAGAAA
Found at i:179299 original size:20 final size:19
Alignment explanation
Indices: 179267--179310 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
179257 AAAAATCAAA
*
179267 TTTTTTCATTTTTTTAATT
1 TTTTTTCAATTTTTTAATT
179286 TTTTTTCCAATTTTTTAATT
1 TTTTTT-CAATTTTTTAATT
179306 TTTTT
1 TTTTT
179311 AAAAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTTCAATTTTTTAATT
Found at i:181312 original size:26 final size:26
Alignment explanation
Indices: 181283--181365 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
181273 ATGTGTCATC
181283 ATGAGTATATGAATCCTTTACGGATT
1 ATGAGTATATGAATCCTTTACGGATT
* * * *
181309 ATGAGGTTTGATGACTAT-GTGT-C--ATC
1 ATGA-GTAT-ATGA--ATCCTTTACGGATT
181335 ATGAGTATATGAATCCTTTACGGATT
1 ATGAGTATATGAATCCTTTACGGATT
181361 ATGAG
1 ATGAG
181366 GTCCGATGAC
Statistics
Matches: 41, Mismatches: 8, Indels: 16
0.63 0.12 0.25
Matches are distributed among these distances:
22 2 0.05
23 2 0.05
24 5 0.12
25 3 0.07
26 17 0.41
27 3 0.07
28 5 0.12
29 2 0.05
30 2 0.05
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (26 bp):
ATGAGTATATGAATCCTTTACGGATT
Found at i:181444 original size:52 final size:52
Alignment explanation
Indices: 181260--181437 Score: 284
Period size: 52 Copynumber: 3.4 Consensus size: 52
181250 GTAAATGAAA
*
181260 AGGTTTGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
1 AGGTTCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
*
181312 AGGTTTGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
1 AGGTTCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
* * * * *
181364 AGGTCCGATGACTATGTGTTATCATGAGTACATGAATCCTCTACAGATTATG
1 AGGTTCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
*
181416 AGGTTCGATAACTATGTGTCAT
1 AGGTTCGATGACTATGTGTCAT
181438 TGTGAGTTTT
Statistics
Matches: 117, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 117 1.00
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (52 bp):
AGGTTCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
Found at i:188495 original size:52 final size:52
Alignment explanation
Indices: 188415--188601 Score: 286
Period size: 52 Copynumber: 3.6 Consensus size: 52
188405 GTAAATGAAA
* *
188415 AGGTCCGATGACTATGTGTCATCGTGAGTATACGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
188467 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
188519 AGGTCCGATGACTATGTTTCATCGTCAGTATATGAATCCTTTACGAATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
188571 AGGTCCGAT-AGCTATATGTCATTGTGAGTAT
1 AGGTCCGATGA-CTATGTGTCATCGTGAGTAT
188602 TAAATGGAAT
Statistics
Matches: 123, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
51 1 0.01
52 122 0.99
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:217418 original size:22 final size:22
Alignment explanation
Indices: 217402--217443 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
217392 CGCACTCTGG
217402 TGCTTAGTGATTTGCACTTCGA
1 TGCTTAGTGATTTGCACTTCGA
217424 TGCTTAGTGATTTGCACTTC
1 TGCTTAGTGATTTGCACTTC
217444 AGAGCCTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (22 bp):
TGCTTAGTGATTTGCACTTCGA
Found at i:217453 original size:22 final size:22
Alignment explanation
Indices: 217406--217454 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
217396 CTCTGGTGCT
*
217406 TAGTGATTTGCACTTCGATGCT
1 TAGTGATTTGCACTTCGATGCC
217428 TAGTGATTTGCACTTCAGA-GCC
1 TAGTGATTTGCACTTC-GATGCC
217450 TAGTG
1 TAGTG
217455 TTCTATTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (22 bp):
TAGTGATTTGCACTTCGATGCC
Found at i:219192 original size:25 final size:23
Alignment explanation
Indices: 219164--219209 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
219154 GTTGGATCCA
219164 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
219189 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
219210 CCCTAATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:221210 original size:6 final size:6
Alignment explanation
Indices: 221201--221278 Score: 61
Period size: 6 Copynumber: 12.8 Consensus size: 6
221191 AAATAGATAA
* * *
221201 TAAAAC TAAAAC TAAAAC TAAAAC TAAAAAAA TAAAAA TAAAA- TAAAAA
1 TAAAAC TAAAAC TAAAAC TAAAAC T--AAAAC TAAAAC TAAAAC TAAAAC
* * *
221250 TAAAAAC GAAAAC GAAAAC GAAAAC -AAAA
1 T-AAAAC TAAAAC TAAAAC TAAAAC TAAAA
221279 ATGAAAATGA
Statistics
Matches: 65, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
5 9 0.14
6 47 0.72
7 4 0.06
8 5 0.08
ACGTcount: A:0.74, C:0.10, G:0.04, T:0.12
Consensus pattern (6 bp):
TAAAAC
Found at i:221237 original size:26 final size:25
Alignment explanation
Indices: 221197--221255 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
221187 ATAAAAATAG
* *
221197 ATAATAAAACTAAAACTAAAACTAAAA
1 ATAA-AAAAATAAAAATAAAA-TAAAA
*
221224 CTAAAAAAATAAAAATAAAATAAAA
1 ATAAAAAAATAAAAATAAAATAAAA
221249 ATAAAAA
1 ATAAAAA
221256 CGAAAACGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 11 0.39
26 14 0.50
27 3 0.11
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (25 bp):
ATAAAAAAATAAAAATAAAATAAAA
Found at i:221245 original size:11 final size:11
Alignment explanation
Indices: 221186--221254 Score: 63
Period size: 11 Copynumber: 6.2 Consensus size: 11
221176 CAACCATAGG
221186 AATAAAAATAGA
1 AATAAAAATA-A
*
221198 TAATAAAACTAA
1 -AATAAAAATAA
*
221210 AACTAAAACTAA
1 AA-TAAAAATAA
221222 AACT--AAA-AA
1 AA-TAAAAATAA
221231 AATAAAAATAA
1 AATAAAAATAA
221242 AATAAAAATAA
1 AATAAAAATAA
221253 AA
1 AA
221255 ACGAAAACGA
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
8 1 0.02
9 4 0.08
10 5 0.10
11 17 0.34
12 14 0.28
13 9 0.18
ACGTcount: A:0.75, C:0.06, G:0.01, T:0.17
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:221256 original size:32 final size:32
Alignment explanation
Indices: 221199--221261 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
221189 AAAAATAGAT
* * *
221199 AATAAAACTAAAACTAAAACTAAAACTAAAAA
1 AATAAAAATAAAACTAAAAATAAAACGAAAAA
221231 AATAAAAATAAAA-TAAAAATAAAAACGAAAA
1 AATAAAAATAAAACTAAAAAT-AAAACGAAAA
221262 CGAAAACGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 6 0.22
32 21 0.78
ACGTcount: A:0.76, C:0.08, G:0.02, T:0.14
Consensus pattern (32 bp):
AATAAAAATAAAACTAAAAATAAAACGAAAAA
Found at i:221285 original size:6 final size:6
Alignment explanation
Indices: 221229--221369 Score: 114
Period size: 6 Copynumber: 23.8 Consensus size: 6
221219 TAAAACTAAA
* * * * * * **
221229 AAAATA AAAAT- AAAATA AAAATA AAAACG AAAACG AAAACG AAAACA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
221276 AAAATG AAAATG AAAATG AAAATG AAAAATG AAAAATG AAAATG -AAA--
1 AAAATG AAAATG AAAATG AAAATG -AAAATG -AAAATG AAAATG AAAATG
* *
221323 AAAATG AAAA-- AAAACG AAAAAATA AAAATG AAAATG AAAATG AAAAT
1 AAAATG AAAATG AAAATG --AAAATG AAAATG AAAATG AAAATG AAAAT
221370 AAATATACTA
Statistics
Matches: 118, Mismatches: 8, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
4 7 0.06
5 8 0.07
6 86 0.73
7 13 0.11
8 4 0.03
ACGTcount: A:0.74, C:0.04, G:0.11, T:0.12
Consensus pattern (6 bp):
AAAATG
Found at i:221350 original size:39 final size:40
Alignment explanation
Indices: 221282--221362 Score: 121
Period size: 39 Copynumber: 2.0 Consensus size: 40
221272 AACAAAAATG
*
221282 AAAATGAAAATGAAAATGAAAAATGAAAAATGAAAATGAAA
1 AAAATGAAAA-GAAAACGAAAAATGAAAAATGAAAATGAAA
221323 AAAATGAAAA-AAAACGAAAAAAT-AAAAATGAAAATGAAA
1 AAAATGAAAAGAAAACG-AAAAATGAAAAATGAAAATGAAA
221362 A
1 A
221363 TGAAAATAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
39 22 0.58
40 6 0.16
41 10 0.26
ACGTcount: A:0.74, C:0.01, G:0.12, T:0.12
Consensus pattern (40 bp):
AAAATGAAAAGAAAACGAAAAATGAAAAATGAAAATGAAA
Found at i:223108 original size:87 final size:87
Alignment explanation
Indices: 222962--223198 Score: 413
Period size: 87 Copynumber: 2.7 Consensus size: 87
222952 TATTTTGAAA
*
222962 TCTAGTTTCAGAAACCGAAA-AAATTTTAGCAAGCATCTCTTCAAGGTTCGATTTCTGCTCTTGT
1 TCTAGTTTTAGAAACCGAAATAAA-TTTAGCAAGCATCTCTTCAAGGTTCGATTTCTGCTCTTGT
*
223026 TGATAAGGTTGTTGAAAAGTCGG
65 TGATAAGGTTGTTGAAAAGTCAG
223049 TCTAGTTTTAGAAACCGAAATAAATTTAGCAAGCATCTCTTCAAGGTTCGATTTCTGCTCTTGTT
1 TCTAGTTTTAGAAACCGAAATAAATTTAGCAAGCATCTCTTCAAGGTTCGATTTCTGCTCTTGTT
223114 GATAAGGTTGTTGAAAAGTCAG
66 GATAAGGTTGTTGAAAAGTCAG
* * *
223136 TCTAGTTTTAGAAACCGAAATAAATTTAGCAAGCATCTCCTAAAGGTTCGATTTTTGCTCTTG
1 TCTAGTTTTAGAAACCGAAATAAATTTAGCAAGCATCTCTTCAAGGTTCGATTTCTGCTCTTG
223199 CTGAAAAGCT
Statistics
Matches: 144, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
87 141 0.98
88 3 0.02
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (87 bp):
TCTAGTTTTAGAAACCGAAATAAATTTAGCAAGCATCTCTTCAAGGTTCGATTTCTGCTCTTGTT
GATAAGGTTGTTGAAAAGTCAG
Found at i:226067 original size:14 final size:13
Alignment explanation
Indices: 226035--226087 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
226025 TCATCTCATC
*
226035 TCATTTACTGTTTA
1 TCATTTA-TTTTTA
* *
226049 CCATTTATTTTTC
1 TCATTTATTTTTA
226062 TGCATTTATATTTTA
1 T-CATTTAT-TTTTA
226077 TCATTTATTTT
1 TCATTTATTTT
226088 CTCGTACTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 7 0.22
14 20 0.62
15 5 0.16
ACGTcount: A:0.21, C:0.13, G:0.04, T:0.62
Consensus pattern (13 bp):
TCATTTATTTTTA
Found at i:237303 original size:21 final size:21
Alignment explanation
Indices: 237274--237315 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
237264 TCAGTCACTT
237274 GAAAAAAAAAAAAAAAAAGAA
1 GAAAAAAAAAAAAAAAAAGAA
* * *
237295 GAAAGAAAAGAAAAAGAAGAA
1 GAAAAAAAAAAAAAAAAAGAA
237316 TAAATTGATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (21 bp):
GAAAAAAAAAAAAAAAAAGAA
Found at i:259472 original size:18 final size:18
Alignment explanation
Indices: 259457--259648 Score: 132
Period size: 18 Copynumber: 10.7 Consensus size: 18
259447 TAATGCTCTT
259457 ACAAGCTAGTATGCTCAA
1 ACAAGCTAGTATGCTCAA
* *
259475 ACAAACCAGTATGCTCAA
1 ACAAGCTAGTATGCTCAA
* *
259493 ACGAGCTAGTATGCGCAA
1 ACAAGCTAGTATGCTCAA
** * *
259511 ATGAGCCAATATGCTCAA
1 ACAAGCTAGTATGCTCAA
** *
259529 ATGAGCTAGTATGCTCTA
1 ACAAGCTAGTATGCTCAA
* * *
259547 ACGAGCCAGTATGTTCAA
1 ACAAGCTAGTATGCTCAA
* * *
259565 ACGAGCCAATATGCTCAA
1 ACAAGCTAGTATGCTCAA
* * **
259583 ACGAGCTAGTATTCTTTA
1 ACAAGCTAGTATGCTCAA
** *
259601 ACGTGCCAGTATGCTCAA
1 ACAAGCTAGTATGCTCAA
* * *
259619 ACGAGCCAATATGCTCAA
1 ACAAGCTAGTATGCTCAA
*
259637 ACGAGCTAGTAT
1 ACAAGCTAGTAT
259649 ACTATTCCTT
Statistics
Matches: 141, Mismatches: 33, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 141 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (18 bp):
ACAAGCTAGTATGCTCAA
Found at i:259500 original size:36 final size:36
Alignment explanation
Indices: 259460--259648 Score: 225
Period size: 36 Copynumber: 5.2 Consensus size: 36
259450 TGCTCTTACA
* *
259460 AGCTAGTATGCTCAAACAAACCAGTATGCTCAAACG
1 AGCTAGTATGCTCAAACGAGCCAGTATGCTCAAACG
* * * *
259496 AGCTAGTATGCGCAAATGAGCCAATATGCTCAAATG
1 AGCTAGTATGCTCAAACGAGCCAGTATGCTCAAACG
* *
259532 AGCTAGTATGCTCTAACGAGCCAGTATGTTCAAACG
1 AGCTAGTATGCTCAAACGAGCCAGTATGCTCAAACG
* * * * **
259568 AGCCAATATGCTCAAACGAGCTAGTATTCTTTAACG
1 AGCTAGTATGCTCAAACGAGCCAGTATGCTCAAACG
* * *
259604 TGCCAGTATGCTCAAACGAGCCAATATGCTCAAACG
1 AGCTAGTATGCTCAAACGAGCCAGTATGCTCAAACG
259640 AGCTAGTAT
1 AGCTAGTAT
259649 ACTATTCCTT
Statistics
Matches: 124, Mismatches: 29, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 124 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (36 bp):
AGCTAGTATGCTCAAACGAGCCAGTATGCTCAAACG
Found at i:259550 original size:54 final size:54
Alignment explanation
Indices: 259466--259648 Score: 258
Period size: 54 Copynumber: 3.4 Consensus size: 54
259456 TACAAGCTAG
* * * * * * *
259466 TATGCTCAAACAAACCAGTATGCTCAAACGAGCTAGTATGCGCAAATGAGCCAA
1 TATGCTCAAACGAGCTAGTATGCTCTAACGAGCCAGTATGCTCAAACGAGCCAA
* *
259520 TATGCTCAAATGAGCTAGTATGCTCTAACGAGCCAGTATGTTCAAACGAGCCAA
1 TATGCTCAAACGAGCTAGTATGCTCTAACGAGCCAGTATGCTCAAACGAGCCAA
* * *
259574 TATGCTCAAACGAGCTAGTATTCTTTAACGTGCCAGTATGCTCAAACGAGCCAA
1 TATGCTCAAACGAGCTAGTATGCTCTAACGAGCCAGTATGCTCAAACGAGCCAA
259628 TATGCTCAAACGAGCTAGTAT
1 TATGCTCAAACGAGCTAGTAT
259649 ACTATTCCTT
Statistics
Matches: 115, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 115 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (54 bp):
TATGCTCAAACGAGCTAGTATGCTCTAACGAGCCAGTATGCTCAAACGAGCCAA
Found at i:262943 original size:102 final size:102
Alignment explanation
Indices: 262767--262971 Score: 410
Period size: 102 Copynumber: 2.0 Consensus size: 102
262757 CCCTCCAAAC
262767 TTAAATCATTGCTCGTCCTGAGTAATGTTCATACATGACAAAGGTCTTGGTAAGGAAAAATTTCT
1 TTAAATCATTGCTCGTCCTGAGTAATGTTCATACATGACAAAGGTCTTGGTAAGGAAAAATTTCT
262832 AAATGTGCAAGTAGCATCAATCTTTGTCTCATAATCA
66 AAATGTGCAAGTAGCATCAATCTTTGTCTCATAATCA
262869 TTAAATCATTGCTCGTCCTGAGTAATGTTCATACATGACAAAGGTCTTGGTAAGGAAAAATTTCT
1 TTAAATCATTGCTCGTCCTGAGTAATGTTCATACATGACAAAGGTCTTGGTAAGGAAAAATTTCT
262934 AAATGTGCAAGTAGCATCAATCTTTGTCTCATAATCA
66 AAATGTGCAAGTAGCATCAATCTTTGTCTCATAATCA
262971 T
1 T
262972 GCATCAACAA
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 103 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (102 bp):
TTAAATCATTGCTCGTCCTGAGTAATGTTCATACATGACAAAGGTCTTGGTAAGGAAAAATTTCT
AAATGTGCAAGTAGCATCAATCTTTGTCTCATAATCA
Found at i:264353 original size:20 final size:20
Alignment explanation
Indices: 264315--264353 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
264305 TGATTGTGGG
* * *
264315 AAGGGTTAATTAGGGTTAAA
1 AAGGATTAATTAAGCTTAAA
264335 AAGGATTAATTAAGCTTAA
1 AAGGATTAATTAAGCTTAA
264354 TGATGAAAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.31
Consensus pattern (20 bp):
AAGGATTAATTAAGCTTAAA
Found at i:266157 original size:92 final size:92
Alignment explanation
Indices: 265998--266172 Score: 296
Period size: 92 Copynumber: 1.9 Consensus size: 92
265988 AACCCATGCA
* * *
265998 TGTATCGGTAGAAGTACAGGGTAGGAGAGAGGTTGTCCATTGACTGGGGTTGTATCGGTAGATGA
1 TGTATCGGTAGAAGTACAGGGTAGGAGAGAGGTTGTCCACTGACTGGGGTTGTATCGATAGAGGA
266063 ATAACAAGTATCGATAGTTTGCATACT
66 ATAACAAGTATCGATAGTTTGCATACT
** *
266090 TGTATCGGTAGAAGTACAGGGTAGGAGAGAGGTTGTTTACTGACTTGGGTTGTATCGATAGAGGA
1 TGTATCGGTAGAAGTACAGGGTAGGAGAGAGGTTGTCCACTGACTGGGGTTGTATCGATAGAGGA
266155 ATAACAAGTATCGATAGT
66 ATAACAAGTATCGATAGT
266173 CATGTGTTTA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
92 77 1.00
ACGTcount: A:0.29, C:0.10, G:0.32, T:0.29
Consensus pattern (92 bp):
TGTATCGGTAGAAGTACAGGGTAGGAGAGAGGTTGTCCACTGACTGGGGTTGTATCGATAGAGGA
ATAACAAGTATCGATAGTTTGCATACT
Found at i:267122 original size:18 final size:18
Alignment explanation
Indices: 267095--267130 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
267085 ACCCTCTTAT
267095 TAAACATAAAAATGAAAA
1 TAAACATAAAAATGAAAA
* *
267113 TAAACGTAAAATTGAAAA
1 TAAACATAAAAATGAAAA
267131 CAAAAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (18 bp):
TAAACATAAAAATGAAAA
Found at i:277273 original size:27 final size:29
Alignment explanation
Indices: 277228--277283 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
277218 TGTACTCAGA
277228 TTGAAGATTTAGATCCCAC-A-CCTTAAT
1 TTGAAGATTTAGATCCCACAATCCTTAAT
*
277255 TTGAAGATTT-GATTGCCACAATCCTTAAT
1 TTGAAGATTTAGA-TCCCACAATCCTTAAT
277284 AGTGATTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 2 0.08
27 15 0.60
28 1 0.04
29 7 0.28
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (29 bp):
TTGAAGATTTAGATCCCACAATCCTTAAT
Found at i:283259 original size:123 final size:123
Alignment explanation
Indices: 283024--283265 Score: 286
Period size: 123 Copynumber: 2.0 Consensus size: 123
283014 TTTAATTCAA
* * *
283024 AGACCAAAACTAGTTTACCAAAAGACAAACTAATTAGACAAAATGATACGATTTCCCGAGCATGG
1 AGACAAAAACTAGTTTACCAAAAGACAAACTAATTAGACAAAATGATACGATATCCCAAGCATGG
* * * ** * *
283089 AATGTTCGAAAAGTTGCTCGAAGGAATGGATCGTCATGAATAATTTAACGAACTATCT
66 AATGTTCAAAAAATTCCTAAAAGGAATGAATCGTCATAAATAATTTAACGAACTATCT
* * * * * ** *
283147 AGACAAAAAGTAGTTTACCAAATGACAAACTATTTAGATAAAATGATGCGATATCTTAAGCATTG
1 AGACAAAAACTAGTTTACCAAAAGACAAACTAATTAGACAAAATGATACGATATCCCAAGCATGG
** * *
283212 AATGTTCAAAAAATTCCTAAAAGGAATGAATTTTCATAAATACTTTAAGGAACT
66 AATGTTCAAAAAATTCCTAAAAGGAATGAATCGTCATAAATAATTTAACGAACT
283266 GAAGTTATAA
Statistics
Matches: 97, Mismatches: 22, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
123 97 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (123 bp):
AGACAAAAACTAGTTTACCAAAAGACAAACTAATTAGACAAAATGATACGATATCCCAAGCATGG
AATGTTCAAAAAATTCCTAAAAGGAATGAATCGTCATAAATAATTTAACGAACTATCT
Found at i:283873 original size:216 final size:216
Alignment explanation
Indices: 283147--286434 Score: 3879
Period size: 216 Copynumber: 15.3 Consensus size: 216
283137 CGAACTATCT
* * * ** * *** *
283147 AGACAAAAAGTAGTTTACCAAATGACAAACTATTTAGATAAAATGATGCGATATCTTAAGCATTG
1 AGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGG
* * ** * * *
283212 AATGTTCAAAAAATTCCTAAAAGGAATGAATTTTCATAAATACTTTAAGGAACTGAAGTTAT-AA
66 AATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACTGAAGTTATAAA
* * * *
283276 AGAACTCGTAAAAATTTGCCAAGTTCGAAAGTTCGTCCTAGAATCAAGAGAGAAACAATTCTCAC
131 AGAACTCGTAAAAGTTTGCCAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCAC
283341 GTAAATAAGTTTTTAATTCAA
196 GTAAATAAGTTTTTAATTCAA
*
283362 AGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGTATGG
1 AGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGG
* * * * ** *
283427 AATGTTTGGAAATTTGCTCAAAGGAATGGATTGTCATGAATACTTTAAGGAACCAAAGTTATAGA
66 AATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACTGAAGTTATAAA
* * * * ** *
283492 AGAACTCGTAAAACTTTGTCAA------AA-TTTGTCGAAGATGCAAGGGAGAAACAATTCTCAC
131 AGAACTCGTAAAAGTTTGCCAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCAC
*
283550 GTAAA-AAATTTTTAATAT-AA
196 GTAAATAAGTTTTTAAT-TCAA
* * * **
283570 AGTA-CAAAAGTTGTCTACCAAATGACAAACTATTTAGA-AAAACAATGCGATTTCCCGAGCATG
1 AG-ACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATG
* * * *
283633 GAATGTTCGGAAAATAGCTCGAAGGAATGGATTGCCATGAATACTTTAAGGAACTGAAGTTATTA
65 GAATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACTGAAGTTATAA
* ** * *
283698 AAGAACTCGAAAAAGTTCACCAAGTTCGGAAGTTAGTCCAAGAACCAAGAGCGAAACAATTCTCA
130 AAGAACTCGTAAAAGTTTGCCAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCA
**
283763 CGTAAATAAAATTTTAATTCAA
195 CGTAAATAAGTTTTTAATTCAA
* * * * *
283785 AGACCAAAAGTTTTTTACAAAATGACAAACTATTTATACAAAAGGATACGATTTCCCGAGCATGG
1 AGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGG
*
283850 AATGTTCAAAAAATTGCTCGAAGGAATGGATCT-TCATGAATACTTTAAGGAACTGAAGTTATAA
66 AATGTTCGAAAAATTGCTCGAAGGAATGGAT-TGTCATGAATACTTTAAGGAACTGAAGTTATAA
* * * * *
283914 AAGAGCACATAAAAGTTTGCCAAGTTCGGAAGTTCATCCAAGAACCAAGAGTGAAACAATTCTCA
130 AAGAACTCGTAAAAGTTTGCCAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCA
* *
283979 AGTAAATAAGTTTTTAATTCAT
195 CGTAAATAAGTTTTTAATTCAA
* * * * *
284001 CGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGTGATTTCTCAAGCATGG
1 AGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGG
* * *** * *
284066 AATGTTCAAAAAATTACTCGAAGGAATGGACCATCATGAATAATTTAACGAACTGAAGTTATAAA
66 AATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACTGAAGTTATAAA
* *
284131 AGAACTCGTAAAAGTTTGCCAAGTTCGGAAGTTCGTCCAAGAAGCAAGAGCGAAACAATTCTCAC
131 AGAACTCGTAAAAGTTTGCCAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCAC
284196 GTAAATAAGTTTTTTAATTCAA
196 GTAAATAAG-TTTTTAATTCAA
* * * * *
284218 AGACCAAAAGTTGTTTGCAAAATTACAAACTATTTAAACCAAATGATGTGATTTCCCGAGCAGGG
1 AGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGG
* * * *** * * * *
284283 TATGTTC-AGAAAGTTACTCGAAGGAACAAATCGTCATGAATAATTTAACGAACTGAAATTATAA
66 AATGTTCGA-AAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACTGAAGTTATAA
* * * *
284347 AAGAACTCGTAAAAGTTTGCCAAGTTTGAAAGTTCGTCTAAGAACCAAGAGCGAAACAATTCTCA
130 AAGAACTCGTAAAAGTTTGCCAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCA
*
284412 CGTAAATAAGTTTTT-ATTTAA
195 CGTAAATAAGTTTTTAATTCAA
* * * * * * *
284433 AGACCAAGAGTTATTTACAAAGTGACAAACTATTTAGATCAATTAATGCGATTTCTCGAGCATGG
1 AGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGG
* * * * * *
284498 AATGTTC-AGAAAATTGCTCAAAGTAATGGATCGTCATGAATAATTTAACGAACTGAAGTTATAC
66 AATGTTCGA-AAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACTGAAGTTATAA
* * * * * * *
284562 AAG-ACTCGTAAATGTTTTCCATGTTTGAAAGTTCGTCCAAGAACCTAGAGCGAAACAATTCTCA
130 AAGAACTCGTAAAAGTTTGCCAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCA
*
284626 CGTAAATAAGATTTTAATTCAA
195 CGTAAATAAGTTTTTAATTCAA
* * *
284648 AGACCAAAAGTTGTTTACAAAATGAAAAACTATTTACACCAAATGATGCGATTTCCAGAGCATGG
1 AGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGG
* * * *
284713 AATATTCGAAAAATTGCTAGAAGGAATGGATTGTCATGAATACTTTAAGGAATTAAAGTTATAAA
66 AATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACTGAAGTTATAAA
* * * *
284778 AGAACTCGTAAAAGTTTTCCAAGTTTGGAAGTTCGTCCAAGAA-CAAGGGGAGAAACACTTCTCA
131 AGAACTCGTAAAAGTTTGCCAAGTTCGGAAGTTCGTCCAAGAACCAA-GAGAGAAACAATTCTCA
284842 CGTAAATAAGTTTTT-ATTCAA
195 CGTAAATAAGTTTTTAATTCAA
* * * *
284863 AGACCAAGAGTTATTTACAAAATGACAAACTATTTAGACCAATTGATGCGATTTCTCGAGCATGG
1 AGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGG
* * *
284928 AAAGTTC-AGAAAATTGCTCAAAGGAATGGATCGTCATGAATACTTTAAGGAACTGAAGTTATAA
66 AATGTTCGA-AAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACTGAAGTTATAA
* * *
284992 AAGAACTCGTAAAAGTTTTCCAA-TCTCGGAAGCTCGTCCAAGAATCAAGAGAGAAACAATTCTC
130 AAGAACTCGTAAAAGTTTGCCAAGT-TCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTC
*
285056 ACGTAAATAAGTTTTTAATTTAA
194 ACGTAAATAAGTTTTTAATTCAA
* * * * **
285079 AGACTAAAAGTTGTTTACAAAATGAAAAACTATTTTGACCAAATGATGTGATTTCCTAAGCATGG
1 AGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGG
* * * *
285144 AATGTTCGGAAAATTTCTCGGAGGAATGGATCT-TCACGAATACTTTAAGGAACTGAAGTTATAA
66 AATGTTCGAAAAATTGCTCGAAGGAATGGAT-TGTCATGAATACTTTAAGGAACTGAAGTTATAA
* * * *
285208 AAGAACTCGTAAAAGTTTGCCAAGTTCAGAAGTTTGTCCAAGTACAAAG-GCAGAAACAATTCTC
130 AAGAACTCGTAAAAGTTTGCCAAGTTCGGAAGTTCGTCCAAGAACCAAGAG-AGAAACAATTCTC
* *
285272 ACGTACATAAGATTTTAATTCAA
194 ACGTAAATAAGTTTTTAATTCAA
* * * *
285295 AGACCAAAAATTGTTTACAAAATGACAAATTATTGAGACTAAATGATGCGATTTCCCGAGCATGG
1 AGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGG
* ** * * * * *
285360 ATTGTTCGGGAAGTTGCTCGAAGGAATGGATCGTCATGAATAATTTAATGAACTGAAGTAATAAA
66 AATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACTGAAGTTATAAA
* * *
285425 AGAACTCGTAAAAGTTTTCCAAGTTCGGAAGTTCGTCCAAGAACCAAGAGCGAAACAATTTTCAC
131 AGAACTCGTAAAAGTTTGCCAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCAC
285490 GTAAATAAGTTTTTAATTCAA
196 GTAAATAAGTTTTTAATTCAA
* * *
285511 AGACCAAAAGTTGCTTACAAAATGACAAACTATTTAGACCAAATGATGCAATTTCTCGAGCATGG
1 AGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGG
* * * * * * * *
285576 AATGTTCGAAAAGTTTCTCAAAGGAATGGATCGTCATGAATAATTTAACGAATTGATGTTATAAA
66 AATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACTGAAGTTATAAA
* * * *
285641 AGAACTCATAAAAGTTTGTCAAGTTCGGAAGTTCGTCCAAGAACCAAAAGTGAAACAATTCTCAC
131 AGAACTCGTAAAAGTTTGCCAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCAC
*
285706 ATAAATAAGTTTTTAATTCAA
196 GTAAATAAGTTTTTAATTCAA
* * * * *
285727 AGAACC-AAATTTGTTTAGAAAATAACAAACTATTTTGACCAAATGATGCGATTTCCTGAGCATG
1 AG-ACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATG
** * *
285791 GAATGTTCGAAAAATTGCTTAAAGGAATGGATCGTCATGAAAACTTTAAGGAACTGAAGTTATAA
65 GAATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACTGAAGTTATAA
* * * *
285856 AAGAACTCGTAAAAGTTTGACAAGTTCGGAATTTTGTCCAATAACCAAGAGAGAAACAATTCTCA
130 AAGAACTCGTAAAAGTTTGCCAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCA
* ***
285921 CGTAAAAAAAAATTTAATAT-AA
195 CGTAAATAAGTTTTTAAT-TCAA
* * * **
285943 AGACCAAAAGTTGTTTACAAAATGATAAACTATTTAGACCAAATGATACAATTTCTTGAGCATGG
1 AGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGG
* * * * * *
286008 -ATAGTTCGAAAAATAT-CTCGAAGGAAGGGATCT-TCTTGAATATTTTATGGAACCGATGTTAT
66 AAT-GTTCGAAAAAT-TGCTCGAAGGAATGGAT-TGTCATGAATACTTTAAGGAACTGAAGTTAT
* ** * * * * * *
286070 AAAAGAACTTGTAAAAGTTTGAAAAGTTTGAAAGTTCGTCCAAGATCCAAAATAGAAACAATTAT
128 AAAAGAACTCGTAAAAGTTTGCCAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCT
286135 CACGTAAATAAGTTTTTAATTCACA
193 CACGTAAATAAGTTTTTAATTCA-A
* * * * ** * *
286160 A-ACCAAAAGTAGTCTATAAAATGACAAACTATTTGGAGGAAATGATGTGATTTCTC-ACGCATG
1 AGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGA-GCATG
* * * * *
286223 G-ATAGGTCGAAAAATAT-CTAGAAGGAATGGATTGTCTTGAATATTTTAAGGAACCGAAGTTAT
65 GAAT-GTTCGAAAAAT-TGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACTGAAGTTAT
* * * * * *
286286 AGAAGAACTCATAAAAGTTT-CTTAAGTTCAGAAGTTCGTCCAAGATCCAAGAGAGAAACACTTC
128 AAAAGAACTCGTAAAAGTTTGC-CAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTC
286350 TCACGTAAATAAGTTTTTAATTCAA
192 TCACGTAAATAAGTTTTTAATTCAA
* * * * * * *
286375 AGACAAAAAGTTGTTTACCAAATGACATACTACTTAAACCAAATGATGTGATTTCTCGAG
1 AGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAG
286435 ACAAATAGGA
Statistics
Matches: 2645, Mismatches: 383, Indels: 89
0.85 0.12 0.03
Matches are distributed among these distances:
207 95 0.04
208 46 0.02
209 35 0.01
210 2 0.00
213 2 0.00
214 107 0.04
215 581 0.22
216 1573 0.59
217 204 0.08
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (216 bp):
AGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGG
AATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACTGAAGTTATAAA
AGAACTCGTAAAAGTTTGCCAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCAC
GTAAATAAGTTTTTAATTCAA
Found at i:288254 original size:22 final size:22
Alignment explanation
Indices: 288213--288254 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
288203 ATATAAACAT
**
288213 TCAATTATATTTGCACAATAAA
1 TCAATTATATTAACACAATAAA
*
288235 TCAATTATATTAACATAATA
1 TCAATTATATTAACACAATA
288255 CATCCATGGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (22 bp):
TCAATTATATTAACACAATAAA
Found at i:292420 original size:7 final size:7
Alignment explanation
Indices: 292389--292419 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
292379 TTTTGGGGTA
292389 TTTTCTT
1 TTTTCTT
292396 TTTTCTT
1 TTTTCTT
292403 TTTTCTT
1 TTTTCTT
292410 TTTT-TT
1 TTTTCTT
292416 TTTT
1 TTTT
292420 TGTATATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTTCTT
Found at i:292839 original size:19 final size:19
Alignment explanation
Indices: 292791--292840 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 19
292781 ATGAAAATAC
292791 AAATATATATTAAATTACTA
1 AAATATATATT-AATTACTA
* *
292811 AAATGT-TATTATTTA-TA
1 AAATATATATTAATTACTA
292828 TAAATATATATTA
1 -AAATATATATTA
292841 CAAAATAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 2 0.08
18 9 0.36
19 9 0.36
20 5 0.20
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
AAATATATATTAATTACTA
Found at i:294520 original size:18 final size:18
Alignment explanation
Indices: 294496--294547 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
294486 GAAACTCTAT
294496 ATCCTTCATGGATTTTAA
1 ATCCTTCATGGATTTTAA
*
294514 TTCCTTC-TAGGATTTTAA
1 ATCCTTCAT-GGATTTTAA
* *
294532 ATCATTCAGGGATTTT
1 ATCCTTCATGGATTTT
294548 CATATAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.04
18 27 0.96
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.46
Consensus pattern (18 bp):
ATCCTTCATGGATTTTAA
Found at i:314909 original size:15 final size:15
Alignment explanation
Indices: 314889--314919 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
314879 GGGAAGTCCC
314889 TCACTACTCGAATCT
1 TCACTACTCGAATCT
314904 TCACTACTCGAATCT
1 TCACTACTCGAATCT
314919 T
1 T
314920 TTCAATCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.32, G:0.06, T:0.35
Consensus pattern (15 bp):
TCACTACTCGAATCT
Found at i:318437 original size:21 final size:21
Alignment explanation
Indices: 318411--318450 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
318401 GGTTTAGGTC
318411 AAAAGGTTTGGGTTTGGTTCA
1 AAAAGGTTTGGGTTTGGTTCA
318432 AAAAGGTTTGGGTTTGGTT
1 AAAAGGTTTGGGTTTGGTT
318451 TGGGTCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.03, G:0.35, T:0.40
Consensus pattern (21 bp):
AAAAGGTTTGGGTTTGGTTCA
Found at i:318453 original size:26 final size:26
Alignment explanation
Indices: 318415--318475 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
318405 TAGGTCAAAA
*
318415 GGTTTGGGTTTGGTTCAAAA-AGGTTTG
1 GGTTT-GGTTTGGGTCAAAAGA-GTTTG
*
318442 GGTTTGGTTTGGGTCTAAAGAGTTTG
1 GGTTTGGTTTGGGTCAAAAGAGTTTG
318468 GGTTTGGT
1 GGTTTGGT
318476 GTTGATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 25 0.81
27 6 0.19
ACGTcount: A:0.15, C:0.03, G:0.39, T:0.43
Consensus pattern (26 bp):
GGTTTGGTTTGGGTCAAAAGAGTTTG
Found at i:322053 original size:142 final size:142
Alignment explanation
Indices: 321797--322082 Score: 491
Period size: 142 Copynumber: 2.0 Consensus size: 142
321787 ACTAAACCTC
* *
321797 GAAAATAAAAAACCCTCAAAACATAAACACTAAATTCTCCAAAAGTGTTAGGAGTTCTAAACTCT
1 GAAAACAAAAAACCCTCAAAACATAAACACTAAATTCTCCAAAAGTGTTAGAAGTTCTAAACTCT
* *
321862 AATGGGTGTATTTTTTAAGGTTGTAAAAGAGCCTATCTATAGGCTAAATTCCAGGTCAATAATAA
66 AATGAGTGTATTTTCTAAGGTTGTAAAAGAGCCTATCTATAGGCTAAATTCCAGGTCAATAATAA
321927 TAAAATAATCTA
131 TAAAATAATCTA
**
321939 GAAAACAAAAAACCCTCAAAATGTAAACACTAAATTCTCCAAAAGTGTTAGAAGTTCTAAACTCT
1 GAAAACAAAAAACCCTCAAAACATAAACACTAAATTCTCCAAAAGTGTTAGAAGTTCTAAACTCT
* *
322004 AATGAGTGTATTTTCTAAGGTTGTAAAAGAGCCTATTTATAGGCTAAATTTCAGGTCAATAATAA
66 AATGAGTGTATTTTCTAAGGTTGTAAAAGAGCCTATCTATAGGCTAAATTCCAGGTCAATAATAA
*
322069 TACAATAATCTA
131 TAAAATAATCTA
322081 GA
1 GA
322083 CTAATAAGAG
Statistics
Matches: 135, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 135 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (142 bp):
GAAAACAAAAAACCCTCAAAACATAAACACTAAATTCTCCAAAAGTGTTAGAAGTTCTAAACTCT
AATGAGTGTATTTTCTAAGGTTGTAAAAGAGCCTATCTATAGGCTAAATTCCAGGTCAATAATAA
TAAAATAATCTA
Found at i:322132 original size:24 final size:24
Alignment explanation
Indices: 322105--322153 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
322095 TGGCTTAAAC
*
322105 AAATAAACAAAGTTTAATTGAAAG
1 AAATAAACAAAGTTTAACTGAAAG
*
322129 AAATAAACAGAGTTTAACTGAAAG
1 AAATAAACAAAGTTTAACTGAAAG
322153 A
1 A
322154 TTATTTCTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.57, C:0.06, G:0.14, T:0.22
Consensus pattern (24 bp):
AAATAAACAAAGTTTAACTGAAAG
Found at i:324085 original size:24 final size:24
Alignment explanation
Indices: 324069--324167 Score: 180
Period size: 24 Copynumber: 4.1 Consensus size: 24
324059 AGTTTGACTC
324069 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
324093 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
324117 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* *
324141 AAACAAATAAATAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
324165 AAA
1 AAA
324168 GATTATTTCT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 73 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:324121 original size:48 final size:48
Alignment explanation
Indices: 324057--324167 Score: 186
Period size: 48 Copynumber: 2.3 Consensus size: 48
324047 TAGACTAATA
* *
324057 AGAGTTTGACTCAAACAAATAAACAGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAACAGAGTTTAATTGAAACAAATAAAC
* *
324105 AGAGTTTAATTGAAACAAATAAACAGAGTTTAATTGAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAACAGAGTTTAATTGAAACAAATAAAC
324153 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
324168 GATTATTTCT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.52, C:0.09, G:0.14, T:0.25
Consensus pattern (48 bp):
AGAGTTTAACTGAAACAAATAAACAGAGTTTAATTGAAACAAATAAAC
Found at i:328305 original size:2 final size:2
Alignment explanation
Indices: 328294--328326 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
328284 TAATTTATGA
328294 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
328327 GAATATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:337721 original size:27 final size:27
Alignment explanation
Indices: 337653--337713 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
337643 AAGGAACTAT
** * *
337653 TGAATGGACTGTCTTTGTGGCGTACTC
1 TGAATGGACTACCTTTGTGACATACTC
337680 TGAATGGACTACCTTTGTGACATACTC
1 TGAATGGACTACCTTTGTGACATACTC
337707 TGAATGG
1 TGAATGG
337714 GTTGCCTTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.34
Consensus pattern (27 bp):
TGAATGGACTACCTTTGTGACATACTC
Found at i:339949 original size:18 final size:19
Alignment explanation
Indices: 339909--339949 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
339899 AATCTAAATA
*
339909 AAACTCTTAATTAAACTAG
1 AAACTCTTAACTAAACTAG
*
339928 -AACTC-TAACTAATCTAG
1 AAACTCTTAACTAAACTAG
339945 AAACT
1 AAACT
339950 TTCTTGTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.46, C:0.20, G:0.05, T:0.29
Consensus pattern (19 bp):
AAACTCTTAACTAAACTAG
Found at i:348699 original size:18 final size:19
Alignment explanation
Indices: 348657--348700 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
348647 GAATATTTTT
*
348657 TATTTTTCTCTTTTTCATG
1 TATTTTTCTCTTTTTCATC
348676 TATTTTTCT-TTTTTC-TC
1 TATTTTTCTCTTTTTCATC
348693 TAGTTTTT
1 TA-TTTTT
348701 TGATCACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 11 0.48
19 9 0.39
ACGTcount: A:0.09, C:0.14, G:0.05, T:0.73
Consensus pattern (19 bp):
TATTTTTCTCTTTTTCATC
Found at i:350564 original size:43 final size:43
Alignment explanation
Indices: 350456--350778 Score: 373
Period size: 43 Copynumber: 7.5 Consensus size: 43
350446 GTGCTTATCT
350456 CACAAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTT-C
1 CACAAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTTCC
* * * * * *
350498 TACAAACACCGCTACAGACCATGGTCTTTAGCGGCGCTTTTCC
1 CACAAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTTCC
* * *
350541 CACAAACGCCGCTAAAAAACATGGTCTTTAGCGGCGCTTTTCC
1 CACAAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTTCC
* * *
350584 CACAAATGCCGCTAAAGAACTTGATCTTAAGCGACGCTTATT-C
1 CACAAACGCCGCTAAAGAACATGATCTTTAGCGACGCTT-TTCC
** * *
350627 CACAAACGCCATTAAAGAACATAATCTTTAGCGATGCTTTTCC
1 CACAAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTTCC
*
350670 CACAAACGCCGCTAAAGAACATGATCTTTAACGACGCTTTTCC
1 CACAAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTTCC
* * ** * *
350713 CATAAATGCTACTAAAGACCATGATCTTTAACGA-GACTTTTCC
1 CACAAACGCCGCTAAAGAACATGATCTTTAGCGACG-CTTTTCC
* * *
350756 CGCAAACACTGCTAAAGAACATG
1 CACAAACGCCGCTAAAGAACATG
350779 GTTTTTAATG
Statistics
Matches: 237, Mismatches: 40, Indels: 7
0.83 0.14 0.02
Matches are distributed among these distances:
42 38 0.16
43 197 0.83
44 2 0.01
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (43 bp):
CACAAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTTCC
Found at i:356054 original size:41 final size:41
Alignment explanation
Indices: 355993--356362 Score: 374
Period size: 41 Copynumber: 9.1 Consensus size: 41
355983 TAAGCGCCGC
* * *
355993 TTTT-CCATAAGCGTCACTATTGCTCTGACCTTTAGCGGCA
1 TTTTCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCG
356033 TTTTCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCG
1 TTTTCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCG
* * * *** *
356074 CTTTCTCAAAAGCGCTATTGTTGCTCTGACCTTTAGCGGCG
1 TTTTCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCG
* * *
356115 CTTGCCCATAAGCGTCGCTATTGCTCTGACCTTTAGCGGCG
1 TTTTCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCG
** * * * * *
356156 CATTCCCGTAAGCACCGCTATTGCTCTAACCTTCAGCAGCG
1 TTTTCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCG
* * *
356197 CTTTTCCC-TCAA-CGTCGGTATTGCTCTGACCTTTAGAGGCG
1 -TTTTCCCAT-AAGCGCCGCTATTGCTCTGACCTTTAGCGGCG
* *
356238 CTTTTCCC-TAAGTGCCGCTATTGCTCTGACCATTAGCGGCG
1 -TTTTCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCG
* * *
356279 TTTTTCCATAAGCGCCACTATTGCTCTGACCTTTAGCGGCAC
1 TTTTCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGC-G
** * *
356321 TTTT-CCATAAGCATCGCTATTGCTCT-ACCTTTTGCAGCG
1 TTTTCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCG
356360 TTT
1 TTT
356363 AAGTAAAAAC
Statistics
Matches: 273, Mismatches: 51, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
39 3 0.01
40 22 0.08
41 237 0.87
42 11 0.04
ACGTcount: A:0.17, C:0.30, G:0.20, T:0.33
Consensus pattern (41 bp):
TTTTCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCG
Found at i:356221 original size:123 final size:124
Alignment explanation
Indices: 355997--356352 Score: 422
Period size: 123 Copynumber: 2.9 Consensus size: 124
355987 CGCCGCTTTT
* *
355997 CCATAAGCGTCACTATTGCTCTGACCTTTAGCGGCATTTTCCCATAAGCGCCGCTATTGCTCTGA
1 CCATAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGTTTTCCCATAAGCGCCGCTATTGCTCTGA
* *
356062 CCTTTAGCGGCGC-TTT--CTCAAAAG-CGCTATTGTTGCTCTGACCTTTAGCGGCGC-TTGC
66 CCTTTAGCGGCGCTTTTCCCTC-AACGTCGCTA---TTGCTCTGACCTTTAGAGGCGCTTTGC
** * * *
356120 CCATAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGCATTCCCGTAAGCACCGCTATTGCTCTAA
1 CCATAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGTTTTCCCATAAGCGCCGCTATTGCTCTGA
* * * *
356185 CCTTCAGCAGCGCTTTTCCCTCAACGTCGGTATTGCTCTGACCTTTAGAGGCGCTTTTC
66 CCTTTAGCGGCGCTTTTCCCTCAACGTCGCTATTGCTCTGACCTTTAGAGGCGCTTTGC
* * * * *
356244 CC-TAAGTGCCGCTATTGCTCTGACCATTAGCGGCGTTTTTCCATAAGCGCCACTATTGCTCTGA
1 CCATAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGTTTTCCCATAAGCGCCGCTATTGCTCTGA
* * *
356308 CCTTTAGCGGCACTTTTCCAT-AAGCATCGCTATTGCTCT-ACCTTT
66 CCTTTAGCGGCGCTTTTCCCTCAA-CGTCGCTATTGCTCTGACCTTT
356353 TGCAGCGTTT
Statistics
Matches: 198, Mismatches: 29, Indels: 13
0.82 0.12 0.05
Matches are distributed among these distances:
122 8 0.04
123 172 0.87
124 8 0.04
125 3 0.02
126 7 0.04
ACGTcount: A:0.17, C:0.31, G:0.20, T:0.32
Consensus pattern (124 bp):
CCATAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGTTTTCCCATAAGCGCCGCTATTGCTCTGA
CCTTTAGCGGCGCTTTTCCCTCAACGTCGCTATTGCTCTGACCTTTAGAGGCGCTTTGC
Found at i:360220 original size:27 final size:27
Alignment explanation
Indices: 360203--360255 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
360193 CTTTGTGGTG
360203 TACTCTGAATGGATTGCCTTTGTGACA
1 TACTCTGAATGGATTGCCTTTGTGACA
* *
360230 TACTCTGATTGGGTTGCCTTTGTGAC
1 TACTCTGAATGGATTGCCTTTGTGAC
360256 GGGTCCTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.40
Consensus pattern (27 bp):
TACTCTGAATGGATTGCCTTTGTGACA
Found at i:361803 original size:27 final size:27
Alignment explanation
Indices: 361773--361826 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
361763 AAAGGAACTA
* *
361773 TTGAATGGACTACCTTTGTGGCATACT
1 TTGAATAGACTACCTTTGTGACATACT
* *
361800 TTGAATAGACTGCCTTTTTGACATACT
1 TTGAATAGACTACCTTTGTGACATACT
361827 CTAAATAGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (27 bp):
TTGAATAGACTACCTTTGTGACATACT
Found at i:361833 original size:27 final size:27
Alignment explanation
Indices: 361780--361834 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
361770 CTATTGAATG
* * *
361780 GACTACCTTTGTGGCATACTTTGAATA
1 GACTACCTTTGTGACATACTCTAAATA
* *
361807 GACTGCCTTTTTGACATACTCTAAATA
1 GACTACCTTTGTGACATACTCTAAATA
361834 G
1 G
361835 GTTTCCTTAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (27 bp):
GACTACCTTTGTGACATACTCTAAATA
Found at i:366359 original size:31 final size:31
Alignment explanation
Indices: 366324--366425 Score: 170
Period size: 31 Copynumber: 3.3 Consensus size: 31
366314 CATGGTCATC
*
366324 AATCATTCATATTTGCATATTCATACCCTAT
1 AATCATTCACATTTGCATATTCATACCCTAT
366355 AATCATTCACATTTGCATATTCATACCCTAT
1 AATCATTCACATTTGCATATTCATACCCTAT
*
366386 AATCATTCACATTTGCATTTTC-TAACCCTAT
1 AATCATTCACATTTGCATATTCAT-ACCCTAT
366417 AATCATTCA
1 AATCATTCA
366426 TATAAATTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
30 1 0.01
31 67 0.99
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.40
Consensus pattern (31 bp):
AATCATTCACATTTGCATATTCATACCCTAT
Found at i:370986 original size:17 final size:17
Alignment explanation
Indices: 370966--370998 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
370956 TCAATAGTCA
370966 TTTTTTCTCCTTACCTG
1 TTTTTTCTCCTTACCTG
370983 TTTTTTCTCCTTACCT
1 TTTTTTCTCCTTACCT
370999 CTATTACGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.30, G:0.03, T:0.61
Consensus pattern (17 bp):
TTTTTTCTCCTTACCTG
Found at i:375380 original size:18 final size:19
Alignment explanation
Indices: 375359--375394 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
375349 TCAAAAAGTA
*
375359 GAGAAAAA-AGAAAAATAC
1 GAGAAAAATAAAAAAATAC
375377 GAGAAAAATAAAAAAATA
1 GAGAAAAATAAAAAAATA
375395 AAAAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.75, C:0.03, G:0.14, T:0.08
Consensus pattern (19 bp):
GAGAAAAATAAAAAAATAC
Found at i:382125 original size:22 final size:22
Alignment explanation
Indices: 382100--382141 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
382090 TAAATTGCTT
382100 ATTTTTTATACTTAAAATAAAC
1 ATTTTTTATACTTAAAATAAAC
* *
382122 ATTTTTTATAGTTTAAATAA
1 ATTTTTTATACTTAAAATAA
382142 TATACCCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTTTTTATACTTAAAATAAAC
Found at i:389223 original size:29 final size:29
Alignment explanation
Indices: 389183--389240 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
389173 AACACAAAAA
*
389183 ATATCAACTTTTCCAGAAAATCAATCCAT
1 ATATAAACTTTTCCAGAAAATCAATCCAT
*
389212 ATATAAACTTTTTCAGAAAATCAATCCAT
1 ATATAAACTTTTCCAGAAAATCAATCCAT
389241 TTTTCAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.43, C:0.21, G:0.03, T:0.33
Consensus pattern (29 bp):
ATATAAACTTTTCCAGAAAATCAATCCAT
Found at i:396378 original size:34 final size:34
Alignment explanation
Indices: 396337--396408 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
396327 TCTTCTCTCT
396337 TTTTTCTCTCAAATTCTTTTTCTTTT-TCAATTTC
1 TTTTTCTCTC-AATTCTTTTTCTTTTCTCAATTTC
* * *
396371 TTTTTCTCTCATTTCTTTTTTTTTTCTCTATTTC
1 TTTTTCTCTCAATTCTTTTTCTTTTCTCAATTTC
396405 TTTT
1 TTTT
396409 ATTTTTCTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 13 0.38
34 21 0.62
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.71
Consensus pattern (34 bp):
TTTTTCTCTCAATTCTTTTTCTTTTCTCAATTTC
Found at i:396396 original size:20 final size:20
Alignment explanation
Indices: 396371--396423 Score: 90
Period size: 19 Copynumber: 2.7 Consensus size: 20
396361 TTTCAATTTC
*
396371 TTTTTCTCTCATTTCTTTTT
1 TTTTTCTCTCATTTCTTTTA
396391 TTTTTCTCT-ATTTCTTTTA
1 TTTTTCTCTCATTTCTTTTA
396410 TTTTTCTCTCATTT
1 TTTTTCTCTCATTT
396424 TCTCTCATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTCTCTCATTTCTTTTA
Found at i:398567 original size:9 final size:9
Alignment explanation
Indices: 398553--398648 Score: 79
Period size: 9 Copynumber: 10.7 Consensus size: 9
398543 TGTAGCACAT
398553 TGCATGGAA
1 TGCATGGAA
398562 TGCATGGAA
1 TGCATGGAA
**
398571 TGCAT-GTT
1 TGCATGGAA
398579 TCGCATGGAA
1 T-GCATGGAA
*
398589 TGCAT-GAGT
1 TGCATGGA-A
*
398598 TGCTTGGAA
1 TGCATGGAA
*
398607 TGCATGAAA
1 TGCATGGAA
* *
398616 TGCAAGAAA
1 TGCATGGAA
398625 TGCATGGAA
1 TGCATGGAA
* *
398634 TACATGAAA
1 TGCATGGAA
398643 TGCATG
1 TGCATG
398649 AACTGTTTGT
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
8 4 0.06
9 60 0.88
10 4 0.06
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.26
Consensus pattern (9 bp):
TGCATGGAA
Found at i:398611 original size:27 final size:27
Alignment explanation
Indices: 398553--398650 Score: 88
Period size: 27 Copynumber: 3.6 Consensus size: 27
398543 TGTAGCACAT
* * ***
398553 TGCATGGAATGCATGGAATGCATGTTT
1 TGCATGAAATGCATGAAATGCATGGAA
* * ** *
398580 CGCATGGAATGCATGAGTTGCTTGGAA
1 TGCATGAAATGCATGAAATGCATGGAA
*
398607 TGCATGAAATGCAAGAAATGCATGGAA
1 TGCATGAAATGCATGAAATGCATGGAA
*
398634 TACATGAAATGCATGAA
1 TGCATGAAATGCATGAA
398651 CTGTTTGTCC
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.26
Consensus pattern (27 bp):
TGCATGAAATGCATGAAATGCATGGAA
Found at i:407490 original size:66 final size:66
Alignment explanation
Indices: 407384--407514 Score: 253
Period size: 66 Copynumber: 2.0 Consensus size: 66
407374 AAAAAAATGA
*
407384 GTAATGAGAAAGAGAATGAACGTTAACGGAGAGTGAGGGAAACGTGAGAGAGAAAATAGGAGATA
1 GTAATGAGAAAGAGAATGAACGTCAACGGAGAGTGAGGGAAACGTGAGAGAGAAAATAGGAGATA
407449 G
66 G
407450 GTAATGAGAAAGAGAATGAACGTCAACGGAGAGTGAGGGAAACGTGAGAGAGAAAATAGGAGATA
1 GTAATGAGAAAGAGAATGAACGTCAACGGAGAGTGAGGGAAACGTGAGAGAGAAAATAGGAGATA
407515 ATCTCTCCCT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.46, C:0.05, G:0.36, T:0.13
Consensus pattern (66 bp):
GTAATGAGAAAGAGAATGAACGTCAACGGAGAGTGAGGGAAACGTGAGAGAGAAAATAGGAGATA
G
Found at i:409571 original size:21 final size:22
Alignment explanation
Indices: 409539--409582 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
409529 AAATAGAGAG
*
409539 AGAACAAAGAAAAA-AAATAAA
1 AGAACAAAGAAAAACAAACAAA
409560 AGAA-AAAGGAAAAACAAACAAA
1 AGAACAAA-GAAAAACAAACAAA
409582 A
1 A
409583 TATGTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 3 0.15
21 10 0.50
22 7 0.35
ACGTcount: A:0.80, C:0.07, G:0.11, T:0.02
Consensus pattern (22 bp):
AGAACAAAGAAAAACAAACAAA
Found at i:411269 original size:27 final size:27
Alignment explanation
Indices: 411239--411366 Score: 139
Period size: 27 Copynumber: 4.7 Consensus size: 27
411229 ACAAACACAA
* * *
411239 AATAATGCTCCTTCAAACCAGATATAG
1 AATAATGCTCTTTCAAGCCAGATACAG
* ** *
411266 AATAATGATCTTTTGAGCCAAATACAG
1 AATAATGCTCTTTCAAGCCAGATACAG
* * *
411293 AATAACGCTCTTTCGAGCCAGATACAA
1 AATAATGCTCTTTCAAGCCAGATACAG
*
411320 AATAATGCTCTTTCAAGCTAGATACAG
1 AATAATGCTCTTTCAAGCCAGATACAG
* *
411347 AATAACGCTCTTTCGAGCCA
1 AATAATGCTCTTTCAAGCCA
411367 AAATTCAAAG
Statistics
Matches: 82, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 82 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.27
Consensus pattern (27 bp):
AATAATGCTCTTTCAAGCCAGATACAG
Found at i:413162 original size:50 final size:50
Alignment explanation
Indices: 413108--413540 Score: 174
Period size: 50 Copynumber: 8.7 Consensus size: 50
413098 CTATAGTAGA
* * * *
413108 AAATCTTATCTCCTTGAAGATGTAGTGGAGCAAGATGAAGCAACAACATC
1 AAATCTTATCTCCTTGAAGATGAAGTGGAGCAAGATAAAGCTACAATATC
* * * * * * * * *
413158 AAATCCTATATCCTTAAAGTTGCAGTGGATCAA-ATTAAA-CTATAGTAGC
1 AAATCTTATCTCCTTGAAGATGAAGTGGAGCAAGA-TAAAGCTACAATATC
*
413207 AAATCTTATCTCCCTGAAGATGAAGTGGAGCAAGATAAAGCTACAATATC
1 AAATCTTATCTCCTTGAAGATGAAGTGGAGCAAGATAAAGCTACAATATC
* * * * * ** *
413257 AAATCATATAT-TCC-TGAAG-TTACA-CGAATC-AGATTAAAACTATGATAGC
1 AAATC-T-TATCTCCTTGAAGATGA-AGTGGAGCAAGA-TAAAGCTACAATATC
* * * ** * * *
413306 AAATATTATCT-CTCCGAAGTTCCAGTAGAGTAAGATGAAGCTACAA-ATC
1 AAATCTTATCTCCT-TGAAGATGAAGTGGAGCAAGATAAAGCTACAATATC
* * * * * * * * * *
413355 AAATCCTATATCCCTGAAG-TTACAATGGATC-GGATTCGAA-CTACAGTAGC
1 AAATCTTATCTCCTTGAAGATGA-AGTGGAGCAAGA-T-AAAGCTACAATATC
* * * * *
413405 AAATCTCATCTGCC-TGAAGATGCAGTGGAGTAAGATGAAGCTACAACATC
1 AAATCTTATCT-CCTTGAAGATGAAGTGGAGCAAGATAAAGCTACAATATC
* * * * * * * *
413455 AAATCCTATATCCCTGAAGTTGAAGTGGATC-AGATTAAAACTACAGTAGC
1 AAATCTTATCTCCTTGAAGATGAAGTGGAGCAAGA-TAAAGCTACAATATC
* *
413505 AAATGTTATCTCCTTGAAGATGTAGTGGAGCAAGAT
1 AAATCTTATCTCCTTGAAGATGAAGTGGAGCAAGAT
413541 TGTAACAGCC
Statistics
Matches: 269, Mismatches: 89, Indels: 50
0.66 0.22 0.12
Matches are distributed among these distances:
47 4 0.01
48 8 0.03
49 93 0.35
50 146 0.54
51 15 0.06
52 3 0.01
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (50 bp):
AAATCTTATCTCCTTGAAGATGAAGTGGAGCAAGATAAAGCTACAATATC
Found at i:413225 original size:99 final size:99
Alignment explanation
Indices: 412965--413540 Score: 618
Period size: 99 Copynumber: 5.9 Consensus size: 99
412955 TGGATCAGCC
* * * *
412965 AATCCTATATCGTTGAAGTTACAGTGGATCAGATCAAAACTA-CGATAGCAAATCTTATCTCTCT
1 AATCCTATATCCTTGAAGTTACAGTGGATCAGATTAAAACTATAG-TAGCAAATCTTATCTCCCT
* * * *
413029 GAAGTTACAATAGAGCAAGATGAAGCT---AA--A
65 GAAGATGCAGTGGAGCAAGATGAAGCTACAAATCA
* * * * *
413059 AAGCCTATATTCTTGAAGTTACAGTGGATCGGATTAAAACTATAGTAGAAAATCTTATCTCCTTG
1 AATCCTATATCCTTGAAGTTACAGTGGATCAGATTAAAACTATAGTAGCAAATCTTATCTCCCTG
* *
413124 AAGATGTAGTGGAGCAAGATGAAGCAACAACATCA
66 AAGATGCAGTGGAGCAAGATGAAGCTACAA-ATCA
* * *
413159 AATCCTATATCCTTAAAGTTGCAGTGGATCAAATT-AAACTATAGTAGCAAATCTTATCTCCCTG
1 AATCCTATATCCTTGAAGTTACAGTGGATCAGATTAAAACTATAGTAGCAAATCTTATCTCCCTG
* *
413223 AAGATGAAGTGGAGCAAGATAAAGCTACAATATCA
66 AAGATGCAGTGGAGCAAGATGAAGCTACAA-ATCA
* * * *
413258 AATCATATATTCC-TGAAGTTACA-CGAATCAGATTAAAACTAT-GATAGCAAATATTATCTCTC
1 AATCCTATA-TCCTTGAAGTTACAGTGGATCAGATTAAAACTATAG-TAGCAAATCTTATCTC-C
* * * *
413320 C-GAAGTTCCAGTAGAGTAAGATGAAGCTACAAATCA
63 CTGAAGATGCAGTGGAGCAAGATGAAGCTACAAATCA
* * * ** * * *
413356 AATCCTATATCCCTGAAGTTACAATGGATCGGATTCGAACTACAGTAGCAAATCTCATCTGCCTG
1 AATCCTATATCCTTGAAGTTACAGTGGATCAGATTAAAACTATAGTAGCAAATCTTATCTCCCTG
*
413421 AAGATGCAGTGGAGTAAGATGAAGCTACAACATCA
66 AAGATGCAGTGGAGCAAGATGAAGCTACAA-ATCA
* * * *
413456 AATCCTATATCCCTGAAGTTGA-AGTGGATCAGATTAAAACTACAGTAGCAAATGTTATCTCCTT
1 AATCCTATATCCTTGAAGTT-ACAGTGGATCAGATTAAAACTATAGTAGCAAATCTTATCTCCCT
*
413520 GAAGATGTAGTGGAGCAAGAT
65 GAAGATGCAGTGGAGCAAGAT
413541 TGTAACAGCC
Statistics
Matches: 402, Mismatches: 63, Indels: 28
0.82 0.13 0.06
Matches are distributed among these distances:
94 74 0.18
95 1 0.00
97 4 0.01
98 34 0.08
99 175 0.44
100 113 0.28
101 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (99 bp):
AATCCTATATCCTTGAAGTTACAGTGGATCAGATTAAAACTATAGTAGCAAATCTTATCTCCCTG
AAGATGCAGTGGAGCAAGATGAAGCTACAAATCA
Found at i:428183 original size:71 final size:68
Alignment explanation
Indices: 428066--428238 Score: 179
Period size: 72 Copynumber: 2.4 Consensus size: 68
428056 GAAACTACGA
428066 AGAGTTGTTCCGAAACAACTCAAGTCAGTAGCCAAGGTATTCATTCCCCTACT-CTTCTACCGAA
1 AGAGTTGTTCCGAAACAACTCAAGTCAGTAGCCAA-G-ATTCATT-CCCTA-TACTTCTACCGAA
*
428130 ACATTAT
62 ACATCAT
* *
428137 AGAGTTGTTTCGAAACAACTCAAGTCAGTAGCTTAA-ATTCCAATTCCCTATGAACTTCTACCGA
1 AGAGTTGTTCCGAAACAACTCAAGTCAGTAGC-CAAGATT-C-ATTCCCTAT--ACTTCTACCGA
* *
428201 TACCTCAT
61 AACATCAT
* * *
428209 ACAGTTGTTCCGAAACAACTTAATTCAGTA
1 AGAGTTGTTCCGAAACAACTCAAGTCAGTA
428239 TCAAAATTTA
Statistics
Matches: 87, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
69 4 0.05
70 6 0.07
71 34 0.39
72 43 0.49
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.29
Consensus pattern (68 bp):
AGAGTTGTTCCGAAACAACTCAAGTCAGTAGCCAAGATTCATTCCCTATACTTCTACCGAAACAT
CAT
Found at i:431423 original size:28 final size:28
Alignment explanation
Indices: 431390--431528 Score: 134
Period size: 29 Copynumber: 4.9 Consensus size: 28
431380 ATTATTTTGA
431390 AAAATAGTGGCAAAACTATAAAATCTAG
1 AAAATAGTGGCAAAACTATAAAATCTAG
* *
431418 AAAATAGTGGCTAAATTATAAAATCTAG
1 AAAATAGTGGCAAAACTATAAAATCTAG
* * * * *
431446 AAAATCAATGGCAAAATTGTAAATTCTGG
1 AAAAT-AGTGGCAAAACTATAAAATCTAG
* * * *
431475 AAAATCGATGGTAAAACTGTAAAATCTGG
1 AAAATAG-TGGCAAAACTATAAAATCTAG
* *
431504 AAAACCAGTGGAAAAACTATAAAAT
1 AAAA-TAGTGGCAAAACTATAAAAT
431529 AGTTGTAGTT
Statistics
Matches: 92, Mismatches: 16, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
28 31 0.34
29 60 0.65
30 1 0.01
ACGTcount: A:0.50, C:0.10, G:0.16, T:0.24
Consensus pattern (28 bp):
AAAATAGTGGCAAAACTATAAAATCTAG
Found at i:432002 original size:3 final size:3
Alignment explanation
Indices: 431994--432026 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
431984 GATGTGGGAA
431994 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
432027 TGGCTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:432555 original size:34 final size:35
Alignment explanation
Indices: 432484--432555 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 35
432474 TATCTACCAT
* *
432484 TCAAGAATTTCAATTCATTCATATATTATAAACAA
1 TCAAGAATTTCAATTCATTCATATATCACAAACAA
* * *
432519 TCAAGAATTT-AATTCTTTCATATATCACGAAGAA
1 TCAAGAATTTCAATTCATTCATATATCACAAACAA
432553 TCA
1 TCA
432556 CAAATTCTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
34 22 0.69
35 10 0.31
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (35 bp):
TCAAGAATTTCAATTCATTCATATATCACAAACAA
Found at i:432684 original size:34 final size:37
Alignment explanation
Indices: 432617--432690 Score: 91
Period size: 38 Copynumber: 2.1 Consensus size: 37
432607 TCATAAATAG
* * *
432617 AAAGATTTTCAATTTATTCATGTATCATATAAACATTC
1 AAAGATTTTCAATTCATTCA-GCATCATATAAACAATC
432655 AAAGATTTTCAATTCATTCA-CAT-AT-TAAACAATC
1 AAAGATTTTCAATTCATTCAGCATCATATAAACAATC
432689 AA
1 AA
432691 GTAAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 10 0.30
35 2 0.06
36 2 0.06
38 19 0.58
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.38
Consensus pattern (37 bp):
AAAGATTTTCAATTCATTCAGCATCATATAAACAATC
Found at i:434131 original size:36 final size:36
Alignment explanation
Indices: 434090--434165 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
434080 TACCAAGCAC
* * * *
434090 ATCATATAGCTTAATTAATCAGATAATATTTACCAT
1 ATCATATAGCATAATCAATCAAATAACATTTACCAT
*
434126 ATCATATAGCATAATCAATCAAATAACATTTATCAT
1 ATCATATAGCATAATCAATCAAATAACATTTACCAT
434162 ATCA
1 ATCA
434166 CGCATATCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.36
Consensus pattern (36 bp):
ATCATATAGCATAATCAATCAAATAACATTTACCAT
Found at i:434411 original size:45 final size:45
Alignment explanation
Indices: 434362--434572 Score: 332
Period size: 45 Copynumber: 4.7 Consensus size: 45
434352 GTCGTAAAGT
*
434362 ATAATCAATCAAATAATATTTACCATATCACGCATATCGTATAAC
1 ATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAAC
* *
434407 ATAATCAATCAAATATTATTTACCATATCATGCATATCGTATAGC
1 ATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAAC
* *
434452 ATAATCAATCAAATAATATTTACCATATCATGCATATTGTATAGC
1 ATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAAC
* *
434497 ATAATCAATCAAATAATATTTATCATATCATGCATATTGTATAAC
1 ATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAAC
* * *
434542 ATACTTAATCAATTAATATTTACCATATCAT
1 ATAATCAATCAAATAATATTTACCATATCAT
434573 AATTAATCAA
Statistics
Matches: 155, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 155 1.00
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (45 bp):
ATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAAC
Found at i:434578 original size:29 final size:29
Alignment explanation
Indices: 434541--434601 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
434531 TATTGTATAA
* * *
434541 CATACTTAATCAATTAATATTTACCATAT
1 CATAATTAATCAAATAATATTTACCACAT
*
434570 CATAATTAATCAAATAGTATTTACCACAT
1 CATAATTAATCAAATAATATTTACCACAT
434599 CAT
1 CAT
434602 GAATATCGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.43, C:0.18, G:0.02, T:0.38
Consensus pattern (29 bp):
CATAATTAATCAAATAATATTTACCACAT
Found at i:434581 original size:74 final size:74
Alignment explanation
Indices: 434496--434647 Score: 198
Period size: 74 Copynumber: 2.1 Consensus size: 74
434486 TATTGTATAG
* * * * * *
434496 CATAATCAATCAAATAATATTTATCATATCATGCATATTGTATAACAT-ACTTAATCAATTAATA
1 CATAATCAATCAAATAATATTTACCACATCATGAATATCGTATAACATGA-TCAATCAAATAATA
*
434560 TTTACCATAT
65 GTTACCATAT
* * *
434570 CATAATTAATCAAATAGTATTTACCACATCATGAATATCGTATAGCATGATCAATCAAATAATAG
1 CATAATCAATCAAATAATATTTACCACATCATGAATATCGTATAACATGATCAATCAAATAATAG
434635 TTACCATAT
66 TTACCATAT
434644 CATA
1 CATA
434648 CATAACGTAT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
74 66 0.99
75 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (74 bp):
CATAATCAATCAAATAATATTTACCACATCATGAATATCGTATAACATGATCAATCAAATAATAG
TTACCATAT
Found at i:434595 original size:119 final size:119
Alignment explanation
Indices: 434451--434680 Score: 334
Period size: 119 Copynumber: 1.9 Consensus size: 119
434441 TATCGTATAG
* * * *
434451 CATAATCAATCAAATAATATTTACCATATCATGCATATTGTATAGCATAATCAATCAAATAATAT
1 CATAATCAATCAAATAATATTTACCACATCATGAATATCGTATAGCATAATCAATCAAATAATAG
* * ** * * *
434516 TTATCATATCATGCATATTGTATAACATACTTAATCAATTAATATTTACCATAT
66 TTACCATATCATACATAACGTATAACATAATCAATCAAATAATATTTACCATAT
* * *
434570 CATAATTAATCAAATAGTATTTACCACATCATGAATATCGTATAGCATGATCAATCAAATAATAG
1 CATAATCAATCAAATAATATTTACCACATCATGAATATCGTATAGCATAATCAATCAAATAATAG
434635 TTACCATATCATACATAACGTATAACATAATCAATCAAATAATATT
66 TTACCATATCATACATAACGTATAACATAATCAATCAAATAATATT
434681 CATCATGTCA
Statistics
Matches: 97, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
119 97 1.00
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (119 bp):
CATAATCAATCAAATAATATTTACCACATCATGAATATCGTATAGCATAATCAATCAAATAATAG
TTACCATATCATACATAACGTATAACATAATCAATCAAATAATATTTACCATAT
Found at i:434628 original size:45 final size:45
Alignment explanation
Indices: 434570--435321 Score: 572
Period size: 45 Copynumber: 17.7 Consensus size: 45
434560 TTTACCATAT
* * *
434570 CATAATTAATCAAATAGTATTTACCACATCATGAATATCGTATAG
1 CATAATCAATCAAATAATATTTACCATATCATGAATATCGTATAG
* * * *
434615 CATGATCAATCAAATAATAGTTACCATATCAT-ACATAACGTATAA
1 CATAATCAATCAAATAATATTTACCATATCATGA-ATATCGTATAG
* * * * *
434660 CATAATCAATCAAATAATATTCATCATGTCATGCATATCATATAG
1 CATAATCAATCAAATAATATTTACCATATCATGAATATCGTATAG
* *
434705 CATAATCAATCAAA-AATATTTAACATATCAT-ACATATTGTATAG
1 CATAATCAATCAAATAATATTTACCATATCATGA-ATATCGTATAG
*
434749 CATAATCAATCAAATAATATTTACCATGTCATG-----C--ATA-
1 CATAATCAATCAAATAATATTTACCATATCATGAATATCGTATAG
* * *
434786 CATAATCAATCAAATAATATTTACCATATCAT-ACATGTCGTACAA
1 CATAATCAATCAAATAATATTTACCATATCATGA-ATATCGTATAG
*
434831 CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAG
1 CATAATCAATCAAATAATATTTACCATATCATGAATATCGTATAG
* * * *
434876 CATAATCAATCTAATAATATTTACCATGTCATGCATATCATATAG
1 CATAATCAATCAAATAATATTTACCATATCATGAATATCGTATAG
* *
434921 CACAATCAATCAAATAATATTTATCATATCAT-ACATATCGTATAG
1 CATAATCAATCAAATAATATTTACCATATCATGA-ATATCGTATAG
* *** *
434966 CATAATAAATCAAATAATATTTAAGGTGTCATG-----C--ATA-
1 CATAATCAATCAAATAATATTTACCATATCATGAATATCGTATAG
* * *
435003 CATAATCAATCAAATAATATTTACCATGTCATGCATATTGTATAG
1 CATAATCAATCAAATAATATTTACCATATCATGAATATCGTATAG
* * * * * * * * *
435048 AACACTTAATCAAATAATATTTACCACATCGTGCATACCATATAG
1 CATAATCAATCAAATAATATTTACCATATCATGAATATCGTATAG
**
435093 CATTGTCAATCAAATAATA-TT----TATCATG----TCGTATAG
1 CATAATCAATCAAATAATATTTACCATATCATGAATATCGTATAG
* * *
435129 CATAAGCAATCAAATAACA-TT----TATC--G--TATTGTATAG
1 CATAATCAATCAAATAATATTTACCATATCATGAATATCGTATAG
* *
435165 CATAATTAATCAAATAATATTTACCATTTCATG-----C--ATA-
1 CATAATCAATCAAATAATATTTACCATATCATGAATATCGTATAG
* * * *
435202 CATAATCAATCAAATAATATTTACAATGTCATGCATATTGTATAG
1 CATAATCAATCAAATAATATTTACCATATCATGAATATCGTATAG
* * * ** * * *
435247 AATACTTAATCGGATAATATTTACCATATCATGCATACCGTATAA
1 CATAATCAATCAAATAATATTTACCATATCATGAATATCGTATAG
* *
435292 CATAGTCAATCAAATAATACTTACCATATC
1 CATAATCAATCAAATAATATTTACCATATC
435322 GTGTAGCATA
Statistics
Matches: 565, Mismatches: 100, Indels: 84
0.75 0.13 0.11
Matches are distributed among these distances:
34 1 0.00
36 50 0.09
37 92 0.16
38 9 0.02
40 6 0.01
41 3 0.01
42 1 0.00
43 1 0.00
44 48 0.08
45 354 0.63
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (45 bp):
CATAATCAATCAAATAATATTTACCATATCATGAATATCGTATAG
Done.