Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007850.1 Hibiscus syriacus cultivar Beakdansim tig00110209_pilon, 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: 1775394
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:148369 original size:18 final size:18
Alignment explanation
Indices: 148346--148387 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
148336 AAGAGAATGA
* *
148346 AAAAATAGGTGAAGTGGG
1 AAAAATAGGTAAAGTGAG
148364 AAAAATAGGTAAAGTGAG
1 AAAAATAGGTAAAGTGAG
148382 AAAAAT
1 AAAAAT
148388 GAAAAAGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.29, T:0.17
Consensus pattern (18 bp):
AAAAATAGGTAAAGTGAG
Found at i:148607 original size:41 final size:41
Alignment explanation
Indices: 148432--148912 Score: 407
Period size: 42 Copynumber: 11.7 Consensus size: 41
148422 TGTAAATTTA
* *
148432 CGGCGTTTGTAAACAAAAATGCCACTAAAGTACGAGTCTATAG
1 CGGCGTTTGT--ATAAAAACGCCACTAAAGTACGAGTCTATAG
* * ** * *
148475 AGGCGTTTGTTCTAAAAACGCCACTAAAACAAGACTCTATAG
1 CGGCGTTTG-TATAAAAACGCCACTAAAGTACGAGTCTATAG
* * * * * * *
148517 TGGCATTTTTTACAAAAACGCCACTAAAGTTATGAGTCTTTAA
1 CGGC-GTTTGTATAAAAACGCCACTAAAG-TACGAGTCTATAG
* *
148560 CGGCGTTTGCATACAAACGCCACTAAAGTACGAGTCTATAG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAG
* * * *
148601 CGGCGTTTAT-TCAAAAAATGCCACTAAAGTACTAGTCTATAA
1 CGGCGTTTGTAT--AAAAACGCCACTAAAGTACGAGTCTATAG
* * * *
148643 CGGCATTTTTATAAAAACGCCACTAAAGTAC-AGTCTTTGG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAG
* *
148683 CGGCGTTTGTATAAAAACACCACTAAAGTACTAGTCTATAG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAG
* *
148724 CGGTGTTTAATATAAAAACGCCACTAAAGTACGAGTCTATAG
1 CGGCGTTT-GTATAAAAACGCCACTAAAGTACGAGTCTATAG
* * *
148766 CGGTGTTTGTATAAAAACGCCACTAAAGTACTAGTCTTTAG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAG
* * * * *
148807 CGGCG--T-TCTAAAAACGTCACTAAAGTAC-ATTTTTTAG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAG
* * ** * * * * *
148844 CGGCATTTATATAAAAATACCACTAAAGTTCAAGTGTTTTG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAG
* *
148885 CGGCGTTTGTTCTAAAAACGCCGCTAAA
1 CGGCGTTTG-TATAAAAACGCCACTAAA
148913 AATGCCACTA
Statistics
Matches: 353, Mismatches: 72, Indels: 27
0.78 0.16 0.06
Matches are distributed among these distances:
37 11 0.03
38 20 0.06
39 2 0.01
40 52 0.15
41 97 0.27
42 147 0.42
43 23 0.07
44 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (41 bp):
CGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAG
Found at i:148668 original size:83 final size:83
Alignment explanation
Indices: 148444--148813 Score: 383
Period size: 83 Copynumber: 4.5 Consensus size: 83
148434 GCGTTTGTAA
* * * * ** *
148444 ACAAAAATGCCACTAAAGTACGAGTCTATAGA-GGCGTTTGTTCTAAAAACGCCACTAAAACAAG
1 ACAAAAACGCCACTAAAGTACTAGTCTATA-ACGGCGTTTATTATAAAAACGCCACTAAAGTACG
* * *
148508 ACTCTATAGTGGCATTTTTT
65 AGTCTATAGCGGC-GTTTTT
* ** *
148528 ACAAAAACGCCACTAAAGTTA-TGAGTCTTTAACGGCGTTT-GCATACAAACGCCACTAAAGTAC
1 ACAAAAACGCCACTAAAG-TACT-AGTCTATAACGGCGTTTATTATAAAAACGCCACTAAAGTAC
148591 GAGTCTATAGCGGCGTTTATT
64 GAGTCTATAGCGGCGTTT-TT
* *
148612 -CAAAAAATGCCACTAAAGTACTAGTCTATAACGGCATTT-TTATAAAAACGCCACTAAAGTAC-
1 AC-AAAAACGCCACTAAAGTACTAGTCTATAACGGCGTTTATTATAAAAACGCCACTAAAGTACG
* * *
148674 AGTCTTTGGCGGCGTTTGT
65 AGTCTATAGCGGCGTTTTT
* * * * *
148693 ATAAAAACACCACTAAAGTACTAGTCTATAGCGGTGTTTAATATAAAAACGCCACTAAAGTACGA
1 ACAAAAACGCCACTAAAGTACTAGTCTATAACGGCGTTTATTATAAAAACGCCACTAAAGTACGA
* *
148758 GTCTATAGCGGTGTTTGT
66 GTCTATAGCGGCGTTTTT
* * *
148776 ATAAAAACGCCACTAAAGTACTAGTCTTTAGCGGCGTT
1 ACAAAAACGCCACTAAAGTACTAGTCTATAACGGCGTT
148814 CTAAAAACGT
Statistics
Matches: 242, Mismatches: 35, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
81 33 0.14
82 37 0.15
83 92 0.38
84 64 0.26
85 16 0.07
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (83 bp):
ACAAAAACGCCACTAAAGTACTAGTCTATAACGGCGTTTATTATAAAAACGCCACTAAAGTACGA
GTCTATAGCGGCGTTTTT
Found at i:148726 original size:123 final size:123
Alignment explanation
Indices: 148453--148912 Score: 454
Period size: 123 Copynumber: 3.7 Consensus size: 123
148443 AACAAAAATG
* * *
148453 CCACTAAAGTACGAGTCTATAGAGGCGTTTGTTCTAAAAACGCCACTAAA--ACAAGACTCTATA
1 CCACTAAAGTACGAGTCTATAGCGGCGTTTATTCAAAAAACGCCACTAAAGTACAAG--TCTATA
* * * * * *
148516 GTGGCATTTTTTACAAAAACGCCACTAAAGTTATGAGTCTTTAACGGCGTTTGCATACAAACG
64 GCGGCA-TTTTTATAAAAACGCCACTAAAG-TA-CAGTCTTTAGCGGCGTTTGCATAAAAACA
* * *
148579 CCACTAAAGTACGAGTCTATAGCGGCGTTTATTCAAAAAATGCCACTAAAGTACTAGTCTATAAC
1 CCACTAAAGTACGAGTCTATAGCGGCGTTTATTCAAAAAACGCCACTAAAGTACAAGTCTATAGC
* *
148644 GGCATTTTTATAAAAACGCCACTAAAGTACAGTCTTTGGCGGCGTTTGTATAAAAACA
66 GGCATTTTTATAAAAACGCCACTAAAGTACAGTCTTTAGCGGCGTTTGCATAAAAACA
* * * *
148702 CCACTAAAGTACTAGTCTATAGCGGTGTTTAAT-ATAAAAACGCCACTAAAGTACGAGTCTATAG
1 CCACTAAAGTACGAGTCTATAGCGGCGTTTATTCA-AAAAACGCCACTAAAGTACAAGTCTATAG
** * *
148766 CGGTGTTTGTATAAAAACGCCACTAAAGTACTAGTCTTTAGCGGCG-TT-C-TAAAAACG
65 CGGCATTTTTATAAAAACGCCACTAAAGTAC-AGTCTTTAGCGGCGTTTGCATAAAAACA
* * * * * * * * *
148823 TCACTAAAGTAC-ATTTTTTAGCGGCATTTATAT-AAAAATA--CCACTAAAGTTCAAGTGTTTT
1 CCACTAAAGTACGAGTCTATAGCGGCGTTTAT-TCAAAAA-ACGCCACTAAAGTACAAGTCTATA
* * *
148884 GCGGCGTTTGTTCTAAAAACGCCGCTAAA
64 GCGGCATTT-TTATAAAAACGCCACTAAA
148913 AATGCCACTA
Statistics
Matches: 285, Mismatches: 42, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
119 24 0.08
120 33 0.12
121 21 0.07
122 1 0.00
123 109 0.38
124 15 0.05
125 22 0.08
126 56 0.20
128 4 0.01
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (123 bp):
CCACTAAAGTACGAGTCTATAGCGGCGTTTATTCAAAAAACGCCACTAAAGTACAAGTCTATAGC
GGCATTTTTATAAAAACGCCACTAAAGTACAGTCTTTAGCGGCGTTTGCATAAAAACA
Found at i:149275 original size:31 final size:31
Alignment explanation
Indices: 149214--149274 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
149204 ATTTAAATTT
* *
149214 TTTCGAGCTCGAGTCGAGTTTCAAATTTTTA
1 TTTCGAGCTCAAGTCGAGCTTCAAATTTTTA
* *
149245 TTTCGAGTTCAAGTCGAGCTTGACAATTTT
1 TTTCGAGCTCAAGTCGAGCTTCA-AATTTT
149275 AAGCTCGTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 19 0.76
32 6 0.24
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (31 bp):
TTTCGAGCTCAAGTCGAGCTTCAAATTTTTA
Found at i:151061 original size:73 final size:73
Alignment explanation
Indices: 150796--151053 Score: 319
Period size: 70 Copynumber: 3.5 Consensus size: 73
150786 CCGGAAATAT
** * * * *
150796 AAAATAGGCGTTATCTATTACATTAAAATACTTACC-AATTTTTT-AAGGTTGTTAATAATGTAA
1 AAAATAGGCACTACCTATTACATTAAAATACCTACCGGATTTTTTGAAGGTTGCTAATAATGTAA
150859 ACGGT-AA
66 ACGGTAAA
* **
150866 AAAATAGGCACTACCTATTACATTAAAATACCTACTGG-TTTTTTGAAAATTGCTAATAATGTAA
1 AAAATAGGCACTACCTATTACATTAAAATACCTACCGGATTTTTTGAAGGTTGCTAATAATGTAA
150930 ACGGTACAAAA
66 ACGGT---AAA
*
150941 AAAATAGGCACTACCTATTATATTAAAATACCTACC-GATTTTTTTGAAGGTTGCTAATAATGTA
1 AAAATAGGCACTACCTATTACATTAAAATACCTACCGGA-TTTTTTGAAGGTTGCTAATAATGTA
151005 AACGGTAAA
65 AACGGTAAA
** * *
151014 AAAATAGGTGCTACCTATTACATTAAACTATCTACCGGAT
1 AAAATAGGCACTACCTATTACATTAAAATACCTACCGGAT
151054 ATGTTGAAAG
Statistics
Matches: 161, Mismatches: 18, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
70 37 0.23
71 21 0.13
73 35 0.22
74 3 0.02
75 36 0.22
76 29 0.18
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (73 bp):
AAAATAGGCACTACCTATTACATTAAAATACCTACCGGATTTTTTGAAGGTTGCTAATAATGTAA
ACGGTAAA
Found at i:158280 original size:24 final size:23
Alignment explanation
Indices: 158252--158314 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 23
158242 GCTCGTATAA
158252 ATTTGCACCGTAGTGCCACGTAG
1 ATTTGCACCGTAGTGCCACGTAG
* *
158275 ATTTTGCACCGAAGTGCCGCGTAG
1 A-TTTGCACCGTAGTGCCACGTAG
**
158299 AAATGCACCGTAGTGC
1 ATTTGCACCGTAGTGC
158315 ATATAAGATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 13 0.38
24 21 0.62
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.24
Consensus pattern (23 bp):
ATTTGCACCGTAGTGCCACGTAG
Found at i:159520 original size:17 final size:17
Alignment explanation
Indices: 159494--159526 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
159484 TTTTGCTTTT
159494 AATTTATTTAAGTATTTA
1 AATTTATTTAA-TATTTA
159512 AATTT-TTTAATATTT
1 AATTTATTTAATATTT
159527 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
AATTTATTTAATATTTA
Found at i:159528 original size:17 final size:19
Alignment explanation
Indices: 159490--159528 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
159480 AATATTTTGC
159490 TTTT-AATTTATTTAAGTA
1 TTTTAAATTTATTTAAGTA
159508 -TTTAAATTT-TTTAA-TA
1 TTTTAAATTTATTTAAGTA
159524 TTTTA
1 TTTTA
159529 TTTAATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
16 2 0.11
17 12 0.63
18 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTAAATTTATTTAAGTA
Found at i:167917 original size:99 final size:99
Alignment explanation
Indices: 167743--167929 Score: 277
Period size: 99 Copynumber: 1.9 Consensus size: 99
167733 TGAGTTTCGA
** *
167743 CTAAAATATTATTGGAGTTTAAGATGATGGAGCCTTGAATTTACTCACGATAAGAAAATAAGTTA
1 CTAAAATATTATAAGAGATTAAGATGATGGAGCCTTGAATTTACTCACGATAAGAAAATAAGTTA
167808 AAAATGGAAAATGTTATGAATATATGGGTTGCAC
66 AAAATGGAAAATGTTATGAATATATGGGTTGCAC
* * * *
167842 CTAAAATGTTATAAGAGATTAAGCTGATGGAGCCTTGAATTTTC-CTACTATAAGAAAATAAGTT
1 CTAAAATATTATAAGAGATTAAGATGATGGAGCCTTGAATTTACTC-ACGATAAGAAAATAAGTT
* *
167906 AAAAGTTGAAAATGTTATGAATAT
65 AAAAATGGAAAATGTTATGAATAT
167930 GTATAATAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
98 1 0.01
99 77 0.99
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (99 bp):
CTAAAATATTATAAGAGATTAAGATGATGGAGCCTTGAATTTACTCACGATAAGAAAATAAGTTA
AAAATGGAAAATGTTATGAATATATGGGTTGCAC
Found at i:169574 original size:99 final size:101
Alignment explanation
Indices: 169314--169574 Score: 264
Period size: 100 Copynumber: 2.6 Consensus size: 101
169304 TAGTGTATTA
* * * * * * *
169314 TTTCATAATATAGACGGTTCCATACTATAACTTAA-TCAGTTAACATAAGAACAAGGCGCAA-CT
1 TTTCATAATATAAACGGTTTCTTCCTATAACTTAACT-AGTTAAAATAACACCAAGGCGCAACCT
* * * *
169377 GATAATGTTATCCAGGAAAATATGTTTGTTTTATTTT
65 GATAATGTTATCCAGGAAAATAGGTATGTATTATCTT
* * * * *
169414 TTTCATAATATACAA-GGTTT-TAGCCTATAACGTAACCAATTAAAATAACACTAAGGCGCAACC
1 TTTCATAATATA-AACGGTTTCT-TCCTATAACTTAACTAGTTAAAATAACACCAAGGCGCAACC
* *
169477 T-ATAATGTTATCTAGGAAACTAGGTATGTATTA-CTT
64 TGATAATGTTATCCAGGAAAATAGGTATGTATTATCTT
* * *
169513 TTTCATAATATAAACAGTTTCTTCCTATAACTTAACTAGTTAATATAACACCAAGGTGCAAC
1 TTTCATAATATAAACGGTTTCTTCCTATAACTTAACTAGTTAAAATAACACCAAGGCGCAAC
169575 TGGTAACGTC
Statistics
Matches: 129, Mismatches: 26, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
98 2 0.02
99 51 0.40
100 73 0.57
101 3 0.02
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (101 bp):
TTTCATAATATAAACGGTTTCTTCCTATAACTTAACTAGTTAAAATAACACCAAGGCGCAACCTG
ATAATGTTATCCAGGAAAATAGGTATGTATTATCTT
Found at i:169576 original size:199 final size:199
Alignment explanation
Indices: 169217--169576 Score: 433
Period size: 199 Copynumber: 1.8 Consensus size: 199
169207 TTAATTTCAA
* * * * * * * *
169217 TCATAATGTATAAGGTTTTAGCCTATAACTTATCCAGTTGACATAACAACAAGGCGTAACCTATA
1 TCATAATATACAAGGTTTTAGCCTATAACGTAACCAATTAAAATAACAACAAGGCGCAACCTATA
* * *
169282 ATATTTTCCAGAAAACAAAGTTTAGTGTATTATTTCATAATATAGACGGTTCCATACTATAACTT
66 ATATTATCCAGAAAACAAAGTTTAGTGTATTATTTCATAATATAAACAGTTCCATACTATAACTT
*
169347 AATCAGTTAACATAAGAACAAGGCGCAACTGATAATGTTATCCAGGAAAATATGTTTGTTTTATT
131 AATCAGTTAACATAACAACAAGGCGCAACTGATAATGTTATCCAGGAAAATATGTTTGTTTTATT
169412 TTTT
196 TTTT
169416 TCATAATATACAAGGTTTTAGCCTATAACGTAACCAATTAAAATAAC-ACTAAGGCGCAACCTAT
1 TCATAATATACAAGGTTTTAGCCTATAACGTAACCAATTAAAATAACAAC-AAGGCGCAACCTAT
* * * * * * * *
169480 AATGTTATCTAGGAAAC-TAG-GTA-TGTATTACTTTTTCATAATATAAACAGTTTCTTCCTATA
65 AATATTATCCAGAAAACAAAGTTTAGTGTATTA---TTTCATAATATAAACAGTTCCATACTATA
* * *
169542 ACTTAA-CTAGTTAATATAACACCAAGGTGCAACTG
127 ACTTAATC-AGTTAACATAACAACAAGGCGCAACTG
169577 GTAACGTCAC
Statistics
Matches: 133, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
196 7 0.05
197 2 0.02
198 5 0.04
199 119 0.89
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.34
Consensus pattern (199 bp):
TCATAATATACAAGGTTTTAGCCTATAACGTAACCAATTAAAATAACAACAAGGCGCAACCTATA
ATATTATCCAGAAAACAAAGTTTAGTGTATTATTTCATAATATAAACAGTTCCATACTATAACTT
AATCAGTTAACATAACAACAAGGCGCAACTGATAATGTTATCCAGGAAAATATGTTTGTTTTATT
TTTT
Found at i:170638 original size:73 final size:74
Alignment explanation
Indices: 170551--170701 Score: 268
Period size: 73 Copynumber: 2.1 Consensus size: 74
170541 TCCAAAGTTA
**
170551 GAATAATATGTTGAACCATGTTTTATAATATTTTGATATAACAAATTAAGGTAAAATGTTTTTGG
1 GAATAATATGTTGAACCATGTTTTATAATATTTTGATATAACAAATTAAGACAAAATGTTTTTGG
170616 ACTTGAATT
66 ACTTGAATT
*
170625 GAATAAT-TGTTGAACCATGTTTTATAATGTTTTGATATAACAAATTAAGACAAAATGTTTTTGG
1 GAATAATATGTTGAACCATGTTTTATAATATTTTGATATAACAAATTAAGACAAAATGTTTTTGG
170689 ACTTGAATT
66 ACTTGAATT
170698 GAAT
1 GAAT
170702 TTGTTCAAAG
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
73 67 0.91
74 7 0.09
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (74 bp):
GAATAATATGTTGAACCATGTTTTATAATATTTTGATATAACAAATTAAGACAAAATGTTTTTGG
ACTTGAATT
Found at i:172392 original size:3 final size:3
Alignment explanation
Indices: 172386--172435 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
172376 TAAAGAAAAA
* *
172386 AAG AAG AAG ATA- AAG -AG AAG AAA AAC AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
172430 AAG AAG
1 AAG AAG
172436 GTAGGCATTG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
2 3 0.07
3 37 0.90
4 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.28, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:180416 original size:33 final size:33
Alignment explanation
Indices: 180352--180470 Score: 123
Period size: 33 Copynumber: 3.6 Consensus size: 33
180342 GTTAACTTAC
* * * * *
180352 CGATGATTTGTTTGTTGGTTGCTCGAGATTTTT
1 CGATGAGTTGTTGGTTGATTGGTTGAGATTTTT
* *
180385 GGATGAGTTGTTGGTTGATTGGTTGATA-TTTT
1 CGATGAGTTGTTGGTTGATTGGTTGAGATTTTT
* *
180417 CCATTGAGTGGTTGGTTGATTGGTTGAGATTTTT
1 CGA-TGAGTTGTTGGTTGATTGGTTGAGATTTTT
* *
180451 CGATGAGCTGTTAGTTGATT
1 CGATGAGTTGTTGGTTGATT
180471 TCTTTATTTT
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
32 5 0.07
33 58 0.84
34 6 0.09
ACGTcount: A:0.15, C:0.06, G:0.31, T:0.48
Consensus pattern (33 bp):
CGATGAGTTGTTGGTTGATTGGTTGAGATTTTT
Found at i:184482 original size:25 final size:24
Alignment explanation
Indices: 184454--184503 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
184444 TGTATTGAAT
*
184454 ATCTTAATAATTGTTTATATTTTTA
1 ATCTAAATAATTGTTTA-ATTTTTA
*
184479 ATCTAAATAATTTTTTAATTTTTA
1 ATCTAAATAATTGTTTAATTTTTA
184503 A
1 A
184504 AAAATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (24 bp):
ATCTAAATAATTGTTTAATTTTTA
Found at i:189550 original size:28 final size:27
Alignment explanation
Indices: 189495--189555 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
189485 CAAATTATAC
*
189495 AATATATTTTAAATAATATAGTATTTT
1 AATATATTATAAATAATATAGTATTTT
189522 AATATATTATAATTATAA-ATAGT-TGTTT
1 AATATATTATAA--ATAATATAGTAT-TTT
189550 AATATA
1 AATATA
189556 GCAATGATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 12 0.40
28 14 0.47
29 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (27 bp):
AATATATTATAAATAATATAGTATTTT
Found at i:191577 original size:20 final size:20
Alignment explanation
Indices: 191530--191779 Score: 224
Period size: 20 Copynumber: 12.2 Consensus size: 20
191520 AATGACCAAC
191530 AAAATCGCAACGCGATATC--
1 AAAATCGCAACGCGAT-TCAG
* *
191549 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* * **
191569 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
* *
191589 AAGATCGCAACACGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* * *
191611 AGAATCGCAATGCGATTCAT
1 AAAATCGCAACGCGATTCAG
*
191631 AAAATCGCAACGCGATTCAT
1 AAAATCGCAACGCGATTCAG
191651 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
191671 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
191691 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
191713 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
191733 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
191755 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
191775 AAAAT
1 AAAAT
191780 GAGTAAATTC
Statistics
Matches: 191, Mismatches: 24, Indels: 31
0.78 0.10 0.13
Matches are distributed among these distances:
18 1 0.01
19 22 0.12
20 118 0.62
21 2 0.01
22 43 0.23
23 5 0.03
ACGTcount: A:0.40, C:0.25, G:0.18, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:191666 original size:40 final size:41
Alignment explanation
Indices: 191613--191779 Score: 225
Period size: 42 Copynumber: 4.1 Consensus size: 41
191603 ATCTTCCAAG
* *
191613 AATCGCAATGCGA-TT-CATAAAATCGCAACGCGATTCATAA
1 AATCGCAACGCGACTTCCA-AAAATCGCAACGCGATTCAGAA
191653 AATCGCAACGCGA-TT-CAGAAAATCGCAACGCGATTCAGAA
1 AATCGCAACGCGACTTCCA-AAAATCGCAACGCGATTCAGAA
*
191693 AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
1 AATCGCAACGCGA-CTTCCAAAAATCGCAACGCGATTCAGAA
* *
191735 AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAA
1 AATCGCAACGCGA-CTTCCAAAAATCGCAACGCGATTCAGAA
191777 AAT
1 AAT
191780 GAGTAAATTC
Statistics
Matches: 119, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
40 50 0.42
42 67 0.56
43 2 0.02
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
AATCGCAACGCGACTTCCAAAAATCGCAACGCGATTCAGAA
Found at i:191707 original size:102 final size:102
Alignment explanation
Indices: 191530--191779 Score: 319
Period size: 102 Copynumber: 2.4 Consensus size: 102
191520 AATGACCAAC
* * * * *
191530 AAAATCGCAACGCGA-T-ATCAAAACCGCAACGCGATTTAGAAAAGCGCAACGTTGAAAAGAAGA
1 AAAATCGCAACGCGATTCAT-AAAATCGCAACGCGATTAAGAAAATCGCAACGTCGAAAAGAAAA
* *
191593 TCGCAACACGATCTTCCAAGAATCGCAATGCGATTCAT
65 TCGCAACACGATCTTCCAAGAATCGCAACGCGATTCAG
* **
191631 AAAATCGCAACGCGATTCATAAAATCGCAACGCGATTCAGAAAATCGCAACG-CGATTCAGAAAA
1 AAAATCGCAACGCGATTCATAAAATCGCAACGCGATTAAGAAAATCGCAACGTCGA-AAAGAAAA
*
191695 TCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAG
65 TCGCAACACGATCTTCCAAGAATCGCAACGCGATTCAG
*
191733 AAAATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATTAAGAAAAT
1 AAAATCGCAACGCGA--TT-CATAAAATCGCAACGCGATTAAGAAAAT
191780 GAGTAAATTC
Statistics
Matches: 131, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
101 17 0.13
102 85 0.65
103 2 0.02
104 25 0.19
105 2 0.02
ACGTcount: A:0.40, C:0.25, G:0.18, T:0.17
Consensus pattern (102 bp):
AAAATCGCAACGCGATTCATAAAATCGCAACGCGATTAAGAAAATCGCAACGTCGAAAAGAAAAT
CGCAACACGATCTTCCAAGAATCGCAACGCGATTCAG
Found at i:191730 original size:42 final size:42
Alignment explanation
Indices: 191633--191779 Score: 237
Period size: 42 Copynumber: 3.5 Consensus size: 42
191623 CGATTCATAA
* *
191633 AATCGCAACGCGATTCATAAAATCGCAACGCGA--TT-CAGAA
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCA-AG
191673 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAG
191715 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAG
*
191757 AATCGCAACGCGATTAAGAAAAT
1 AATCGCAACGCGATTCAGAAAAT
191780 GAGTAAATTC
Statistics
Matches: 101, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
40 32 0.32
42 67 0.66
43 2 0.02
ACGTcount: A:0.39, C:0.26, G:0.18, T:0.17
Consensus pattern (42 bp):
AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAG
Found at i:191886 original size:6 final size:6
Alignment explanation
Indices: 191875--191977 Score: 192
Period size: 6 Copynumber: 17.5 Consensus size: 6
191865 GACACGTATT
191875 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
191923 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
191970 ACC-CG ACC
1 ACCACG ACC
191978 CGAGACGAGA
Statistics
Matches: 97, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 10 0.10
6 87 0.90
ACGTcount: A:0.32, C:0.51, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:192493 original size:6 final size:6
Alignment explanation
Indices: 192477--192598 Score: 237
Period size: 6 Copynumber: 20.5 Consensus size: 6
192467 TCTCGTCTCG
192477 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
192524 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
192572 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
192599 AATACGTGTC
Statistics
Matches: 116, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.04
6 111 0.96
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:192750 original size:20 final size:20
Alignment explanation
Indices: 192701--193083 Score: 435
Period size: 20 Copynumber: 18.8 Consensus size: 20
192691 CTCATTTTCT
192701 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
192721 GAAGATCGCGTTGCGATTCTTG
1 G-A-ATCGCGTTGCGATTCTTG
*
192743 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
192763 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
192783 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
192803 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
192823 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
192843 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
192863 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
192883 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
192904 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
192923 GAAGATCGCGTTGCGATT-TTCT
1 G-A-ATCGCGTTGCGATTCTT-G
* * *
192945 AAATCGCGTTGTGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
*
192965 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
*
192985 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
193005 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
193025 GAAGATCGCGTTGCGATT-TTAT
1 G-A-ATCGCGTTGCGATTCTT-G
*
193047 GAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
193067 GAAGATCGCGTTGCGAT
1 G-A-ATCGCGTTGCGAT
193084 CTTCTTTTCA
Statistics
Matches: 325, Mismatches: 16, Indels: 42
0.85 0.04 0.11
Matches are distributed among these distances:
18 5 0.02
19 6 0.02
20 228 0.70
21 21 0.06
22 65 0.20
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:192780 original size:40 final size:40
Alignment explanation
Indices: 192701--193088 Score: 502
Period size: 40 Copynumber: 9.5 Consensus size: 40
192691 CTCATTTTCT
*
192701 GAATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGCGATTCTTG
192743 GAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTG
192783 GAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTG
192823 GAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTG
*
192863 GAATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGATT-TTCTGAATCGCGTTGCGA--TTCTTG
* *
192904 -AATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGCGATTCTT-G
* * *
192945 AAATCGCGTTGTGATTTTCTGAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTT-G
192985 GAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTG
* *
193025 GAAGATCGCGTTGCGATTTTATGAATCGCATTGCGATTCTTG
1 G-A-ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTG
*
193067 GAAGATCGCGTTGCGATCTTCT
1 G-A-ATCGCGTTGCGATTTTCT
193089 TTTCAACGTT
Statistics
Matches: 322, Mismatches: 11, Indels: 26
0.90 0.03 0.07
Matches are distributed among these distances:
39 2 0.01
40 203 0.63
41 12 0.04
42 105 0.33
ACGTcount: A:0.16, C:0.19, G:0.27, T:0.37
Consensus pattern (40 bp):
GAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTG
Found at i:192818 original size:60 final size:58
Alignment explanation
Indices: 192694--193143 Score: 435
Period size: 60 Copynumber: 7.4 Consensus size: 58
192684 GAATTTACTC
*
192694 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTT-TGAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATT-TTTGAATCGCGTTGCG
192756 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCGTTGCG
1 ATTTT-TGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTT-TGAATCGCGTTGCG
* * *
192816 ATTCTTGGAATCGCGTTGCGATT-TTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATT-TTTGAATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATT-TTTGAATCGCGTTGCG
* *
192876 ATTCTTGGAATCGCGTTGCGATTTTCTT--AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATT-TTTGAATCGCGTTGCGA--TTCTTGGAATCGCGTTGCGATT-TTTG-A-ATCGCGTTGCG
* * *
192938 ATTTTCTAAATCGCGTTGTGATT-TTCTGAATCGCGTTGCGATTTTCTGAATCGCGTTGCG
1 ATTTT-TGAATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATTTT-TGAATCGCGTTGCG
*
192998 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTATGAATCGCATTGCG
1 ATTTT-TGAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTT-TGAATCGCGTTGCG
* **** * * *
193060 ATTCTTGGAAGATCGCGTTGCGA-TCTTCTTTTCAACGTTGCGCTTTTCTAAATCGCGTTGCG
1 ATT-TTTG-A-ATCGCGTTGCGATTCTTGGAATC-GCGTTGCGATTTT-TGAATCGCGTTGCG
*
193122 -GTTTTGATATCGCGTTGCGATT
1 ATTTTTGA-ATCGCGTTGCGATT
193144 TTGTTGGTCA
Statistics
Matches: 340, Mismatches: 26, Indels: 46
0.83 0.06 0.11
Matches are distributed among these distances:
59 19 0.06
60 155 0.46
61 17 0.05
62 128 0.38
63 9 0.03
64 12 0.04
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.38
Consensus pattern (58 bp):
ATTTTTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTTGAATCGCGTTGCG
Found at i:193118 original size:20 final size:20
Alignment explanation
Indices: 193095--193145 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
193085 TTCTTTTCAA
* *
193095 CGTTGCGCTTTTCTAAATCG
1 CGTTGCGATTTTCTGAATCG
*
193115 CGTTGCG-GTTT-TGATATCG
1 CGTTGCGATTTTCTGA-ATCG
193134 CGTTGCGATTTT
1 CGTTGCGATTTT
193146 GTTGGTCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 14 0.54
20 10 0.38
ACGTcount: A:0.12, C:0.20, G:0.25, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCTGAATCG
Found at i:199909 original size:9 final size:9
Alignment explanation
Indices: 199895--199928 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
199885 TCTATACATT
199895 TCCCAAATA
1 TCCCAAATA
199904 TCCCAAATA
1 TCCCAAATA
199913 TCCCAAATA
1 TCCCAAATA
199922 TCCCAAA
1 TCCCAAA
199929 AGATCTGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (9 bp):
TCCCAAATA
Found at i:204614 original size:406 final size:406
Alignment explanation
Indices: 203856--204644 Score: 1499
Period size: 406 Copynumber: 1.9 Consensus size: 406
203846 AAAATATAAC
*
203856 CGCGTTACTTAACGAGTTTTTTAATGACCGTTATGATCAGGACAACTAAAGTGATAGCGCTTATA
1 CGCGTCACTTAACGAGTTTTTTAATGACCGTTATGATCAGGACAACTAAAGTGATAGCGCTTATA
203921 ACATTAACCAGCTGAATGATTCGAAAAAAGTTACACTTATTGGAGAAAAATGATATGATTTATAT
66 ACATTAACCAGCTGAATGATTCGAAAAAAGTTACACTTATTGGAGAAAAATGATATGATTTATAT
203986 ATTTATTTTATAATTAAACCTATCAAATCTGAAAACTATCATATCGTATACTGTTAATTATTTTA
131 ATTTATTTTATAATTAAACCTATCAAATCTGAAAACTATCATATCGTATACTGTTAATTATTTTA
204051 ATAAAAATAAATTATATTATAAATTCCAATAATTTATATATTTTATCATCAGATGATCTAACTAA
196 ATAAAAATAAATTATATTATAAATTCCAATAATTTATATATTTTATCATCAGATGATCTAACTAA
*
204116 ATAAAAAATTAGCTAATCCTTATTCCCATATGTAATGAGGTAAGAGGGAGGTAAGATAGTAAGCT
261 ATAAAAAATTAGCTAATCATTATTCCCATATGTAATGAGGTAAGAGGGAGGTAAGATAGTAAGCT
*
204181 GCCCCCAACGCCAGGTTGAGAGTAGCTTCCGTGGGAGACCTCCAAATTATGAAATGCCCTCCGTT
326 GCCCCCAACGCCAGGTTGAGAGTAGCTTCCGTAGGAGACCTCCAAATTATGAAATGCCCTCCGTT
204246 AGACTCGATCACACGA
391 AGACTCGATCACACGA
204262 CGCGTCACTTAACGAGTTTTTTAATGACCGTTATGATCAGGACAACTAAAGTGATAGCGCTTATA
1 CGCGTCACTTAACGAGTTTTTTAATGACCGTTATGATCAGGACAACTAAAGTGATAGCGCTTATA
204327 ACATTAACCAGCTGAATGATTCGAAAAAAGTTACACTTATTGGAGAAAAATGATATGATTTATAT
66 ACATTAACCAGCTGAATGATTCGAAAAAAGTTACACTTATTGGAGAAAAATGATATGATTTATAT
* * *
204392 ATTTATTTTATAATTAAACCTATCAAATCTGTAAACTGTCATATTGTATACTGTTAATTATTTTA
131 ATTTATTTTATAATTAAACCTATCAAATCTGAAAACTATCATATCGTATACTGTTAATTATTTTA
204457 ATAAAAATAAATTATATTATAAATTCCAATAATTTATATATTTTATCATCAGATGATCTAACTAA
196 ATAAAAATAAATTATATTATAAATTCCAATAATTTATATATTTTATCATCAGATGATCTAACTAA
*
204522 ATAAAAAATTAGCTAATCATTATTCTCATATGTAAT-AGGGTAAGAGGGAGGTAAGATAGTAAGC
261 ATAAAAAATTAGCTAATCATTATTCCCATATGTAATGA-GGTAAGAGGGAGGTAAGATAGTAAGC
204586 TGCCCCCAACGCCAGGTTGAGAGTAGCTTCCGTAGGAGACCTCCAAATTATGAAATGCC
325 TGCCCCCAACGCCAGGTTGAGAGTAGCTTCCGTAGGAGACCTCCAAATTATGAAATGCC
204645 TTGTGTTAAA
Statistics
Matches: 375, Mismatches: 7, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
405 1 0.00
406 374 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (406 bp):
CGCGTCACTTAACGAGTTTTTTAATGACCGTTATGATCAGGACAACTAAAGTGATAGCGCTTATA
ACATTAACCAGCTGAATGATTCGAAAAAAGTTACACTTATTGGAGAAAAATGATATGATTTATAT
ATTTATTTTATAATTAAACCTATCAAATCTGAAAACTATCATATCGTATACTGTTAATTATTTTA
ATAAAAATAAATTATATTATAAATTCCAATAATTTATATATTTTATCATCAGATGATCTAACTAA
ATAAAAAATTAGCTAATCATTATTCCCATATGTAATGAGGTAAGAGGGAGGTAAGATAGTAAGCT
GCCCCCAACGCCAGGTTGAGAGTAGCTTCCGTAGGAGACCTCCAAATTATGAAATGCCCTCCGTT
AGACTCGATCACACGA
Found at i:209011 original size:15 final size:15
Alignment explanation
Indices: 208991--209028 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
208981 AGAGCCTCTA
*
208991 AATCATTTAGCACTT
1 AATCATTCAGCACTT
*
209006 AATCATTCAGCGCTT
1 AATCATTCAGCACTT
209021 AATCATTC
1 AATCATTC
209029 TGAAATAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.37
Consensus pattern (15 bp):
AATCATTCAGCACTT
Found at i:218552 original size:405 final size:405
Alignment explanation
Indices: 217799--219013 Score: 2362
Period size: 405 Copynumber: 3.0 Consensus size: 405
217789 ATATTTATTG
217799 AGGCTCATAGATCTAACATTGCTCTCTCAATCCTAACATTACTGAGTTTACAAGGGATAGTAAAC
1 AGGCTCATAGATCTAACATTGCTCTCTCAATCCTAACATTACTGAGTTTACAAGGGATAGTAAAC
* * *
217864 ATACTTGGATCCTTGCACTTGGGGGGTAATTTTTTTTCTGAGGACAGCTGAAACATTCTCCCCCA
66 ATACCTAGATCCTTGCACTTGGGGGGTAA--TATTTTCTGAGGACAGCTGAAACATTCTCCCCCA
217929 TACTTACCTTTTTATTACCCTTGAGCTTTCTCTTGTTGGTGCACAATTCTTTAAGAAATTTAGCA
129 TACTTACCTTTTTATTACCCTTGAGCTTTCTCTTGTTGGTGCACAATTCTTTAAGAAATTTAGCA
217994 TATCGAGGTACTTGTTTAATTACATCAAGTAAAGGAATATTTACCTCGATCTTGCGAAATATCTC
194 TATCGAGGTACTTGTTTAATTACATCAAGTAAAGGAATATTTACCTCGATCTTGCGAAATATCTC
218059 AAGAATTTCTTTCTCTTTTGCTTCTTTCTTGGACTTAGCGAACCTAGCGGGAAAATGAGGATTTA
259 AAGAATTTCTTTCTCTTTTGCTTCTTTCTTGGACTTAGCGAACCTAGCGGGAAAATGAGGATTTA
218124 TGACAAATTCCTTCGGTTGTTCACTTTTGAGTCCTTTGGGTTGGTCTTTCTAAGTATAGGGATCA
324 TGACAAATTCCTTCGGTTGTTCACTTTTGAGTCCTTTGGGTTGGTCTTTCTAAGTATAGGGATCA
218189 ACAACTTCCTTTTCAGT
389 ACAACTTCCTTTTCAGT
218206 AGGCTCATAGATCTAACATTGCTCTCTCAATCCTAACATTACTGAGTTTACAAGGGATAGTAAAC
1 AGGCTCATAGATCTAACATTGCTCTCTCAATCCTAACATTACTGAGTTTACAAGGGATAGTAAAC
218271 ATACCTAGATCCTTGCACTTGGGGGGTAATATTTTCTGAGGACAGCTGAAACATTCTCCCCCATA
66 ATACCTAGATCCTTGCACTTGGGGGGTAATATTTTCTGAGGACAGCTGAAACATTCTCCCCCATA
218336 CTTACCTTTTTATTACCCTTGAGCTTTCTCTTGTTGGTGCACAATTCTTTAAGAAATTTAGCATA
131 CTTACCTTTTTATTACCCTTGAGCTTTCTCTTGTTGGTGCACAATTCTTTAAGAAATTTAGCATA
*
218401 TTGAGGTACTTGTTTAATTACATCAAGTAAAGGAATATTTACCTCGATCTTGCGAAATATCTCAA
196 TCGAGGTACTTGTTTAATTACATCAAGTAAAGGAATATTTACCTCGATCTTGCGAAATATCTCAA
218466 GAATTTCTTTCTCTTTTGCTTCTTTCTTGGACTTAGCGAACCTAGCGGGAAAATGAGGATTTATG
261 GAATTTCTTTCTCTTTTGCTTCTTTCTTGGACTTAGCGAACCTAGCGGGAAAATGAGGATTTATG
218531 ACAAATTCCTTCGGTTGTTCACTTTTGAGTCCTTTGGGTTGGTCTTTCTAAGTATAGGGATCAAC
326 ACAAATTCCTTCGGTTGTTCACTTTTGAGTCCTTTGGGTTGGTCTTTCTAAGTATAGGGATCAAC
218596 AACTTCCTTTTCAGT
391 AACTTCCTTTTCAGT
218611 AGGCTCATAGATCTAACATTGCTCTCTCAATCCTAACATTACTGAGTTTACAAGGGATAGTAAAC
1 AGGCTCATAGATCTAACATTGCTCTCTCAATCCTAACATTACTGAGTTTACAAGGGATAGTAAAC
218676 ATACCTAGATCCTTGCACTTGGGGGGTAATATTTTCTGAGGACAGCTGAAACATTCTCCCCCATA
66 ATACCTAGATCCTTGCACTTGGGGGGTAATATTTTCTGAGGACAGCTGAAACATTCTCCCCCATA
218741 CTTACCTTTTTATTACCCTTGAGCTTTCTCTTGTTGGTGCACAATTCTTTAAGAAATTTAGCATA
131 CTTACCTTTTTATTACCCTTGAGCTTTCTCTTGTTGGTGCACAATTCTTTAAGAAATTTAGCATA
218806 TCGAGGTACTTGTTTAATTACATCAAGTAAAGGAATATTTACCTCGATCTTGCGAAATATCTCAA
196 TCGAGGTACTTGTTTAATTACATCAAGTAAAGGAATATTTACCTCGATCTTGCGAAATATCTCAA
218871 GAATTTC--TCTCTTTTGCTTCTTTCTTGGACTTAGCGAACCTAGCGGGAAAATGAGGATTTATG
261 GAATTTCTTTCTCTTTTGCTTCTTTCTTGGACTTAGCGAACCTAGCGGGAAAATGAGGATTTATG
218934 ACAAATTCCTTCGGTTGTTCACTTTTGAGTCCTTTGGGTTGGTCTTTCTAAGTATAGGGATCAAC
326 ACAAATTCCTTCGGTTGTTCACTTTTGAGTCCTTTGGGTTGGTCTTTCTAAGTATAGGGATCAAC
218999 AACTTCCTTTTCAGT
391 AACTTCCTTTTCAGT
219014 TTCTTCCTCT
Statistics
Matches: 803, Mismatches: 5, Indels: 4
0.99 0.01 0.00
Matches are distributed among these distances:
403 136 0.17
405 575 0.72
407 92 0.11
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (405 bp):
AGGCTCATAGATCTAACATTGCTCTCTCAATCCTAACATTACTGAGTTTACAAGGGATAGTAAAC
ATACCTAGATCCTTGCACTTGGGGGGTAATATTTTCTGAGGACAGCTGAAACATTCTCCCCCATA
CTTACCTTTTTATTACCCTTGAGCTTTCTCTTGTTGGTGCACAATTCTTTAAGAAATTTAGCATA
TCGAGGTACTTGTTTAATTACATCAAGTAAAGGAATATTTACCTCGATCTTGCGAAATATCTCAA
GAATTTCTTTCTCTTTTGCTTCTTTCTTGGACTTAGCGAACCTAGCGGGAAAATGAGGATTTATG
ACAAATTCCTTCGGTTGTTCACTTTTGAGTCCTTTGGGTTGGTCTTTCTAAGTATAGGGATCAAC
AACTTCCTTTTCAGT
Found at i:224044 original size:3 final size:3
Alignment explanation
Indices: 224036--224073 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
224026 GCTGAAACAG
*
224036 CTT CTT CTT CTT CTT CTT CTT CTT CGT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
224074 CAAATTATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.34, G:0.03, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:230228 original size:158 final size:154
Alignment explanation
Indices: 229983--230563 Score: 613
Period size: 158 Copynumber: 3.7 Consensus size: 154
229973 TTAGTCTCTG
* * * * * *
229983 TTTTCATTATTTATTCGATTCCTCCTTCATTTTAAGT-CAATTTTTATCAAATTTTAACCACATG
1 TTTTC-TTATTTCTTCAATTCATCCTTTATTTTAAGTCCAATTTTTATCAAATTTAAACAACATG
* * *
230047 CTCATAAATCATC-ATAGAATACATATGT-ACTTTCAATTCCTCTTTTTGATGATAAATTTTTTT
65 CTCATATA-CAACAATAGAATACATATGTAAC-TTCAATTCCTCTTTTTGATAAT-AA-TTTTTT
230110 ATTTTTCAATTTAGTCTTTAATGTTTCATAA
126 ATTTTTCAATTTAGTC-TTAAT-TTTCATAA
* * *
230141 -TTTCTTTTTTTCTTCAATTCATCATTTATTTTAAGTCCAATATTTA-CTAAATTTAAACAACAT
1 TTTTC-TTATTTCTTCAATTCATCCTTTATTTTAAGTCCAATTTTTATC-AAATTTAAACAACAT
230204 GCTCATATACAACAATAGAATACATATGTAACTTCAATTCCTCTTTTTGATAATAACTTTTTTAT
64 GCTCATATACAACAATAGAATACATATGTAACTTCAATTCCTCTTTTTGATAATAA-TTTTTTAT
* * * * *
230269 CTTTCAGTGTA-ACTCAATTTTTCATAA
128 TTTTCAATTTAGTCTTAA-TTTTCATAA
* * * * *
230296 TTTTCTAATTTCTTCGATTCAACCTTTATTTTAAGTCC-GTTTTTATCAAATTTGAATCAA-ATG
1 TTTTCTTATTTCTTCAATTCATCCTTTATTTTAAGTCCAATTTTTATCAAATTT-AAACAACATG
* * * * * *
230359 CTCATATACCACAATAGAATACCTATATAACTTTAATTTCTCTTTTTGACAATAATTTTTTATTT
65 CTCATATACAACAATAGAATACATATGTAACTTCAATTCCTCTTTTTGATAATAATTTTTTATTT
230424 TTCAATTTAGTCCCTTAATTTCTCATAA
130 TTCAATTTAGT--CTTAATTT-TCATAA
*** * *
230452 TTTTCTTATTTCTTCAATTCATCCTTTATTTTAAGTACGTTTTTTTATCAAATTTGAACCACATG
1 TTTTCTTATTTCTTCAATTCATCCTTTATTTTAAGT-CCAATTTTTATCAAATTTAAACAACATG
* * * *
230517 CTCCTATACCACAATAGAATA-TTATGTAACTTCAATTTCTACTTTTT
65 CTCATATACAACAATAGAATACATATGTAACTTCAATTCCT-CTTTTT
230564 TTACTTAATA
Statistics
Matches: 357, Mismatches: 50, Indels: 32
0.81 0.11 0.07
Matches are distributed among these distances:
153 16 0.04
154 63 0.18
155 48 0.13
156 49 0.14
157 71 0.20
158 108 0.30
159 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.05, T:0.48
Consensus pattern (154 bp):
TTTTCTTATTTCTTCAATTCATCCTTTATTTTAAGTCCAATTTTTATCAAATTTAAACAACATGC
TCATATACAACAATAGAATACATATGTAACTTCAATTCCTCTTTTTGATAATAATTTTTTATTTT
TCAATTTAGTCTTAATTTTCATAA
Found at i:233743 original size:20 final size:20
Alignment explanation
Indices: 233720--233760 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
233710 CTCTATCTCT
233720 ATATAATATATTCCATCTAA
1 ATATAATATATTCCATCTAA
233740 ATATAATATATTCCATCTAA
1 ATATAATATATTCCATCTAA
233760 A
1 A
233761 ACCAAACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (20 bp):
ATATAATATATTCCATCTAA
Found at i:240273 original size:29 final size:29
Alignment explanation
Indices: 240241--240307 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
240231 TTTTTAATAA
240241 AATTCCCAAAATAACACCCATTTCGAATT
1 AATTCCCAAAATAACACCCATTTCGAATT
*
240270 AATTCCCAAAATAGCACCCATTTCGAATT
1 AATTCCCAAAATAACACCCATTTCGAATT
240299 AATTCCCAA
1 AATTCCCAA
240308 CATGTCACCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.40, C:0.28, G:0.04, T:0.27
Consensus pattern (29 bp):
AATTCCCAAAATAACACCCATTTCGAATT
Found at i:240316 original size:29 final size:28
Alignment explanation
Indices: 240241--240317 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 28
240231 TTTTTAATAA
*
240241 AATTCCCAAAATAACACCCATTTCGAATT
1 AATTCCCAAAAT-GCACCCATTTCGAATT
240270 AATTCCCAAAATAGCACCCATTTCGAATT
1 AATTCCCAAAAT-GCACCCATTTCGAATT
*
240299 AATTCCCAACATGTCACCC
1 AATTCCCAAAATG-CACCC
240318 GGTCAACGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 1 0.02
29 44 0.98
ACGTcount: A:0.38, C:0.31, G:0.05, T:0.26
Consensus pattern (28 bp):
AATTCCCAAAATGCACCCATTTCGAATT
Found at i:247447 original size:29 final size:29
Alignment explanation
Indices: 247322--247449 Score: 177
Period size: 29 Copynumber: 4.4 Consensus size: 29
247312 CATTTTACAG
**
247322 AAATAGCACCC-TTTTTAATTAAATTCCCA
1 AAATAGCACCCATTTCGAATT-AATTCCCA
*
247351 AAATAGCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCCATTTCGAATTAATTCCCA
*
247380 AAATAGCACCCATTTCGATTTAATTCCCA
1 AAATAGCACCCATTTCGAATTAATTCCCA
*
247409 AAATAGCACCCATTTCGAATTAATTCCTA
1 AAATAGCACCCATTTCGAATTAATTCCCA
* *
247438 ACATATCACCCA
1 AAATAGCACCCA
247450 GTCAACGGGT
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
29 83 0.92
30 7 0.08
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.30
Consensus pattern (29 bp):
AAATAGCACCCATTTCGAATTAATTCCCA
Found at i:258062 original size:29 final size:29
Alignment explanation
Indices: 258030--258088 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
258020 ATTTCAAAAT
*
258030 TATAATTATGAAAAAAACATATTAATTTATA
1 TATATTTAT-AAAAAAA-ATATTAATTTATA
* *
258061 TATATTTATAAATAAAATATTTATTTAT
1 TATATTTATAAAAAAAATATTAATTTAT
258089 TTAGAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 11 0.44
30 6 0.24
31 8 0.32
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (29 bp):
TATATTTATAAAAAAAATATTAATTTATA
Found at i:258296 original size:120 final size:120
Alignment explanation
Indices: 258043--258289 Score: 286
Period size: 120 Copynumber: 2.0 Consensus size: 120
258033 AATTATGAAA
* *
258043 AAAACATATTAATTTATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCATAAAAGG
1 AAAACA-ATTAA--TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAAAAAAGG
* * * * * *
258108 ACTTCTAGGTGCCTTAAGACAGCTCTTTTCTTCGATATTAAAAAATAAATAATTAATT
63 ACATCCAGGTGCCTTAAAACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATT
**
258166 AAAACAATTAATATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAATATCAAAAAATGGA
1 AAAACAATTAATATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAAAAAA-GGA
* ** * *
258230 CATCCAGTTGTTTTAAAACTGC-CCTTTCTT-AATATTGAAAAATAAATAAAT-ATT
64 CATCCAGGTGCCTTAAAACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATT
258284 AAAACA
1 AAAACA
258290 GGATTAAAAT
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
118 9 0.08
119 24 0.22
120 45 0.42
121 18 0.17
122 5 0.05
123 6 0.06
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.38
Consensus pattern (120 bp):
AAAACAATTAATATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAAAAAAGGACA
TCCAGGTGCCTTAAAACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATT
Found at i:259855 original size:3 final size:3
Alignment explanation
Indices: 259840--259903 Score: 76
Period size: 3 Copynumber: 21.3 Consensus size: 3
259830 ATATTTAATT
*
259840 TAA TAA TAT TAA TAA T-A TATA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
** *
259885 TAA TTT TAA AAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
259904 TTAAATAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:260334 original size:74 final size:76
Alignment explanation
Indices: 260067--260397 Score: 587
Period size: 76 Copynumber: 4.4 Consensus size: 76
260057 AGGTCCTAAA
* * * *
260067 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAACTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
260132 AGGCTTTTTGG
66 AGGCTTTTTGG
260143 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
260208 AGGCTTTTTGG
66 AGGCTTTTTGG
260219 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT-CCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
260283 AGGC-TTTTGG
66 AGGCTTTTTGG
*
260293 AAACATCATGCACTGTAGGACTTACATATGACCCTAAGGCTTTGAAAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
260357 AGGCTTTTTGG
66 AGGCTTTTTGG
*
260368 AAACATCATGCACTGCAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
260398 TGGGAAATAG
Statistics
Matches: 246, Mismatches: 7, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
73 7 0.03
74 65 0.26
75 42 0.17
76 132 0.54
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:260340 original size:150 final size:151
Alignment explanation
Indices: 260067--260397 Score: 585
Period size: 150 Copynumber: 2.2 Consensus size: 151
260057 AGGTCCTAAA
* *
260067 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAACTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGA
260132 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-A
260197 AAAGCTCCCGAAGGCTTTTTGG
130 AAAGCTCCCGAAGGCTTTTTGG
* *
260219 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT-CCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGA
*
260283 AGGC-TTTTGGAAACATCATGCACTGTAGGACTTACATATGACCCTAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
260347 AAGCTCCCGAAGGCTTTTTGG
131 AAGCTCCCGAAGGCTTTTTGG
*
260368 AAACATCATGCACTGCAGGACTTACAGATG
1 AAACATCATGCACTGAAGGACTTACAGATG
260398 TGGGAAATAG
Statistics
Matches: 173, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
149 52 0.30
150 57 0.33
151 8 0.05
152 56 0.32
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (151 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGA
AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
AAGCTCCCGAAGGCTTTTTGG
Found at i:265754 original size:9 final size:9
Alignment explanation
Indices: 265736--265800 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
265726 CCCCTTTTTC
*
265736 TTTTTCCCT
1 TTTTTTCCT
265745 TTTTTTCC-
1 TTTTTTCCT
265753 TTTTTT-CT
1 TTTTTTCCT
*
265761 CATTTTT-CT
1 -TTTTTTCCT
*
265770 TTTTTTCAT
1 TTTTTTCCT
265779 CTTTTTT-C-
1 -TTTTTTCCT
265787 TTTTTTCCT
1 TTTTTTCCT
265796 TTTTT
1 TTTTT
265801 CTCATTTTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
7 7 0.16
8 12 0.27
9 20 0.44
10 6 0.13
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTTCCT
Found at i:265803 original size:42 final size:41
Alignment explanation
Indices: 265745--265834 Score: 171
Period size: 41 Copynumber: 2.2 Consensus size: 41
265735 CTTTTTCCCT
265745 TTTTTTCCTTTTTTCTCATTTTTCTTTTTTTCATCTTTTTTC
1 TTTTTTCCTTTTTTCTCATTTTTC-TTTTTTCATCTTTTTTC
265787 TTTTTTCCTTTTTTCTCATTTTTCTTTTTTCATCTTTTTTC
1 TTTTTTCCTTTTTTCTCATTTTTCTTTTTTCATCTTTTTTC
265828 TTTTTTC
1 TTTTTTC
265835 TTTCTTTGCT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 24 0.50
42 24 0.50
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (41 bp):
TTTTTTCCTTTTTTCTCATTTTTCTTTTTTCATCTTTTTTC
Found at i:265834 original size:17 final size:17
Alignment explanation
Indices: 265730--265834 Score: 81
Period size: 17 Copynumber: 6.8 Consensus size: 17
265720 ATTTCTCCCC
* *
265730 TTTTTCTTTTTCCCT-T
1 TTTTTCTTTTTTCATCT
*
265746 TTTTTCCTTTTTTC-TCA
1 TTTTT-CTTTTTTCATCT
265763 TTTTTCTTTTTTTCATCT
1 TTTTTC-TTTTTTCATCT
265781 TTTTTCTTTTTTC--CT
1 TTTTTCTTTTTTCATCT
265796 TTTTTC-----TCA---
1 TTTTTCTTTTTTCATCT
265805 TTTTTCTTTTTTCATCT
1 TTTTTCTTTTTTCATCT
265822 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
265835 TTTCTTTGCT
Statistics
Matches: 73, Mismatches: 3, Indels: 25
0.72 0.03 0.25
Matches are distributed among these distances:
9 6 0.08
10 2 0.03
14 3 0.04
15 8 0.11
16 7 0.10
17 39 0.53
18 8 0.11
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCTTTTTTCATCT
Found at i:268761 original size:36 final size:36
Alignment explanation
Indices: 268684--268773 Score: 94
Period size: 36 Copynumber: 2.5 Consensus size: 36
268674 GTAAATGCGA
* *
268684 AAATGCATAA-ATGCAAAAATAAGAATGCAAACTGTG
1 AAATGCA-AAGATGCAAAAATAAGAATACAAAATGTG
* *
268720 TAATGCAAAGATGTAAAAAGTAAGAATACAAAATG-G
1 AAATGCAAAGATGCAAAAA-TAAGAATACAAAATGTG
* *
268756 AAATGCACAGATACAAAA
1 AAATGCAAAGATGCAAAA
268774 TGTAAATGCA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
35 2 0.05
36 29 0.66
37 13 0.30
ACGTcount: A:0.56, C:0.10, G:0.17, T:0.18
Consensus pattern (36 bp):
AAATGCAAAGATGCAAAAATAAGAATACAAAATGTG
Found at i:270493 original size:2 final size:2
Alignment explanation
Indices: 270488--270523 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
270478 CTAATGAAAA
270488 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
270524 CAAGGTATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:271727 original size:18 final size:18
Alignment explanation
Indices: 271704--271742 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
271694 TTTCTTCGAT
271704 ATTAAAAAAAAATAAATA
1 ATTAAAAAAAAATAAATA
* * *
271722 ATTAAAATAATATATATA
1 ATTAAAAAAAAATAAATA
271740 ATT
1 ATT
271743 TATAAAATAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATTAAAAAAAAATAAATA
Found at i:271826 original size:114 final size:110
Alignment explanation
Indices: 271619--271844 Score: 260
Period size: 114 Copynumber: 2.0 Consensus size: 110
271609 AAAAACATTA
* * *
271619 AATATATATATTTATAAATAAAATTTTATTTATTTAGAAATATCAAAAGGACTTCTAGGTGCATT
1 AATATATATATTTATAAATAAAATTTTATTTATTTAAAAATATCAAAAGGACATCCAGGTGCATT
*
271684 AAGACAGCTCTTTCTTCGATATTAAAAAA-AAATAAATAATTAAAAT
66 AAGACAGCCCTTTCTTC-ATATTAAAAAATAAATAAAT-ATTAAAAT
** *
271730 AATATATATAATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGT
1 AATATATAT-ATTTAT-AAATAAAAT-TTTATTTATTTAAAAATATC--AAAA-GGACATCCAGG
** * *
271795 TGTTTTAAGACTGCCCTTTCTT-A-ATTGAAAAATAAATAAATATTAAAAT
60 TGCATTAAGACAGCCCTTTCTTCATATTAAAAAATAAATAAATATTAAAAT
271844 A
1 A
271845 GGATTAAAAT
Statistics
Matches: 97, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
111 9 0.09
112 6 0.06
113 7 0.07
114 36 0.37
115 9 0.09
116 4 0.04
117 26 0.27
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.37
Consensus pattern (110 bp):
AATATATATATTTATAAATAAAATTTTATTTATTTAAAAATATCAAAAGGACATCCAGGTGCATT
AAGACAGCCCTTTCTTCATATTAAAAAATAAATAAATATTAAAAT
Found at i:271913 original size:17 final size:18
Alignment explanation
Indices: 271891--271924 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
271881 TAATAAATAA
271891 AATAAATAT-TATTTATT
1 AATAAATATATATTTATT
271908 AATAAATATATATTTAT
1 AATAAATATATATTTAT
271925 GGCTAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATAAATATATATTTATT
Found at i:272026 original size:21 final size:20
Alignment explanation
Indices: 271993--272045 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
271983 CTAAACAATG
**
271993 AATAAATTAAAACTATATTTAA
1 AATAAA-TAAAACT-TATAAAA
*
272015 AATAAATAAAACTTGTAAAA
1 AATAAATAAAACTTATAAAA
272035 AATAAATAAAA
1 AATAAATAAAA
272046 ATTGAATTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 15 0.54
21 7 0.25
22 6 0.21
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (20 bp):
AATAAATAAAACTTATAAAA
Found at i:273369 original size:21 final size:23
Alignment explanation
Indices: 273358--273414 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 23
273348 TATTTAATTT
*
273358 AATAATATTAATAATATATATTAT
1 AATAATAATAAT-ATATATATTAT
*
273382 AATAATAATAATA-ATA-ATTTT
1 AATAATAATAATATATATATTAT
*
273403 AAAAATAATAAT
1 AATAATAATAAT
273415 TTAAATAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.50
22 3 0.10
23 1 0.03
24 11 0.37
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AATAATAATAATATATATATTAT
Found at i:273372 original size:3 final size:3
Alignment explanation
Indices: 273357--273414 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
273347 ATATTTAATT
* * **
273357 TAA TAA TAT TAA TAA T-A TATA TTA TAA TAA TAA TAA TAA TAA TTT
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
273402 TAA AAA TAA TAA T
1 TAA TAA TAA TAA T
273415 TTAAATAATT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:273373 original size:24 final size:24
Alignment explanation
Indices: 273357--273414 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
273347 ATATTTAATT
*
273357 TAATAATATTAATAATATATATTA
1 TAATAATAATAATAATATATATTA
273381 TAATAATAATAATAATA-AT-TT-
1 TAATAATAATAATAATATATATTA
*
273402 TAAAAATAATAAT
1 TAATAATAATAAT
273415 TTAAATAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 12 0.38
22 2 0.06
23 2 0.06
24 16 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TAATAATAATAATAATATATATTA
Found at i:275305 original size:60 final size:60
Alignment explanation
Indices: 275231--275353 Score: 192
Period size: 60 Copynumber: 2.0 Consensus size: 60
275221 AATGCACTGT
* * * ** *
275231 TTTTCATGTAACTTGCATTAGTGGCACCTTTATGCCAAAATGCATTGTTAGGCATTTAAC
1 TTTTCATCTAACTTGCATTAGTGACACCTTTATACCAAAATGCACCGTTAGACATTTAAC
275291 TTTTCATCTAACTTGCATTAGTGACACCTTTATACCAAAATGCACCGTTAGACATTTAAC
1 TTTTCATCTAACTTGCATTAGTGACACCTTTATACCAAAATGCACCGTTAGACATTTAAC
275351 TTT
1 TTT
275354 CATTTTAGAA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (60 bp):
TTTTCATCTAACTTGCATTAGTGACACCTTTATACCAAAATGCACCGTTAGACATTTAAC
Found at i:280800 original size:12 final size:12
Alignment explanation
Indices: 280783--280807 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
280773 TCATTGATTG
280783 GAAGAAGATGAA
1 GAAGAAGATGAA
280795 GAAGAAGATGAA
1 GAAGAAGATGAA
280807 G
1 G
280808 GGTCACTTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.36, T:0.08
Consensus pattern (12 bp):
GAAGAAGATGAA
Found at i:290034 original size:42 final size:42
Alignment explanation
Indices: 289987--290072 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 42
289977 ATATATCTAT
* ** * *
289987 TAAAATTATAGGTATGGTCAATATAAAACATATATTATGAGA
1 TAAAATTACAGGTATAATCAACATAAAACATAAATTATGAGA
* *
290029 TAAAATTACATGTATAATTAACATAAAACATAAATTATGAGA
1 TAAAATTACAGGTATAATCAACATAAAACATAAATTATGAGA
290071 TA
1 TA
290073 GAAACTAATG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.33
Consensus pattern (42 bp):
TAAAATTACAGGTATAATCAACATAAAACATAAATTATGAGA
Found at i:293324 original size:41 final size:41
Alignment explanation
Indices: 293279--293515 Score: 240
Period size: 41 Copynumber: 5.9 Consensus size: 41
293269 TATTGAGTGT
* *
293279 CATGATTGAATT-AAGTAGAATTGTGAATCATTGCATGCTTC
1 CATGATTGAATTGAA-TCGAATTGTGAATTATTGCATGCTTC
* *
293320 CATGATTGAATT-AAGTTGAATTGTGAATTATTGCATGTTTC
1 CATGATTGAATTGAA-TCGAATTGTGAATTATTGCATGCTTC
*
293361 CATGCTTGAATTGAATCGAATTGTGAATTATTGCATG-TGTC
1 CATGATTGAATTGAATCGAATTGTGAATTATTGCATGCT-TC
*
293402 CATGATTGAATTGAATCGAATTATGAATTATTGCATGC-T-
1 CATGATTGAATTGAATCGAATTGTGAATTATTGCATGCTTC
* ** *
293441 -A--ATCGAATTGAGCCGAATGGTGAATTATTGCATG-TTGC
1 CATGATTGAATTGAATCGAATTGTGAATTATTGCATGCTT-C
* * * * *
293479 CATGATTGAACTGAAACGAATTTTTAATTAGTGCATG
1 CATGATTGAATTGAATCGAATTGTGAATTATTGCATG
293516 TTGCCAAGAT
Statistics
Matches: 167, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
36 29 0.17
38 1 0.01
39 1 0.01
40 2 0.01
41 132 0.79
42 2 0.01
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.38
Consensus pattern (41 bp):
CATGATTGAATTGAATCGAATTGTGAATTATTGCATGCTTC
Found at i:293468 original size:77 final size:77
Alignment explanation
Indices: 293368--293515 Score: 208
Period size: 77 Copynumber: 1.9 Consensus size: 77
293358 TTCCATGCTT
* * * *
293368 GAATTGAATCGAATTGTGAATTATTGCATG-TGTCCATGATTGAATTGAATCGAATTATGAATTA
1 GAATTGAACCGAATGGTGAATTATTGCATGTTG-CCATGATTGAACTGAAACGAATTATGAATTA
*
293432 TTGCATGCTAATC
65 GTGCATGCTAATC
* * *
293445 GAATTGAGCCGAATGGTGAATTATTGCATGTTGCCATGATTGAACTGAAACGAATTTTTAATTAG
1 GAATTGAACCGAATGGTGAATTATTGCATGTTGCCATGATTGAACTGAAACGAATTATGAATTAG
293510 TGCATG
66 TGCATG
293516 TTGCCAAGAT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
77 60 0.97
78 2 0.03
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.36
Consensus pattern (77 bp):
GAATTGAACCGAATGGTGAATTATTGCATGTTGCCATGATTGAACTGAAACGAATTATGAATTAG
TGCATGCTAATC
Found at i:296264 original size:18 final size:18
Alignment explanation
Indices: 296241--296280 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
296231 AGGGATTATA
*
296241 AGTGGTTTTTTGGGATAT
1 AGTGGTTTTTCGGGATAT
296259 AGTGGTTTTTCGGGATAT
1 AGTGGTTTTTCGGGATAT
296277 AGTG
1 AGTG
296281 TTCCTTCGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.03, G:0.35, T:0.45
Consensus pattern (18 bp):
AGTGGTTTTTCGGGATAT
Found at i:296288 original size:18 final size:18
Alignment explanation
Indices: 296252--296309 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
296242 GTGGTTTTTT
*
296252 GGGATATAGTGGTT-TTTC
1 GGGATATAGT-GTTCCTTC
296270 GGGATATAGTGTTCCTTC
1 GGGATATAGTGTTCCTTC
* * *
296288 GGGACAAAGTGGTCCTTC
1 GGGATATAGTGTTCCTTC
296306 GGGA
1 GGGA
296310 CAAATTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 3 0.09
18 32 0.91
ACGTcount: A:0.19, C:0.14, G:0.34, T:0.33
Consensus pattern (18 bp):
GGGATATAGTGTTCCTTC
Found at i:296310 original size:18 final size:18
Alignment explanation
Indices: 296267--296313 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
296257 ATAGTGGTTT
* * *
296267 TTCGGGATATAGTGTTCC
1 TTCGGGACAAAGTGGTCC
296285 TTCGGGACAAAGTGGTCC
1 TTCGGGACAAAGTGGTCC
296303 TTCGGGACAAA
1 TTCGGGACAAA
296314 TTTAAATGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (18 bp):
TTCGGGACAAAGTGGTCC
Found at i:297509 original size:31 final size:31
Alignment explanation
Indices: 297474--297540 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
297464 GGGTGACCAC
* * *
297474 ATCTTAATTAAATAAAAATGAAGGTCATTAT
1 ATCTTAATTAAATAAAAACGAAAGTCACTAT
*
297505 ATCTTAATTAAATAAAAACGAAAGTGACTAT
1 ATCTTAATTAAATAAAAACGAAAGTCACTAT
297536 ATCTT
1 ATCTT
297541 GTATTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACGAAAGTCACTAT
Found at i:305197 original size:35 final size:35
Alignment explanation
Indices: 305158--305228 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
305148 AAGAAATAAG
* *
305158 TTTATGGG-CTCTGCTTCTAATTTAGTTTATTAATA
1 TTTATGGGTCT-TGCTTCTAATTTAATATATTAATA
*
305193 TTTATGGGTCTTGCTTTTAATTTAATATATTAATA
1 TTTATGGGTCTTGCTTCTAATTTAATATATTAATA
305228 T
1 T
305229 AATTTTTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 30 0.94
36 2 0.06
ACGTcount: A:0.25, C:0.08, G:0.13, T:0.54
Consensus pattern (35 bp):
TTTATGGGTCTTGCTTCTAATTTAATATATTAATA
Found at i:307022 original size:88 final size:88
Alignment explanation
Indices: 306758--306992 Score: 452
Period size: 88 Copynumber: 2.7 Consensus size: 88
306748 GTAAGAAAAA
*
306758 TATAAAGAAGAAAGATATAGGAATAAAGGGAGAGAATTATATTATTATCTTAATATAATCTGTGT
1 TATAAAGAAGAAAGATATAGGAATAAAGGGAGAGAATTATATTATTATCTTAATATAATCTGTAT
306823 ACAATATTTTCTCTTCATTATTG
66 ACAATATTTTCTCTTCATTATTG
306846 TATAAAGAAGAAAGATATAGGAATAAAGGGAGAGAATTATATTATTATCTTAATATAATCTGTAT
1 TATAAAGAAGAAAGATATAGGAATAAAGGGAGAGAATTATATTATTATCTTAATATAATCTGTAT
306911 ACAATATTTTCTCTTCATTATTG
66 ACAATATTTTCTCTTCATTATTG
*
306934 TATAAAGAATAAAGATATAGGAATAAAGGGAGAGAATTATATTATTATCTTAATATAAT
1 TATAAAGAAGAAAGATATAGGAATAAAGGGAGAGAATTATATTATTATCTTAATATAAT
306993 ATATATAATC
Statistics
Matches: 145, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 145 1.00
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (88 bp):
TATAAAGAAGAAAGATATAGGAATAAAGGGAGAGAATTATATTATTATCTTAATATAATCTGTAT
ACAATATTTTCTCTTCATTATTG
Found at i:318347 original size:19 final size:21
Alignment explanation
Indices: 318315--318357 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
318305 ACATATCATA
*
318315 CAAATATTTAGCATCCAAAGT
1 CAAATATTTAGCATACAAAGT
*
318336 CAAAT-TTT-GCATAGAAAGT
1 CAAATATTTAGCATACAAAGT
318355 CAA
1 CAA
318358 CTTAAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.60
20 3 0.15
21 5 0.25
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (21 bp):
CAAATATTTAGCATACAAAGT
Found at i:320163 original size:24 final size:24
Alignment explanation
Indices: 320136--320197 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
320126 CGTTCGTGAA
320136 CGTTCGGTTATGTTCGTTTATATG
1 CGTTCGGTTATGTTCGTTTATATG
** *
320160 CGTTTAGTTATGTTCGTTTATGTG
1 CGTTCGGTTATGTTCGTTTATATG
*
320184 CGTTCGTTTATGTT
1 CGTTCGGTTATGTT
320198 TAACCTAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.11, C:0.11, G:0.24, T:0.53
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGTTTATATG
Found at i:321722 original size:10 final size:10
Alignment explanation
Indices: 321707--321781 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
321697 GGGTCTCCAA
321707 CGTTTATGTT
1 CGTTTATGTT
321717 CGTTTATGTT
1 CGTTTATGTT
321727 CG----TGTT
1 CGTTTATGTT
*
321733 CATTTATGTT
1 CGTTTATGTT
321743 CGTGTT-TGTTT
1 CGT-TTATG-TT
* *
321754 ATGTTTGTGTT
1 -CGTTTATGTT
*
321765 CATTTATGTT
1 CGTTTATGTT
321775 CGTTTAT
1 CGTTTAT
321782 TTATTAAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 5 0.10
10 33 0.66
11 8 0.16
12 4 0.08
ACGTcount: A:0.11, C:0.09, G:0.20, T:0.60
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:321738 original size:16 final size:16
Alignment explanation
Indices: 321713--321785 Score: 96
Period size: 16 Copynumber: 4.7 Consensus size: 16
321703 CCAACGTTTA
*
321713 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
321729 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
** *
321745 TGTTTGTTTATGTTTG
1 TGTTCATTTATGTTCG
321761 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
321777 T-TT-ATTTAT
1 TGTTCATTTAT
321786 TAAATGAACG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 6 0.12
15 2 0.04
16 42 0.84
ACGTcount: A:0.11, C:0.08, G:0.19, T:0.62
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:321755 original size:32 final size:32
Alignment explanation
Indices: 321713--321777 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
321703 CCAACGTTTA
321713 TGTTCGTTTATGTTCGTGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCGTGTTCATTTATGTTCG
* *
321745 TGTTTGTTTATGTTTGTGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCGTGTTCATTTATGTTCG
321777 T
1 T
321778 TTATTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.09, C:0.09, G:0.22, T:0.60
Consensus pattern (32 bp):
TGTTCGTTTATGTTCGTGTTCATTTATGTTCG
Found at i:321868 original size:16 final size:16
Alignment explanation
Indices: 321847--321878 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
321837 AAATTTTTTT
321847 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
321863 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
321879 CTTATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.12, G:0.25, T:0.56
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:323585 original size:74 final size:74
Alignment explanation
Indices: 323452--323594 Score: 164
Period size: 74 Copynumber: 1.9 Consensus size: 74
323442 TGAAGGATTA
* * * * *
323452 TTTGGATGGCCCCCCTTTGCGGGTTTAAGCCAAACAAGATTACTCCCCTTCACGATTTAAG-CTA
1 TTTGGATGACCCCCCTTTACGGGTCTAAGCCAAACAAGAATACTCCCCATCACGATTTAAGTC-A
323516 GTCTTAATTC
65 GTCTTAATTC
* ** * *
323526 TTTGGATGACTCCCCTTTACGGGTCTAATTCAAATAAGAATACTCCCCATCATTG-TTTAAGTCA
1 TTTGGATGACCCCCCTTTACGGGTCTAAGCCAAACAAGAATACTCCCCATCA-CGATTTAAGTCA
323590 GTCTT
65 GTCTT
323595 GGTACTTCAG
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
74 55 0.96
75 2 0.04
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.34
Consensus pattern (74 bp):
TTTGGATGACCCCCCTTTACGGGTCTAAGCCAAACAAGAATACTCCCCATCACGATTTAAGTCAG
TCTTAATTC
Found at i:327308 original size:23 final size:24
Alignment explanation
Indices: 327282--327326 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
327272 TATTGTTCAC
327282 GAACATGTTCATTTA-ATGTTCGT
1 GAACATGTTCATTTATATGTTCGT
*
327305 GAACATGTTCGTTTATATGTTC
1 GAACATGTTCATTTATATGTTC
327327 ACAAACGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.44
Consensus pattern (24 bp):
GAACATGTTCATTTATATGTTCGT
Found at i:327383 original size:24 final size:23
Alignment explanation
Indices: 327350--327402 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 23
327340 TGAACCGTTT
*
327350 GTTTAATGTTCGCGAACATGTTC
1 GTTTAATGTTCACGAACATGTTC
*
327373 GTTTATATGTTCACGAACATGTTT
1 GTTTA-ATGTTCACGAACATGTTC
327397 GTTTAA
1 GTTTAA
327403 ATTTTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (23 bp):
GTTTAATGTTCACGAACATGTTC
Found at i:327419 original size:58 final size:58
Alignment explanation
Indices: 327275--327395 Score: 170
Period size: 58 Copynumber: 2.1 Consensus size: 58
327265 GTTTAATTAT
* * * *
327275 TGTTCACGAACATGTTCATTTAATGTTCGTGAACATGTTCGTTTATATGTTCACAAACG
1 TGTTCATGAACA-GTTTATTTAATGTTCGCGAACATGTTCGTTTATATGTTCACAAACA
* * *
327334 TGTTCATGAACCGTTTGTTTAATGTTCGCGAACATGTTCGTTTATATGTTCACGAACA
1 TGTTCATGAACAGTTTATTTAATGTTCGCGAACATGTTCGTTTATATGTTCACAAACA
327392 TGTT
1 TGTT
327396 TGTTTAAATT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
58 45 0.82
59 10 0.18
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (58 bp):
TGTTCATGAACAGTTTATTTAATGTTCGCGAACATGTTCGTTTATATGTTCACAAACA
Found at i:327981 original size:16 final size:18
Alignment explanation
Indices: 327960--327992 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
327950 AAATTACCTT
327960 AAATGTT-TA-AAATTTA
1 AAATGTTATACAAATTTA
327976 AAATGTTATACAAATTT
1 AAATGTTATACAAATTT
327993 TTAATATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (18 bp):
AAATGTTATACAAATTTA
Found at i:329202 original size:20 final size:20
Alignment explanation
Indices: 329177--329269 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
329167 TTTTCCCAAT
329177 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
329197 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
329217 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
329238 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
329259 TCGCAATGCGA
1 TCGCAATGCGA
329270 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:329219 original size:41 final size:41
Alignment explanation
Indices: 329174--329269 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
329164 CGATTTTCCC
329174 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
329215 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
329256 AAATCGCAATGCGA
1 AATTCGCAATGCGA
329270 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:329223 original size:21 final size:20
Alignment explanation
Indices: 329177--329269 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
329167 TTTTCCCAAT
*
329177 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
329197 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
329217 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
329238 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
329259 TCGCAATGCGA
1 TCGCAATGCGA
329270 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:329282 original size:41 final size:41
Alignment explanation
Indices: 329196--329330 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
329186 GAATAAGTAA
* * *
329196 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
329237 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
329278 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
329319 TTCGCAACGCGA
1 ATCGCAACGCGA
329331 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:329283 original size:20 final size:20
Alignment explanation
Indices: 329258--329352 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
329248 AATTGGGAAA
*
329258 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
329278 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
329299 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
329319 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
329339 TTCGCAACGCGATA
1 ATCGCAACGCGATA
329353 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:329568 original size:22 final size:22
Alignment explanation
Indices: 329540--329583 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
329530 CACTCTCTCA
*
329540 CCCATCTCCGACGAAATTCGTC
1 CCCATCTCCGACGAAATCCGTC
*
329562 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
329584 TATCTAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:329872 original size:20 final size:20
Alignment explanation
Indices: 329847--329884 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
329837 CGATTCTCTC
329847 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
329867 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
329885 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:331225 original size:18 final size:18
Alignment explanation
Indices: 331204--331248 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
331194 TCCACTTCGG
*
331204 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
331222 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
331240 GAGCCATCA
1 GAGCCATCA
331249 TCTGATCAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:331746 original size:20 final size:20
Alignment explanation
Indices: 331721--331766 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
331711 TAGTTTACTT
331721 TCGCAACACAAAAATGACTA
1 TCGCAACACAAAAATGACTA
* ** *
331741 TCGCAACGCGGAAATGGCTA
1 TCGCAACACAAAAATGACTA
331761 TCGCAA
1 TCGCAA
331767 TGCGAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACAAAAATGACTA
Found at i:331782 original size:19 final size:18
Alignment explanation
Indices: 331760--331855 Score: 66
Period size: 19 Copynumber: 5.6 Consensus size: 18
331750 GGAAATGGCT
*
331760 ATCGCAATGCGAAATAAAA
1 ATCGCAA-GCGAAATCAAA
331779 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATCAAA
*
331793 ATCGCAACGCGAAAT-GAA
1 ATCGCAA-GCGAAATCAAA
331811 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATCAAA
*
331825 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATCAAA
331844 ATCGCAATGCGA
1 ATCGCAA-GCGA
331856 TTTGTGTTTC
Statistics
Matches: 61, Mismatches: 5, Indels: 22
0.69 0.06 0.25
Matches are distributed among these distances:
14 20 0.33
15 1 0.02
16 6 0.10
17 2 0.03
18 11 0.18
19 21 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATCAAA
Found at i:331795 original size:14 final size:14
Alignment explanation
Indices: 331776--331833 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
331766 ATGCGAAATA
331776 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
331790 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
331806 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
331822 AAAATCGCAACG
1 AAAATCGCAACG
331834 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:331818 original size:32 final size:32
Alignment explanation
Indices: 331760--331850 Score: 146
Period size: 32 Copynumber: 2.8 Consensus size: 32
331750 GGAAATGGCT
* *
331760 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAACGCGAAAT-GAAATCGCAACGACAAA
331793 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
331825 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATG-AAATCGCAA
331851 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 32 0.58
33 23 0.42
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:331886 original size:14 final size:14
Alignment explanation
Indices: 331867--331924 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
331857 TTGTGTTTCG
331867 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
331881 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
331897 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
331913 CGTTGCGATTTT
1 CGTTGCGATTTT
331925 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:331901 original size:32 final size:33
Alignment explanation
Indices: 331862--331940 Score: 151
Period size: 32 Copynumber: 2.4 Consensus size: 33
331852 GCGATTTGTG
331862 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
331894 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
331927 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
331941 AGTCATATTC
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 27 0.59
33 19 0.41
ACGTcount: A:0.09, C:0.19, G:0.25, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:333797 original size:33 final size:33
Alignment explanation
Indices: 333750--333942 Score: 282
Period size: 33 Copynumber: 5.8 Consensus size: 33
333740 GGAAATTACT
333750 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
333783 ATCGTAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
333815 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
333849 ATCGCAATGCGAAATGAAAATCGCAACGCGA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
333881 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
333915 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
333943 CGAATTTAAT
Statistics
Matches: 141, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
32 2 0.01
33 137 0.97
34 2 0.01
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:333833 original size:66 final size:66
Alignment explanation
Indices: 333751--333949 Score: 371
Period size: 66 Copynumber: 3.0 Consensus size: 66
333741 GAAATTACTA
* * *
333751 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGTAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
333816 T
66 T
333817 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
333882 T
66 T
333883 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
333948 T
66 T
333949 T
1 T
333950 AATTTCGCGT
Statistics
Matches: 130, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 130 1.00
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:333964 original size:19 final size:20
Alignment explanation
Indices: 333942--333986 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
333932 AAATCGCAAC
333942 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
333961 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
333981 GC-AATT
1 GCGAATT
333987 CTCTCGTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:334144 original size:14 final size:14
Alignment explanation
Indices: 334125--334161 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
334115 CATCAATTAA
334125 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
334139 ACAAATCACCTTTT
1 ACAAATCAACTTTT
334153 ACAAATCAA
1 ACAAATCAA
334162 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:335911 original size:20 final size:20
Alignment explanation
Indices: 335826--335919 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
335816 CGCTATGTAA
*
335826 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
335846 ATTGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
335866 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
335887 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
335907 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
335920 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:335938 original size:41 final size:41
Alignment explanation
Indices: 335908--336003 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
335898 ATAGTCAGTA
* * *
335908 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* *
335949 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
335990 TCGCATTGCGAATT
1 TCGCATTGCGAATT
336004 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:335952 original size:20 final size:20
Alignment explanation
Indices: 335908--336000 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
335898 ATAGTCAGTA
* **
335908 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
335929 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
335949 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
335970 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
335990 TCGCATTGCGA
1 TCGCATTGCGA
336001 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:341440 original size:21 final size:21
Alignment explanation
Indices: 341414--341456 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
341404 TTTCTGGGCT
* *
341414 AGGGGAATCGGTACCCACTCA
1 AGGGGAACCGATACCCACTCA
*
341435 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
341456 A
1 A
341457 ACGAACCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.33, G:0.26, T:0.12
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:343104 original size:23 final size:22
Alignment explanation
Indices: 343049--343115 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
343039 GGACATTATT
343049 ATATGGCACTACGGTGCAATTC
1 ATATGGCACTACGGTGCAATTC
* *
343071 -TACGCGACACTCCGGTGCAATTCC
1 ATATG-G-CACTACGGTGCAATT-C
* *
343095 ATATGGCACTTCGGTGTAATT
1 ATATGGCACTACGGTGCAATT
343116 ATACGAGTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
21 3 0.08
22 1 0.03
23 27 0.75
24 2 0.06
25 3 0.08
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.28
Consensus pattern (22 bp):
ATATGGCACTACGGTGCAATTC
Found at i:344305 original size:17 final size:17
Alignment explanation
Indices: 344280--344313 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
344270 AGTTGTTTCC
* *
344280 ATCACATTTCTCAAAGT
1 ATCAAATTTCCCAAAGT
344297 ATCAAATTTCCCAAAGT
1 ATCAAATTTCCCAAAGT
344314 CTAGAGCATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (17 bp):
ATCAAATTTCCCAAAGT
Found at i:350886 original size:2 final size:2
Alignment explanation
Indices: 350879--350920 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
350869 ACAATGGGCG
350879 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
350920 A
1 A
350921 ATTACATTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:352232 original size:49 final size:49
Alignment explanation
Indices: 352158--352257 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 49
352148 ACGATTATTA
* * * *
352158 TATAGTGATAATGGCATCATATGTAATTATATTAAATGATTGTAAGATT
1 TATAGTGATAATGACATCATATGTAATTATACTAAATAATTATAAGATT
* * *
352207 TATAGTGATAATGATATCATCTGTAATTATACTAAATAATTATAATATT
1 TATAGTGATAATGACATCATATGTAATTATACTAAATAATTATAAGATT
352256 TA
1 TA
352258 AAATTATATT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.42
Consensus pattern (49 bp):
TATAGTGATAATGACATCATATGTAATTATACTAAATAATTATAAGATT
Found at i:363658 original size:21 final size:22
Alignment explanation
Indices: 363632--363672 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
363622 CCAGGACAGG
*
363632 GAGTATTAATAC-TCCTTTAAT
1 GAGTATCAATACTTCCTTTAAT
*
363653 GAGTATCGATACTTCCTTTA
1 GAGTATCAATACTTCCTTTA
363673 TAATGTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (22 bp):
GAGTATCAATACTTCCTTTAAT
Found at i:365576 original size:2 final size:2
Alignment explanation
Indices: 365569--365593 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
365559 TTTGTTATTA
365569 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
365594 CATCCTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:367333 original size:116 final size:116
Alignment explanation
Indices: 367208--367424 Score: 407
Period size: 116 Copynumber: 1.9 Consensus size: 116
367198 CGCGAGCCAC
367208 ATTACTAATTTAAACTATAACATATATTTGATATAATATCTACGTATACATATAGCACTAAATGT
1 ATTACTAATTTAAACTATAACATATATTTGATATAATATCTACGTATACATATAGCACTAAATGT
367273 ATAAAAACAAAGTTGGACATATTTACATATAAAATTCACACACACACACAT
66 ATAAAAACAAAGTTGGACATATTTACATATAAAATTCACACACACACACAT
**
367324 ATTACTAATTTAAACTATAACATATATTTGATATAATATCTACGTATACATATAGTTCTAAATGT
1 ATTACTAATTTAAACTATAACATATATTTGATATAATATCTACGTATACATATAGCACTAAATGT
*
367389 ATAAAAACAAAGTTGGACATATTTACTTATAAAATT
66 ATAAAAACAAAGTTGGACATATTTACATATAAAATT
367425 ATATATTATA
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 98 1.00
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (116 bp):
ATTACTAATTTAAACTATAACATATATTTGATATAATATCTACGTATACATATAGCACTAAATGT
ATAAAAACAAAGTTGGACATATTTACATATAAAATTCACACACACACACAT
Found at i:369955 original size:4 final size:4
Alignment explanation
Indices: 369948--370019 Score: 69
Period size: 4 Copynumber: 17.8 Consensus size: 4
369938 TAAAACAAAC
*
369948 AATA AATA AAT- AATA AGAT- AATA AATA AATAA AATAA AATA AACA AATA
1 AATA AATA AATA AATA A-ATA AATA AATA AAT-A AAT-A AATA AATA AATA
*
369997 AA-A AAGA AATAA AATA AATA AAT
1 AATA AATA AAT-A AATA AATA AAT
370020 TATAAAAAAC
Statistics
Matches: 59, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
3 8 0.14
4 36 0.61
5 15 0.25
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:369982 original size:5 final size:5
Alignment explanation
Indices: 369970--370096 Score: 54
Period size: 5 Copynumber: 26.0 Consensus size: 5
369960 ATAAGATAAT
* *
369970 AAAT- AAATA AAATA AAAT- AAA-C AAATA AAAAA GAAATA AAAT- AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA -AAATA AAATA AAATA
* ** **
370017 AATTA TAAA-A AACCA AACGA AAATA AAA-A AAATGA AAATA CAAAT-
1 AAATA -AAATA AAATA AAATA AAATA AAATA AAAT-A AAATA -AAATA
* * * *
370062 ATA-A AAATT AAATA AAAGA AAAAA ATAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA A-AATA AAATA
370097 TGAGTACCTA
Statistics
Matches: 94, Mismatches: 16, Indels: 25
0.70 0.12 0.19
Matches are distributed among these distances:
4 24 0.26
5 51 0.54
6 19 0.20
ACGTcount: A:0.76, C:0.04, G:0.03, T:0.17
Consensus pattern (5 bp):
AAATA
Found at i:370028 original size:29 final size:30
Alignment explanation
Indices: 369948--370028 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 30
369938 TAAAACAAAC
*
369948 AATAAATAAATAATAAGATAATAAATAAATAA
1 AATAAATAAATAATAAGA-AA-AAAGAAATAA
* *
369980 AATAAAATAAA-CA-AATAAAAAAGAAATAA
1 AAT-AAATAAATAATAAGAAAAAAGAAATAA
*
370009 AATAAATAAATTATAA-AAAA
1 AATAAATAAATAATAAGAAAA
370029 CCAAACGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
28 7 0.17
29 17 0.40
30 4 0.10
31 3 0.07
32 4 0.10
33 7 0.17
ACGTcount: A:0.75, C:0.01, G:0.02, T:0.21
Consensus pattern (30 bp):
AATAAATAAATAATAAGAAAAAAGAAATAA
Found at i:371985 original size:24 final size:23
Alignment explanation
Indices: 371915--371986 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 23
371905 ATTTTCTTTG
*
371915 TTTTTATATTTTTTATTCATGTATA
1 TTTTTAT-TTTTTTATTC-TTTATA
*** *
371940 TTTTTATTTACCTATCTATTTATA
1 TTTTTATTTTTTTAT-TCTTTATA
371964 TTTTTATTCTTTTTATTCTTTAT
1 TTTTTATT-TTTTTATTCTTTAT
371987 TTGAATTTTC
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
24 24 0.67
25 12 0.33
ACGTcount: A:0.21, C:0.08, G:0.01, T:0.69
Consensus pattern (23 bp):
TTTTTATTTTTTTATTCTTTATA
Found at i:382510 original size:45 final size:46
Alignment explanation
Indices: 382443--382530 Score: 151
Period size: 45 Copynumber: 1.9 Consensus size: 46
382433 AATATTTCGC
*
382443 TTAGGATGAAAACCCGAGAGGGCGCCCTAAATT-AAAAAAAAACGT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAACGT
*
382488 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAA
382531 TAAAAAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 31 0.77
46 9 0.22
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (46 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAACGT
Found at i:383575 original size:98 final size:98
Alignment explanation
Indices: 383324--383996 Score: 1093
Period size: 98 Copynumber: 6.8 Consensus size: 98
383314 TACCCAGAGT
*
383324 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGGCGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* **
383389 GGACCGCTGGTTGTCAACAGACATTTCTCAATTTCAAAGC
66 GGACCGCTGGTTGTCAATA-A-A-----CAATTTCAGGGC
* *
383429 CAATTCCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
383494 GGACCGCTGGTTGTCAATAAAAAATTTCAGGGC
66 GGACCGCTGGTTGTCAATAAACAATTTCAGGGC
383527 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
383592 GGACCGCTGGTTGTCCATAAACAATTTCAGGGC
66 GGACCGCTGGTTGTCAATAAACAATTTCAGGGC
*
383625 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
383690 GGACGGCTGGTTGTCAATAAACAATTTTAGGGC
66 GGACCGCTGGTTGTCAATAAACAATTTCAGGGC
*
383723 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
383788 GGACCGCTGGTTGTCAATAAATAATTTCAGAGC
66 GGACCGCTGGTTGTCAATAAACAATTTCAGGGC
*
383821 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
383886 GGACCGCTGGTTGTCAATAAATAATTTC----C
66 GGACCGCTGGTTGTCAATAAACAATTTCAGGGC
* *
383915 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAATGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
383980 GGACCGCTGGTTGTCAA
66 GGACCGCTGGTTGTCAA
383997 CAAGTAATTT
Statistics
Matches: 542, Mismatches: 26, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
94 80 0.15
98 380 0.70
103 1 0.00
104 1 0.00
105 80 0.15
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.23
Consensus pattern (98 bp):
CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
GGACCGCTGGTTGTCAATAAACAATTTCAGGGC
Found at i:383592 original size:43 final size:43
Alignment explanation
Indices: 383531--383690 Score: 122
Period size: 43 Copynumber: 3.4 Consensus size: 43
383521 CAGGGCCAAT
383531 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *** ** * *
383574 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCCATAAACAATTTCAGGGCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTCC--AGACAA---C---G-CAAG
383629 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
**
383672 TTCAACTTCATGACGAAGG
1 TTCAACTTCACAACGAAGG
383691 GACGGCTGGT
Statistics
Matches: 87, Mismatches: 18, Indels: 24
0.67 0.14 0.19
Matches are distributed among these distances:
43 36 0.41
44 4 0.05
45 3 0.03
46 3 0.03
47 1 0.01
48 5 0.06
50 5 0.06
51 1 0.01
52 3 0.03
53 3 0.03
54 4 0.05
55 19 0.22
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:390429 original size:18 final size:17
Alignment explanation
Indices: 390392--390442 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
390382 TATGGAATTG
*
390392 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
*
390409 GATTTCAATTCCTTCACA
1 GATTCCAATTCC-TCACA
390427 GATTCCAATTTCCTCA
1 GATTCCAA-TTCCTCA
390443 GAAACATTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 11 0.38
18 14 0.48
19 4 0.14
ACGTcount: A:0.27, C:0.29, G:0.08, T:0.35
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:395668 original size:27 final size:27
Alignment explanation
Indices: 395616--395669 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
395606 GCTTGATTAG
*
395616 GGTAACAGGGTATAGTTTGAGAAACTT
1 GGTAACAGGGTATAGTTCGAGAAACTT
* *
395643 GGTAACATGGTAT-GATTCGAGCAACTT
1 GGTAACAGGGTATAG-TTCGAGAAACTT
395670 TATCGGGGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.30
Consensus pattern (27 bp):
GGTAACAGGGTATAGTTCGAGAAACTT
Found at i:396687 original size:24 final size:24
Alignment explanation
Indices: 396660--396718 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
396650 TATGGCTATG
* *
396660 GTATCGGTACTACTATACAAAGTA
1 GTATTGGTACCACTATACAAAGTA
396684 GTATTGGTACCACTATACAAAGTA
1 GTATTGGTACCACTATACAAAGTA
396708 GTATTGGTACC
1 GTATTGGTACC
396719 TCTTTGGGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (24 bp):
GTATTGGTACCACTATACAAAGTA
Found at i:398522 original size:15 final size:15
Alignment explanation
Indices: 398498--398531 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
398488 CCGTAGGACC
398498 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
398513 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
398528 ACTA
1 ACTA
398532 TTATACCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:398659 original size:29 final size:29
Alignment explanation
Indices: 398616--398745 Score: 226
Period size: 29 Copynumber: 4.5 Consensus size: 29
398606 TTTTATATGT
* *
398616 TCATGTA-CTCATGTCATTTATCTTGTGG
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
398644 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
398673 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
398702 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
398731 TCATGTAGCTCATGT
1 TCATGTAGCTCATGT
398746 TCTCATATCA
Statistics
Matches: 97, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
28 7 0.07
29 90 0.93
ACGTcount: A:0.18, C:0.19, G:0.18, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:405451 original size:15 final size:15
Alignment explanation
Indices: 405427--405460 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
405417 ACGTAGGACC
405427 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
405442 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
405457 ACTA
1 ACTA
405461 TTATACCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:405591 original size:29 final size:29
Alignment explanation
Indices: 405545--405674 Score: 244
Period size: 29 Copynumber: 4.5 Consensus size: 29
405535 TTTTATATGT
*
405545 TCATGTA-CTCATGTCATTTCTCTTATGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
405573 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
405602 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
405631 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
405660 TCATGTAGCTCATGT
1 TCATGTAGCTCATGT
405675 TCTCATATCA
Statistics
Matches: 100, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
28 7 0.07
29 93 0.93
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:410048 original size:26 final size:28
Alignment explanation
Indices: 410019--410079 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
410009 TATATTATAG
* *
410019 ATATTA-ATTTTA-ATA-TTAATTTTTT
1 ATATTATATTATAGATATTTAATTTTAT
410044 AATATTATATTATAGATATTTAATTTTAT
1 -ATATTATATTATAGATATTTAATTTTAT
410073 ATATTAT
1 ATATTAT
410080 TAAAATTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 6 0.20
27 5 0.17
28 10 0.33
29 9 0.30
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (28 bp):
ATATTATATTATAGATATTTAATTTTAT
Done.