Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008011.1 Hibiscus syriacus cultivar Beakdansim tig00110474_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: 1648842
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:278447 original size:13 final size:14
Alignment explanation
Indices: 278429--278467 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
278419 TACTTTGATC
278429 TTATAATTTTTT-A
1 TTATAATTTTTTAA
278442 TTATAATTTTATTAA
1 TTATAATTTT-TTAA
278457 TTA-AATTTTTT
1 TTATAATTTTTT
278468 TGTAGCTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 8 0.33
15 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATAATTTTTTAA
Found at i:281758 original size:20 final size:20
Alignment explanation
Indices: 281704--281761 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
281694 ATTTTCTAAC
* * *
281704 ATCGGTACTGTTCACACAAT
1 ATCGATACTATTCATACAAT
*
281724 ATCGATACTATTCATACATT
1 ATCGATACTATTCATACAAT
281744 ATCGATACTATTCATACA
1 ATCGATACTATTCATACA
281762 GTGTAGTACT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.34
Consensus pattern (20 bp):
ATCGATACTATTCATACAAT
Found at i:281773 original size:19 final size:20
Alignment explanation
Indices: 281727--281778 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
281717 ACACAATATC
* *
281727 GATACTATTCATACATTATC
1 GATACTATTCATACAGTATA
*
281747 GATACTATTCATACAGTGTA
1 GATACTATTCATACAGTATA
281767 G-TACTATTCATA
1 GATACTATTCATA
281779 AAAACATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (20 bp):
GATACTATTCATACAGTATA
Found at i:286985 original size:25 final size:25
Alignment explanation
Indices: 286930--286988 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
286920 ATAAGTCTAG
* **
286930 ATTCAATATTTTGATACATGATGACA
1 ATTC-ATATTATGATACATGACCACA
* *
286956 TTTCATATTATGATACATGACCAGA
1 ATTCATATTATGATACATGACCACA
286981 ATTCATAT
1 ATTCATAT
286989 CATATGAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 24 0.89
26 3 0.11
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (25 bp):
ATTCATATTATGATACATGACCACA
Found at i:287094 original size:30 final size:31
Alignment explanation
Indices: 287037--287096 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
287027 TATGAGCTAC
287037 GTGATAAAGATATGGAAAATGACATGTCTAT
1 GTGATAAAGATATGGAAAATGACATGTCTAT
* *
287068 GTGATAAAGGTATGG-AAATGATATGTCTA
1 GTGATAAAGATATGGAAAATGACATGTCTA
287097 CGCGATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30
Consensus pattern (31 bp):
GTGATAAAGATATGGAAAATGACATGTCTAT
Found at i:287372 original size:23 final size:23
Alignment explanation
Indices: 287340--287423 Score: 82
Period size: 23 Copynumber: 3.6 Consensus size: 23
287330 ATATTATATT
*
287340 GCACTACGATGCAATTCTACGTG
1 GCACTTCGATGCAATTCTACGTG
* *
287363 GCACTTCGATACAATTCTACGCG
1 GCACTTCGATGCAATTCTACGTG
*
287386 GTC-CTTCG-GGACAAATTCTACGTG
1 G-CACTTCGATG-C-AATTCTACGTG
*
287410 GCACTTCGGTGCAA
1 GCACTTCGATGCAA
287424 ATTTATACGA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
23 30 0.61
24 18 0.37
25 1 0.02
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (23 bp):
GCACTTCGATGCAATTCTACGTG
Found at i:287416 original size:24 final size:24
Alignment explanation
Indices: 287352--287426 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
287342 ACTACGATGC
**
287352 AATTCTACGTGGCACTTCGATAC-
1 AATTCTACGTGGCACTTCGGGACA
*
287375 AATTCTACGCGGTC-CTTCGGGACA
1 AATTCTACGTGG-CACTTCGGGACA
287399 AATTCTACGTGGCACTTCGGTG-CA
1 AATTCTACGTGGCACTTCGG-GACA
287423 AATT
1 AATT
287427 TATACGAGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
23 19 0.43
24 24 0.55
25 1 0.02
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.29
Consensus pattern (24 bp):
AATTCTACGTGGCACTTCGGGACA
Found at i:288086 original size:20 final size:20
Alignment explanation
Indices: 288049--288087 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
288039 ATGCATCGAT
* *
288049 GCACTGTAGCACTATTCACG
1 GCACTGTAACAATATTCACG
*
288069 GCACTGTAACAATGTTCAC
1 GCACTGTAACAATATTCAC
288088 ATTACTGTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (20 bp):
GCACTGTAACAATATTCACG
Found at i:288457 original size:19 final size:20
Alignment explanation
Indices: 288401--288457 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
288391 AGAATTATAC
*
288401 ATAATTAATACATCAAAATTA
1 ATAATTAAT-TATCAAAATTA
*
288422 ATAATTACTTAAT-AAAATT-
1 ATAATTAATT-ATCAAAATTA
*
288441 TTAATTAATTATCAAAA
1 ATAATTAATTATCAAAA
288458 GAAAAATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
18 2 0.07
19 12 0.40
20 6 0.20
21 10 0.33
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAATTAATTATCAAAATTA
Found at i:288766 original size:24 final size:24
Alignment explanation
Indices: 288739--288793 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
288729 GATTAAAAAG
288739 GACAAATGATGATTTGGAACTATT
1 GACAAATGATGATTTGGAACTATT
288763 GACAAATGATGATTTGGAACTATT
1 GACAAATGATGATTTGGAACTATT
*
288787 GTCAAAT
1 GACAAAT
288794 AATAATAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (24 bp):
GACAAATGATGATTTGGAACTATT
Found at i:296159 original size:12 final size:12
Alignment explanation
Indices: 296142--296167 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
296132 ACTAATTCTA
296142 ATATTAAAAATT
1 ATATTAAAAATT
296154 ATATTAAAAATT
1 ATATTAAAAATT
296166 AT
1 AT
296168 TATCAAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATTAAAAATT
Found at i:301231 original size:172 final size:170
Alignment explanation
Indices: 301000--301323 Score: 501
Period size: 172 Copynumber: 1.9 Consensus size: 170
300990 GATTAGTCTT
* *
301000 TTAGAAATTTCAGTCATAATTGTGTCTTTTTTAATTTGTTATTTTCTTATTGGCTACCTAAAAAT
1 TTAGAAATTTCAGTCATAAATGTGTCTTTTTTAATTTGTTATTTTCTTATTGACTACCTAAAAAT
*
301065 TGCAATGAACAACTTTTGAGAACTGATCTCATTTCATTTTTAGATCCTTTTTTTAAGCACTGT-A
66 TGCAATGAACAACTTTTGAGAACTGATCTCATGTCA-TTTTAGAT-C-TTTTTTAA-CACTGTAA
*
301129 TAG-TTGTTGATATTGAATATTATGATATCTGTCCTTTTTTTTA
127 TAGTTTGTTGATATTGAAAATTATGATATCTGTCCTTTTTTTTA
* *
301172 TTAG-AATTTCCAGTCATAAATGTTTCTTTTTTAATTTGTTGTTTTCTTATTGACTACCTAAAAA
1 TTAGAAATTT-CAGTCATAAATGTGTCTTTTTTAATTTGTTATTTTCTTATTGACTACCTAAAAA
* *
301236 TTGCACTGAACAACTTTTGAGAACTGATCTCATGTCATTTTAGATCTTTTTTAACATTGTAAATA
65 TTGCAATGAACAACTTTTGAGAACTGATCTCATGTCATTTTAGATCTTTTTTAACACTGT-AATA
301301 GTTTGTTGATATTGAAAATTATG
129 GTTTGTTGATATTGAAAATTATG
301324 GAACTCTTTC
Statistics
Matches: 140, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
168 5 0.04
169 8 0.06
170 5 0.04
171 33 0.24
172 89 0.64
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (170 bp):
TTAGAAATTTCAGTCATAAATGTGTCTTTTTTAATTTGTTATTTTCTTATTGACTACCTAAAAAT
TGCAATGAACAACTTTTGAGAACTGATCTCATGTCATTTTAGATCTTTTTTAACACTGTAATAGT
TTGTTGATATTGAAAATTATGATATCTGTCCTTTTTTTTA
Found at i:309926 original size:16 final size:17
Alignment explanation
Indices: 309904--309945 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
309894 TTAAATTTAA
309904 ATTTAATTGTAT-ATATT
1 ATTTAATT-TATGATATT
309921 -TTTAATATTATGATATT
1 ATTTAAT-TTATGATATT
309938 ATTTAATT
1 ATTTAATT
309946 CTAATTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 9 0.41
17 7 0.32
18 6 0.27
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (17 bp):
ATTTAATTTATGATATT
Found at i:310818 original size:20 final size:21
Alignment explanation
Indices: 310787--310825 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
310777 TATATGTTTT
*
310787 TTATTATAAATTTTATTGTAG
1 TTATTATAAATTATATTGTAG
310808 TTATT-TAAATTATATTGT
1 TTATTATAAATTATATTGT
310826 TTGGAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (21 bp):
TTATTATAAATTATATTGTAG
Found at i:315471 original size:76 final size:76
Alignment explanation
Indices: 315356--315511 Score: 296
Period size: 76 Copynumber: 2.1 Consensus size: 76
315346 TTAAAATTTA
*
315356 ATAATATATTTTATATTTACAAAAGTAAGTTAATGTACTAATTTTTTATTTGAGGATATACAATA
1 ATAATATATTTTATATTTACAAAAGTAAGTTAATGTACTAATTTTTTATTTGAGAATATACAATA
315421 TTTAATTTTTT
66 TTTAATTTTTT
315432 ATAATATATTTTATATTTACAAAAGTAAGTTAATGTACTAATTTTTTATTTGAGAATATACAATA
1 ATAATATATTTTATATTTACAAAAGTAAGTTAATGTACTAATTTTTTATTTGAGAATATACAATA
315497 TTTAATTTTTT
66 TTTAATTTTTT
315508 -TAAT
1 ATAAT
315512 CATCATATAT
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
75 4 0.05
76 75 0.95
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (76 bp):
ATAATATATTTTATATTTACAAAAGTAAGTTAATGTACTAATTTTTTATTTGAGAATATACAATA
TTTAATTTTTT
Found at i:320000 original size:2 final size:2
Alignment explanation
Indices: 319993--320026 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
319983 GAAAACAACA
319993 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
320027 GTTTAATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:322924 original size:24 final size:23
Alignment explanation
Indices: 322866--322925 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
322856 AAATCCAGCA
*
322866 AAGAAAATCAAAGCACTCAAAAG
1 AAGAAAATGAAAGCACTCAAAAG
*
322889 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATGAAAGCACTC-AAAAG
*
322913 AAGAAAAAGAAAG
1 AAGAAAATGAAAG
322926 AAAGAAAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 16 0.50
24 16 0.50
ACGTcount: A:0.62, C:0.12, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAATGAAAGCACTCAAAAG
Found at i:328034 original size:2 final size:2
Alignment explanation
Indices: 328027--328054 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
328017 AATTTAAGAT
328027 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
328055 AGGAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:330855 original size:22 final size:22
Alignment explanation
Indices: 330808--330855 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
330798 TTGTACGTCT
*
330808 TTTATGATATAATTATATTTTA
1 TTTATGATATAATTATATTTCA
*
330830 -TTATCGATATCATTA-ATTTCA
1 TTTAT-GATATAATTATATTTCA
330851 TTTAT
1 TTTAT
330856 TTAATTGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTATGATATAATTATATTTCA
Found at i:334952 original size:12 final size:13
Alignment explanation
Indices: 334929--334954 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
334919 ATCTCTACCA
334929 TTTTTCCTTTTTT
1 TTTTTCCTTTTTT
334942 TTTTTCCTTTTTT
1 TTTTTCCTTTTTT
334955 CTTTCGGGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTCCTTTTTT
Found at i:336147 original size:29 final size:28
Alignment explanation
Indices: 336114--336201 Score: 68
Period size: 29 Copynumber: 3.0 Consensus size: 28
336104 GATGAATTTG
336114 GGGATAAAATTAGAATATTTAAAAGTTT
1 GGGATAAAATTAGAATATTTAAAAGTTT
* * * ** * *
336142 GAGGATTAATTTAGAAAGAGGGTCATAGTTT
1 G-GGATAAAATTAG-AATA-TTTAAAAGTTT
*
336173 GGGAATGAAATTAGAATATTTAAAAGTTT
1 GGG-ATAAAATTAGAATATTTAAAAGTTT
336202 AAAAACCAAT
Statistics
Matches: 42, Mismatches: 14, Indels: 7
0.67 0.22 0.11
Matches are distributed among these distances:
28 1 0.02
29 17 0.40
30 8 0.19
31 16 0.38
ACGTcount: A:0.42, C:0.01, G:0.23, T:0.34
Consensus pattern (28 bp):
GGGATAAAATTAGAATATTTAAAAGTTT
Found at i:337648 original size:2 final size:2
Alignment explanation
Indices: 337643--337693 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
337633 ATCATATTAT
337643 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
337685 TC TC TC TC T
1 TC TC TC TC T
337694 ATATATATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:337698 original size:2 final size:2
Alignment explanation
Indices: 337693--337745 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
337683 TCTCTCTCTC
337693 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
337735 TA TA TA TA TA T
1 TA TA TA TA TA T
337746 TAATTAAAGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:339584 original size:20 final size:20
Alignment explanation
Indices: 339559--339664 Score: 85
Period size: 20 Copynumber: 5.4 Consensus size: 20
339549 CGGTCTCAAA
339559 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
339579 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
**
339599 TTCGCAACGCGAAGTTGTAA-
1 TTCGCAACGCGAA-TTCCAAT
* * * *
339619 ATCGCAAC-TGAATTTCAAA
1 TTCGCAACGCGAATTCCAAT
*
339638 TTCGCAACGCGAATT-TAAT
1 TTCGCAACGCGAATTCCAAT
339657 TTCGCAAC
1 TTCGCAAC
339665 AGGTTTTAGT
Statistics
Matches: 67, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
18 4 0.06
19 22 0.33
20 35 0.52
21 6 0.09
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.27
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:340045 original size:14 final size:14
Alignment explanation
Indices: 340026--340059 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
340016 TGTTTTGGAG
340026 GGTCATGTGAGAAT
1 GGTCATGTGAGAAT
340040 GGTCATGTGAGAAT
1 GGTCATGTGAGAAT
340054 -GTCATG
1 GGTCATG
340060 ATGTTTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.26, C:0.09, G:0.35, T:0.29
Consensus pattern (14 bp):
GGTCATGTGAGAAT
Found at i:340443 original size:12 final size:12
Alignment explanation
Indices: 340422--340455 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
340412 ACCACATTTC
*
340422 CAATACCAAACA
1 CAATATCAAACA
*
340434 TAATATCAAACA
1 CAATATCAAACA
340446 CAATATCAAA
1 CAATATCAAA
340456 ACCCACAACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.24, G:0.00, T:0.18
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:340609 original size:24 final size:24
Alignment explanation
Indices: 340582--340635 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
340572 GTATTCAAAA
340582 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
340606 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
340630 TTTGAT
1 TTTGAT
340636 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:342918 original size:18 final size:18
Alignment explanation
Indices: 342895--342930 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
342885 AAGAAAAAGG
*
342895 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
342913 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
342931 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:343356 original size:25 final size:25
Alignment explanation
Indices: 343318--343367 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
343308 AAATCAATTA
*
343318 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
*
343343 AACATTTTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
343368 GAAAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.26, C:0.08, G:0.20, T:0.46
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:343734 original size:18 final size:18
Alignment explanation
Indices: 343713--343749 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
343703 ATAATTGGAG
343713 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
343731 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
343749 T
1 T
343750 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:343756 original size:24 final size:24
Alignment explanation
Indices: 343694--343757 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
343684 TTTCAAATTC
*
343694 ATTTC-ATATATAATTGGAGTTTGA
1 ATTTCAATATA-AATTTGAGTTTGA
* * *
343718 ATTTAAATTTCAATTTGAGTTTGA
1 ATTTCAATATAAATTTGAGTTTGA
343742 ATTTCAATATAAATTT
1 ATTTCAATATAAATTT
343758 CGGCTCCACT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
24 29 0.91
25 3 0.09
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (24 bp):
ATTTCAATATAAATTTGAGTTTGA
Found at i:344291 original size:20 final size:20
Alignment explanation
Indices: 344262--344311 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
344252 ATGTTGCGAT
*
344262 CAACGTGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
*
344282 CAACGCGAAAGTCAAATTTG
1 CAACGCGAAAGTCAAATTCG
*
344302 CAACACGAAA
1 CAACGCGAAA
344312 TAAGCGTTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.16
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:344366 original size:20 final size:20
Alignment explanation
Indices: 344315--344368 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
344305 CACGAAATAA
344315 GCGTTGCGAATTTGACTTTC
1 GCGTTGCGAATTTGACTTTC
* * *
344335 GTGTTACGAATTTTACTTTC
1 GCGTTGCGAATTTGACTTTC
*
344355 GCGTTGCAAATTTG
1 GCGTTGCGAATTTG
344369 TACCTTCAAC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.43
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTTTC
Found at i:344557 original size:61 final size:62
Alignment explanation
Indices: 344426--344566 Score: 169
Period size: 61 Copynumber: 2.2 Consensus size: 62
344416 TTTTTAGAAA
*
344426 TAACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACAAATCAAATT
1 TAACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAATAAATCTTATTTACAAATCAAATT
* * * * **
344491 AAACAAATCAATTTTTACAAATCAATT-AATCAAAAAATAAATCTTATTTCCTCATC-AATT
1 TAACAAATCAACTTTTACAAATCAATTAAAGCAAAAAATAAATCTTATTTACAAATCAAATT
344551 GTAACAAATCAACTTT
1 -TAACAAATCAACTTT
344567 CAATGTAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
60 4 0.06
61 37 0.56
65 25 0.38
ACGTcount: A:0.50, C:0.16, G:0.01, T:0.33
Consensus pattern (62 bp):
TAACAAATCAACTTTTACAAATCAATTAAAGCAAAAAATAAATCTTATTTACAAATCAAATT
Found at i:346024 original size:21 final size:21
Alignment explanation
Indices: 345946--346041 Score: 79
Period size: 21 Copynumber: 4.6 Consensus size: 21
345936 GACGAGACCA
*
345946 CTTGAACGATGATAGGGGCCT
1 CTTGAACGATGAGAGGGGCCT
* * * *
345967 CTTAAACGGTGGGAGGGGCTT
1 CTTGAACGATGAGAGGGGCCT
*
345988 CTTCG-ATGATGAGAGGGGCCT
1 CTT-GAACGATGAGAGGGGCCT
**
346009 CTTGAACGAT-AGGAGGCACCT
1 CTTGAACGATGA-GAGGGGCCT
*
346030 CTTGAATGATGA
1 CTTGAACGATGA
346042 TAGGTGCATC
Statistics
Matches: 57, Mismatches: 14, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.04
21 54 0.95
22 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.24
Consensus pattern (21 bp):
CTTGAACGATGAGAGGGGCCT
Found at i:346039 original size:42 final size:42
Alignment explanation
Indices: 345946--346041 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 42
345936 GACGAGACCA
* * * * ** *
345946 CTTGAACGATGATAGGGGCCTCTTAAACGGTGGGAGGGGCTT
1 CTTGAATGATGAGAGGGGCCTCTTAAACGATAGGAGGCACCT
*
345988 CTTCG-ATGATGAGAGGGGCCTCTTGAACGATAGGAGGCACCT
1 CTT-GAATGATGAGAGGGGCCTCTTAAACGATAGGAGGCACCT
346030 CTTGAATGATGA
1 CTTGAATGATGA
346042 TAGGTGCATC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
41 1 0.02
42 42 0.95
43 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.24
Consensus pattern (42 bp):
CTTGAATGATGAGAGGGGCCTCTTAAACGATAGGAGGCACCT
Found at i:348219 original size:19 final size:20
Alignment explanation
Indices: 348195--348234 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
348185 AATTTGCAAC
348195 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
*
348214 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
348234 G
1 G
348235 TGAATTTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.10, C:0.17, G:0.25, T:0.47
Consensus pattern (20 bp):
GCGATTTTCAGTTTCGCGTT
Found at i:348714 original size:20 final size:20
Alignment explanation
Indices: 348689--348756 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
348679 TGACTTATGT
348689 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
** *
348709 GTTGCGAATTTGGAAAATCGC
1 GTTGCG-ATTTACAAATTCGC
** *
348730 AATGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGC
348750 GTTGCGA
1 GTTGCGA
348757 AATTGGAAAC
Statistics
Matches: 36, Mismatches: 11, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
20 21 0.58
21 15 0.42
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:348793 original size:20 final size:20
Alignment explanation
Indices: 348744--348797 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
348734 CGATTTACAT
348744 ATTCGCGTTGCGAAATTGGA
1 ATTCGCGTTGCGAAATTGGA
* *
348764 A-ACTGGGTTGCGAAATTGGA
1 ATTC-GCGTTGCGAAATTGGA
348784 ATTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
348798 TTTGTTGGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (20 bp):
ATTCGCGTTGCGAAATTGGA
Found at i:349094 original size:25 final size:25
Alignment explanation
Indices: 349066--349115 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
349056 CAATCCTCCA
*
349066 ACATTTAGTTCGTTTGCAATATGGT
1 ACATTTAGTCCGTTTGCAATATGGT
349091 ACATTTAGTCCGTTTGCAATATGGT
1 ACATTTAGTCCGTTTGCAATATGGT
349116 CCCCAACGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (25 bp):
ACATTTAGTCCGTTTGCAATATGGT
Found at i:350033 original size:31 final size:31
Alignment explanation
Indices: 349995--350116 Score: 131
Period size: 31 Copynumber: 3.9 Consensus size: 31
349985 GATCCTTGGC
* *
349995 AACTGTCCATAGGTTCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
** *
350026 AACTGTCCATATGTTCCTTAGAGCATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
*
350057 TACTGTCCATATG-TCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
* *
350088 ATTCTGTCCATATGTTCCGTAGAACATAG
1 A-ACTGTCCATATGTTCCGAAGAACATAG
350117 TTATACCCTC
Statistics
Matches: 74, Mismatches: 12, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
30 3 0.04
31 48 0.65
32 20 0.27
33 3 0.04
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:351167 original size:64 final size:65
Alignment explanation
Indices: 351051--351282 Score: 240
Period size: 64 Copynumber: 3.6 Consensus size: 65
351041 TCATCTTTTA
* * * ** *
351051 ATTAA-GGTATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAAT-ATT
1 ATTAATGGGATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAATCATT
** * ** *
351114 ATTGCTGGGATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATT
1 ATTAATGGGATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAATCATT
* * *
351178 ATTAATGGGATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTATTTATT
1 ATTAATGGGATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAATCATT
** ** *
351243 -TTAA-AAGAGTGCATCGATGCACTACCAATGCATCGGTGCA
1 ATTAATGGGA-TGCATCGATGCACTACTTATGCATCGATGCA
351283 CATTCAAACA
Statistics
Matches: 142, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
63 6 0.04
64 131 0.92
65 5 0.04
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (65 bp):
ATTAATGGGATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAATCATT
Found at i:351256 original size:128 final size:127
Alignment explanation
Indices: 351051--351283 Score: 285
Period size: 128 Copynumber: 1.8 Consensus size: 127
351041 TCATCTTTTA
* * *
351051 ATTAAGGTATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAATATTAT
1 ATTAAGGGATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGCATTCGATGTAATATTAT
** *
351116 TGCTGGGATGCATCGATGCACT-CCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATT
66 TGCTAAGATGCATCGATGCACTACC-AATGCATCGATGCACCAATTGCATTCGATGTTTCATT
* * **
351178 ATTAATGGGATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGT-AT-TTA
1 ATTAA-GGGATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGCATTCGATGTAATATTA
* *
351241 TT-TTAAAAGAGTGCATCGATGCACTACCAATGCATCGGTGCAC
65 TTGCT--AAGA-TGCATCGATGCACTACCAATGCATCGATGCAC
351284 ATTCAAACAA
Statistics
Matches: 89, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
125 1 0.01
126 5 0.06
127 9 0.10
128 72 0.81
129 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (127 bp):
ATTAAGGGATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGCATTCGATGTAATATTAT
TGCTAAGATGCATCGATGCACTACCAATGCATCGATGCACCAATTGCATTCGATGTTTCATT
Found at i:353051 original size:31 final size:31
Alignment explanation
Indices: 353016--353074 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
353006 ACAGTCCCCC
**
353016 AACATTTAGT-TTGTTTGTGATATGGTCCTCT
1 AACATTTAGTCTT-TTTGCAATATGGTCCTCT
353047 AACATTTAGTCTTTTTGCAATATGGTCC
1 AACATTTAGTCTTTTTGCAATATGGTCC
353075 CCAACGTAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (31 bp):
AACATTTAGTCTTTTTGCAATATGGTCCTCT
Found at i:369417 original size:21 final size:21
Alignment explanation
Indices: 369366--369418 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
369356 ATTATGACTA
369366 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
369387 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
369408 TCGCAATGCGA
1 TCGCAATGCGA
369419 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:369473 original size:20 final size:20
Alignment explanation
Indices: 369448--369501 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
369438 AATTGGGAAA
*
369448 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
369468 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
369488 TTCGCAACGAGATA
1 ATCGCAACGCGATA
369502 ATACATAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:369684 original size:19 final size:19
Alignment explanation
Indices: 369657--369695 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
369647 AAAATCACAA
*
369657 CTCAGTCTCATCA-CCATCT
1 CTCACTCTC-TCACCCATCT
369676 CTCACTCTCTCACCCATCT
1 CTCACTCTCTCACCCATCT
369695 C
1 C
369696 CGACGAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.18, C:0.49, G:0.03, T:0.31
Consensus pattern (19 bp):
CTCACTCTCTCACCCATCT
Found at i:370042 original size:20 final size:20
Alignment explanation
Indices: 369996--370044 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
369986 TTTATTCTCT
369996 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
370016 CGCTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
370036 TGTTGCGAT
1 CGTTGCGAT
370045 TTTCATTGTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:370245 original size:25 final size:24
Alignment explanation
Indices: 370191--370245 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
370181 TGTTTATTAT
* *
370191 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
370215 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
370241 TGTTT
1 TGTTT
370246 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:371397 original size:16 final size:18
Alignment explanation
Indices: 371373--371418 Score: 69
Period size: 16 Copynumber: 2.7 Consensus size: 18
371363 TCCACTTCGG
371373 GAGCCATCACCTCA-C-A
1 GAGCCATCACCTCACCTA
*
371389 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCTA
371407 GAGCCATCACCT
1 GAGCCATCACCT
371419 AATCGACCCG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 13 0.50
17 1 0.04
18 12 0.46
ACGTcount: A:0.28, C:0.41, G:0.13, T:0.17
Consensus pattern (18 bp):
GAGCCATCACCTCACCTA
Found at i:372013 original size:19 final size:20
Alignment explanation
Indices: 371959--372025 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
371949 TAGTTTACTT
* *
371959 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
371979 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* * **
371999 TCGCTATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
372018 TCGCAACG
1 TCGCAACG
372026 ACAAAATCGC
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
19 13 0.35
20 24 0.65
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:372033 original size:14 final size:14
Alignment explanation
Indices: 372014--372072 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
372004 ATGCGAAATG
372014 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
372028 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
372047 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
372061 AAAATTGCAACG
1 AAAATCGCAACG
372073 CGAAATAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 21 0.57
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.27
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:372041 original size:33 final size:33
Alignment explanation
Indices: 371998--372089 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
371988 GGAAATGGCT
*
371998 ATCGCTATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
372031 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* * *
372064 ATTGCAACGCGAAATAAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
372090 TGCGTCGCGT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.48, C:0.21, G:0.17, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:372052 original size:19 final size:19
Alignment explanation
Indices: 371998--372093 Score: 68
Period size: 19 Copynumber: 5.6 Consensus size: 19
371988 GGAAATGGCT
* *
371998 ATCGCTATGCGAAATGAAA
1 ATCGCAATGCGAAATCAAA
372017 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATCAAA
*
372031 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATCAAA
372050 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATCAAA
* * *
372064 ATTGCAACGCGAAATAAAA
1 ATCGCAATGCGAAATCAAA
372083 ATCGCAATGCG
1 ATCGCAATGCG
372094 TCGCGTTGCG
Statistics
Matches: 59, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
14 19 0.32
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 28 0.47
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATCAAA
Found at i:372116 original size:14 final size:14
Alignment explanation
Indices: 372097--372155 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
372087 CAATGCGTCG
372097 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
372111 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
372128 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
372144 CGTTGCGGTTTT
1 CGTTGCGATTTT
372156 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 17 0.46
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.08, C:0.17, G:0.25, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:372137 original size:19 final size:19
Alignment explanation
Indices: 372113--372229 Score: 91
Period size: 20 Copynumber: 6.3 Consensus size: 19
372103 GATTTTGTCG
372113 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
372132 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
*
372146 TTGCGGTTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
372165 TCGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
*** *
372184 TTGCGATAGCCATTTTCGCG
1 TTGCGATTTTCA-TTTCGCA
**
372204 TTGCGATAGTCATTTTCGCA
1 TTGCGATTTTCA-TTTCGCA
372224 TTGCGA
1 TTGCGA
372230 AAGTAAGTTT
Statistics
Matches: 80, Mismatches: 12, Indels: 11
0.78 0.12 0.11
Matches are distributed among these distances:
14 5 0.06
15 3 0.04
16 4 0.05
17 4 0.05
18 3 0.04
19 30 0.38
20 31 0.39
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:372141 original size:33 final size:33
Alignment explanation
Indices: 372094--372174 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
372084 TCGCAATGCG
*
372094 TCGCGTTGCGATTTTGTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTGTCGTTGCGATTTTCATT
*
372127 TCGCATTGCGATTTTGTCGTTGCGGTTTTCATT
1 TCGCATTGCGATTTTGTCGTTGCGATTTTCATT
*
372160 TCGCATCGCGATTTT
1 TCGCATTGCGATTTT
372175 CATTTCGCGT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TCGCATTGCGATTTTGTCGTTGCGATTTTCATT
Found at i:372240 original size:20 final size:20
Alignment explanation
Indices: 372177--372255 Score: 77
Period size: 20 Copynumber: 4.0 Consensus size: 20
372167 GCGATTTTCA
* ** *
372177 TTTCGCGTTGCGATAGCCAT
1 TTTCGCGTTGCGAAAGTAAG
* * *
372197 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGAAAGTAAG
*
372217 TTTCGCATTGCGAAAGTAAG
1 TTTCGCGTTGCGAAAGTAAG
*
372237 TTTCGTGTTGCGAAAGTAA
1 TTTCGCGTTGCGAAAGTAA
372256 ACTATTCTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (20 bp):
TTTCGCGTTGCGAAAGTAAG
Found at i:372684 original size:41 final size:42
Alignment explanation
Indices: 372595--372684 Score: 128
Period size: 41 Copynumber: 2.2 Consensus size: 42
372585 CCGACTCACT
* * *
372595 TGTCATCCCTCAAGAGTCCCATCCAATCGTTCAAGAGGCCCC
1 TGTCATCCCTCAAGAGTCCCACCCAACCGTTCAAGAGGCCAC
* *
372637 TATCATCCCTCAAGAGTCCC-CCCCACCGTTCAAGAGGCCAC
1 TGTCATCCCTCAAGAGTCCCACCCAACCGTTCAAGAGGCCAC
372678 TGTCATC
1 TGTCATC
372685 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 23 0.55
42 19 0.45
ACGTcount: A:0.23, C:0.40, G:0.16, T:0.21
Consensus pattern (42 bp):
TGTCATCCCTCAAGAGTCCCACCCAACCGTTCAAGAGGCCAC
Found at i:372693 original size:41 final size:42
Alignment explanation
Indices: 372597--372714 Score: 114
Period size: 42 Copynumber: 2.8 Consensus size: 42
372587 GACTCACTTG
* * * *
372597 TCATCCCTCAAGA-GTCCCATCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGGTCCC-CCCCACCGTTCAAGAGGCCACTA
*
372639 TCATCCCTCAAGA-GTCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGGTCCCCCCCACCGTTCAAGAGGCCACTA
** * * * *
372680 TCATCGTTGAAGAGGTCCCTCCCACCATTCTAGAG
1 TCATCCCTCAAGAGGTCCCCCCCACCGTTCAAGAG
372715 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 28 0.44
42 36 0.56
ACGTcount: A:0.24, C:0.38, G:0.17, T:0.21
Consensus pattern (42 bp):
TCATCCCTCAAGAGGTCCCCCCCACCGTTCAAGAGGCCACTA
Found at i:374125 original size:14 final size:14
Alignment explanation
Indices: 374091--374129 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
374081 TTGATTGTTT
374091 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
374105 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
374119 TGTTGATTTGT
1 AATTGATTTGT
374130 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:374293 original size:19 final size:19
Alignment explanation
Indices: 374269--374333 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
374259 ACAACGAGAG
374269 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
374288 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
374307 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
374321 AATCGCAATGCGA
1 AATCGCAATGCGA
374334 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
19 27 0.63
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:374377 original size:20 final size:20
Alignment explanation
Indices: 374352--374407 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
374342 TCGCATTGCG
*
374352 ATTTTCTCGTTACAATAGCC
1 ATTTTCGCGTTACAATAGCC
*
374372 ATTTTCGCGTTACGATAGCC
1 ATTTTCGCGTTACAATAGCC
*
374392 ATTTTCGCGTTGCAAT
1 ATTTTCGCGTTACAAT
374408 TTCCCCGTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTACAATAGCC
Found at i:376704 original size:12 final size:12
Alignment explanation
Indices: 376687--376711 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
376677 TCTTCGGGGA
376687 CTTTTTCTTCTT
1 CTTTTTCTTCTT
376699 CTTTTTCTTCTT
1 CTTTTTCTTCTT
376711 C
1 C
376712 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:376920 original size:24 final size:24
Alignment explanation
Indices: 376886--376939 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
376876 CTGAAACATC
*
376886 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
376910 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
376934 ATCAAA
1 ATCAAA
376940 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:377743 original size:19 final size:20
Alignment explanation
Indices: 377683--377768 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
377673 TGTATTATCT
* *
377683 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
377703 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
377723 CGTTGCGAAAGTCAG-ATCG
1 CGTTGCGAAAGTCAGAATCG
*
377742 CGTTGCG-AAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
*
377761 CATTGCGA
1 CGTTGCGA
377769 TTTTGTATTC
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
18 7 0.11
19 21 0.34
20 33 0.54
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:377767 original size:38 final size:40
Alignment explanation
Indices: 377685--377768 Score: 118
Period size: 38 Copynumber: 2.1 Consensus size: 40
377675 TATTATCTCG
* * *
377685 TTGCGATAGTCAGAATCTCGTTGCGAAAGTCAGAATCGCG
1 TTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGAATCGCA
*
377725 TTGCGAAAGTCAG-ATCGCGTTGCG-AAGTCAGTATCGCA
1 TTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGAATCGCA
377763 TTGCGA
1 TTGCGA
377769 TTTTGTATTC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 18 0.45
39 10 0.25
40 12 0.30
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (40 bp):
TTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGAATCGCA
Found at i:379446 original size:40 final size:40
Alignment explanation
Indices: 379386--379463 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
379376 TAAAATACAT
* * *
379386 ACATGTTACTCGTTTAATCTTATTTATGAAGTTGAAAAAC
1 ACATATTACTCATTTAATCTTACTTATGAAGTTGAAAAAC
*
379426 ACATATTACTCATTTTATCTTACTTATGAAGTTGAAAA
1 ACATATTACTCATTTAATCTTACTTATGAAGTTGAAAA
379464 CTTAATGCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (40 bp):
ACATATTACTCATTTAATCTTACTTATGAAGTTGAAAAAC
Found at i:382103 original size:16 final size:16
Alignment explanation
Indices: 382079--382110 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
382069 AGAATCAATT
382079 CTTTATTTACTTTTTA
1 CTTTATTTACTTTTTA
*
382095 CTTTTTTTACTTTTTA
1 CTTTATTTACTTTTTA
382111 TTATATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (16 bp):
CTTTATTTACTTTTTA
Found at i:388267 original size:17 final size:18
Alignment explanation
Indices: 388241--388278 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
388231 CAAAAAATTA
*
388241 AAAAAAATAACAAG-AAG
1 AAAAAAATAAAAAGAAAG
*
388258 AAAAACATAAAAAGAAAG
1 AAAAAAATAAAAAGAAAG
388276 AAA
1 AAA
388279 GAATACAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.79, C:0.05, G:0.11, T:0.05
Consensus pattern (18 bp):
AAAAAAATAAAAAGAAAG
Found at i:389305 original size:17 final size:17
Alignment explanation
Indices: 389268--389306 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
389258 AGCACTTAAC
389268 TTTTT-AAAAAACCAAA
1 TTTTTAAAAAAACCAAA
* *
389284 ATTTTAAAAAAACCAAT
1 TTTTTAAAAAAACCAAA
389301 TTTTTA
1 TTTTTA
389307 GAAATTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (17 bp):
TTTTTAAAAAAACCAAA
Found at i:391117 original size:64 final size:64
Alignment explanation
Indices: 391004--391127 Score: 169
Period size: 64 Copynumber: 1.9 Consensus size: 64
390994 GTGCACCAAG
* ** *
391004 TGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGGTGCATTGCT
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAACCCAAGTGCATCGATGCATTGCT
* * *
391068 TGTGCATCGATGCATGAAATGCATTCTATGTTTTAATAA-AACCCAAGTGCATCGATGCAT
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTGAA-AATAACCCAAGTGCATCGATGCAT
391128 AGAGAGTACA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
64 50 0.96
65 2 0.04
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (64 bp):
TGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAACCCAAGTGCATCGATGCATTGCT
Found at i:391140 original size:64 final size:64
Alignment explanation
Indices: 391008--391147 Score: 156
Period size: 64 Copynumber: 2.2 Consensus size: 64
390998 ACCAAGTGTG
* ** * * *** *
391008 CATCGATGCATAAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGGTGCATTGCTTGTG
1 CATCGATGCATAAAATGCATTCGATGTTTGAAAATAACCCAAGTGCATCGATGCATAGAGAGTA
* * *
391072 CATCGATGCATGAAATGCATTCTATGTTTTAATAA-AACCCAAGTGCATCGATGCATAGAGAGTA
1 CATCGATGCATAAAATGCATTCGATGTTTGAA-AATAACCCAAGTGCATCGATGCATAGAGAGTA
391136 CATCGATGCATA
1 CATCGATGCATA
391148 TAGAGTACAT
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
64 60 0.97
65 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (64 bp):
CATCGATGCATAAAATGCATTCGATGTTTGAAAATAACCCAAGTGCATCGATGCATAGAGAGTA
Found at i:391141 original size:19 final size:19
Alignment explanation
Indices: 391117--391203 Score: 147
Period size: 19 Copynumber: 4.6 Consensus size: 19
391107 AACCCAAGTG
391117 CATCGATGCATAGAGAGTA
1 CATCGATGCATAGAGAGTA
*
391136 CATCGATGCATATAGAGTA
1 CATCGATGCATAGAGAGTA
*
391155 CATCGATGCATAGAGAGTG
1 CATCGATGCATAGAGAGTA
*
391174 CATCGATGCATAGAGAGTG
1 CATCGATGCATAGAGAGTA
391193 CATCGATGCAT
1 CATCGATGCAT
391204 GAAATGCATT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 65 1.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.23
Consensus pattern (19 bp):
CATCGATGCATAGAGAGTA
Found at i:393720 original size:18 final size:18
Alignment explanation
Indices: 393697--393731 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
393687 TGATTTTCCA
*
393697 ATGATTTTGAGTAAGAGT
1 ATGATTTAGAGTAAGAGT
*
393715 ATGATTTAGAGTGAGAG
1 ATGATTTAGAGTAAGAG
393732 AGGACGATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (18 bp):
ATGATTTAGAGTAAGAGT
Found at i:393860 original size:23 final size:23
Alignment explanation
Indices: 393830--393894 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
393820 TGCATGACCC
**
393830 TGTGCATCGATGCACATTCAAGG
1 TGTGCATCGATGCACATTCAACA
*
393853 TGTGCATCG--GTACA-TCAACA
1 TGTGCATCGATGCACATTCAACA
*
393873 TGATGAATCGATGCACATTCAA
1 TG-TGCATCGATGCACATTCAA
393895 AGGGATGCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
20 6 0.18
21 10 0.30
23 13 0.39
24 4 0.12
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (23 bp):
TGTGCATCGATGCACATTCAACA
Found at i:399777 original size:64 final size:62
Alignment explanation
Indices: 399669--399846 Score: 198
Period size: 64 Copynumber: 2.8 Consensus size: 62
399659 TGGAACACTT
* * **
399669 AGTGCATCGATGCACCA-AGTGTGCATCATGCATAAAATGCATTCGATGTTTGAA-AATAGCCTG
1 AGTGCATCGATGCA-TAGAGTGTGCATCATGCATGAAATGCATTCGATGTTTGAAGAA-A-CCCA
* * ** *
399732 AGTGCATCGGTGCATTGCTTGTGCATCGATGCATGAAATGCATTCGATGTTTTAATGAAACCCA
1 AGTGCATCGATGCATAGAGTGTGCATC-ATGCATGAAATGCATTCGATGTTTGAA-GAAACCCA
*
399796 AGTGCATCGATGCATAGAGAGTGCATCAATGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCATAGAGTGTGCATC-ATGCATGAAATGCATTCGATGTT
399847 CAATTTATTC
Statistics
Matches: 96, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
63 21 0.22
64 72 0.75
65 1 0.01
66 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.29
Consensus pattern (62 bp):
AGTGCATCGATGCATAGAGTGTGCATCATGCATGAAATGCATTCGATGTTTGAAGAAACCCA
Found at i:402999 original size:2 final size:2
Alignment explanation
Indices: 402992--403020 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
402982 TCTCTGATAC
402992 AT AT 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 AT AT A
403021 ACATTGTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:410334 original size:25 final size:25
Alignment explanation
Indices: 410300--410374 Score: 150
Period size: 25 Copynumber: 3.0 Consensus size: 25
410290 GTCTGGAGGA
410300 TTCATTCTTTAGGATAAACTAACTT
1 TTCATTCTTTAGGATAAACTAACTT
410325 TTCATTCTTTAGGATAAACTAACTT
1 TTCATTCTTTAGGATAAACTAACTT
410350 TTCATTCTTTAGGATAAACTAACTT
1 TTCATTCTTTAGGATAAACTAACTT
410375 ATGAAGTTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (25 bp):
TTCATTCTTTAGGATAAACTAACTT
Found at i:419621 original size:22 final size:22
Alignment explanation
Indices: 419604--419670 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
419594 CTCGTATAAA
419604 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
419626 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
419648 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
419670 T
1 T
419671 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:421334 original size:21 final size:21
Alignment explanation
Indices: 421310--421354 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
421300 TCTTGTTCGT
* *
421310 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
421331 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
421352 TTG
1 TTG
421355 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:424642 original size:22 final size:22
Alignment explanation
Indices: 424625--424691 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
424615 CTCGTATAAA
424625 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
424647 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
424669 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
424691 T
1 T
424692 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:426351 original size:21 final size:21
Alignment explanation
Indices: 426327--426371 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
426317 TCTTGTTCGT
* *
426327 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
426348 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
426369 TTG
1 TTG
426372 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:427230 original size:21 final size:21
Alignment explanation
Indices: 427204--427444 Score: 287
Period size: 21 Copynumber: 11.6 Consensus size: 21
427194 GTTTCCAGAT
*
427204 TCGCAACGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
427225 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
427246 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
427267 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* * *
427288 TCGCAATGTGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
427308 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
427329 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
427350 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
* *
427371 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
427391 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
*
427412 TCGCAATGCCAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
427433 TCGCAATGCGAA
1 TCGCAATGCGAA
427445 TATGTAAATC
Statistics
Matches: 187, Mismatches: 25, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
20 31 0.17
21 156 0.83
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:427311 original size:83 final size:83
Alignment explanation
Indices: 427224--427444 Score: 372
Period size: 83 Copynumber: 2.7 Consensus size: 83
427214 AACTTGGACT
* * *
427224 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTA
1 ATCGCAATGCGATA-GTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTA
*
427288 TCGCAATGTGAATATGTAA
65 TCGCAATGCGAATATGTAA
*
427307 ATCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTAT
1 ATCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTAT
427372 CGCAATGCGAATATGTAA
66 CGCAATGCGAATATGTAA
*
427390 ATCGCAATGCGATAGTCGACTATCGCAATGCCAACTTGGACTATCGCAATGCGAA
1 ATCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAA
427445 TATGTAAATC
Statistics
Matches: 130, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
83 129 0.99
84 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (83 bp):
ATCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTAT
CGCAATGCGAATATGTAA
Found at i:427394 original size:62 final size:63
Alignment explanation
Indices: 427204--427463 Score: 311
Period size: 62 Copynumber: 4.2 Consensus size: 63
427194 GTTTCCAGAT
* * *
427204 TCGCAACGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACT-TGGACTA
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAA-TATGTACAA
* * * *
427267 TCGCAATGCGAACTTGGACTATCGCAATGTGAA-TATGTA-AATCGCAATGCG-ATA-GTCGACT
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAACT-TGGACTATCGCAATGCGAATATGT--ACA
427328 A
63 A
* *
427329 TCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTA-AA
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTACAA
* * *
427391 TCGCAATGCGATA-GTCGACTATCGCAATGCCAACTTGGACTATCGCAATGCGAATATGTA-AA
1 TCGCAATGCGA-ACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTACAA
427453 TCGCAATGCGA
1 TCGCAATGCGA
427464 TAGTCGAAGT
Statistics
Matches: 172, Mismatches: 16, Indels: 19
0.83 0.08 0.09
Matches are distributed among these distances:
60 2 0.01
61 1 0.01
62 116 0.67
63 48 0.28
64 3 0.02
65 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.23
Consensus pattern (63 bp):
TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTACAA
Found at i:427483 original size:21 final size:21
Alignment explanation
Indices: 427453--427629 Score: 184
Period size: 21 Copynumber: 8.6 Consensus size: 21
427443 AATATGTAAA
*
427453 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
427474 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
427495 TCGCGTTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
* *
427516 TCGCGTTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
*
427537 TCGCATTGCGAT-TTAC-ATA-T
1 TCGCATTGCGATAGT-CGA-AGT
**
427557 TCGCATTGTAATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
* ** * *
427578 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATAGTCGAAGT
427599 TCG--TTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
427618 TCGCGTTGCGAT
1 TCGCATTGCGAT
427630 TTATTCTAAA
Statistics
Matches: 130, Mismatches: 19, Indels: 14
0.80 0.12 0.09
Matches are distributed among these distances:
19 15 0.12
20 15 0.12
21 100 0.77
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:427505 original size:62 final size:63
Alignment explanation
Indices: 427367--427548 Score: 176
Period size: 62 Copynumber: 2.9 Consensus size: 63
427357 GCGAACTTCG
* * * * *
427367 ACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCG-ACTATCGCAATGCCA-ACTTGG
1 ACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGT-TCGCATTGCGATACTCGA
*
427429 ACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCATTGCGATAGTCGA
1 ACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCATTGCGATACTCGA
* ** * ** *
427492 AGT-TCGCGTTGCG-ATA-GTCGAAGTTCGCGTTGCGATAGTCCAAGTTCGCATTGCGAT
1 ACTATCGCAATGCGAATATGT--AA-ATCGCAATGCGATAGTCGAAGTTCGCATTGCGAT
427549 TTACATATTC
Statistics
Matches: 102, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
60 2 0.02
61 3 0.03
62 60 0.59
63 37 0.36
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (63 bp):
ACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCATTGCGATACTCGA
Found at i:427605 original size:19 final size:19
Alignment explanation
Indices: 427581--427650 Score: 59
Period size: 21 Copynumber: 3.5 Consensus size: 19
427571 TCGAAGTTCG
427581 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
** * *
427600 CGTTGCGATAGTCGAAGTT
1 CGTTGCGATTTTCCAAATT
*
427619 CGCGTTGCGATTTATTCTAAATT
1 --CGTTGCGA-TT-TTCCAAATT
427642 CGTTGCGAT
1 CGTTGCGAT
427651 AGTCCAAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
19 15 0.38
20 1 0.03
21 16 0.41
22 1 0.03
23 6 0.15
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.39
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:427642 original size:42 final size:40
Alignment explanation
Indices: 427479--427654 Score: 187
Period size: 42 Copynumber: 4.3 Consensus size: 40
427469 GAAGTTCGCA
* *
427479 TTGCGATAGTCGAAGTTCGCGTTGCGA-TAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTATTC-AAATT--CG
* * * *
427521 TTGCGATAGTCCAAGTTCGCATTGCGATT-TACATATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTATTCAAATTCG
**
427560 CATTGTAATAGTCGAAGTTCGCGTTGCGATT-TTCCAAATTCG
1 --TTGCGATAGTCGAAGTTCGCGTTGCGATTATT-CAAATTCG
427602 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTC-AAATTCG
427644 TTGCGATAGTC
1 TTGCGATAGTC
427655 CAAAATCGCA
Statistics
Matches: 113, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
39 2 0.02
40 25 0.22
41 32 0.28
42 53 0.47
43 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (40 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTATTCAAATTCG
Found at i:427761 original size:6 final size:6
Alignment explanation
Indices: 427747--427784 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
427737 GACACGTATT
* *
427747 ACCATG ACCACG ACCACG ACCACG ACCCCG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
427785 CGAGACGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.29, C:0.53, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:428435 original size:131 final size:131
Alignment explanation
Indices: 428201--428441 Score: 437
Period size: 131 Copynumber: 1.8 Consensus size: 131
428191 TTTAAGACTT
*
428201 GGCTTTCCCACTTCCTTGTTGAGTGATAGAGAACAAGGGAGACTCTCGCGAGCCGCCGCCGCCGC
1 GGCTTTCCCACTTACTTGTTGAGTGATAGAGAACAAGGGAGACTCTCGCGAGCCGCCGCCGCCGC
428266 CGTCCGTCTCGTCTCGGGTCGGGTCGTGGTCGTGGTCGTGGTAATACGTGTATTCGACACGTCTT
66 CGTCCGTCTCGTCTCGGGTCGGGTCGTGGTCGTGGTCGTGGTAATACGTGTATTCGACACGTCTT
428331 G
131 G
* * *
428332 GGCTTTCCCACTTACTTGTTGAGTGATAGAGAACAAGGGGGACTCTCGCGCGCCGCCGGCGCCGC
1 GGCTTTCCCACTTACTTGTTGAGTGATAGAGAACAAGGGAGACTCTCGCGAGCCGCCGCCGCCGC
*
428397 CGTCCGTCTCTTCTCGGGTCGGGTCGTGGTCGTGGTCGTGGTAAT
66 CGTCCGTCTCGTCTCGGGTCGGGTCGTGGTCGTGGTCGTGGTAAT
428442 GCGAATACTA
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
131 105 1.00
ACGTcount: A:0.13, C:0.28, G:0.33, T:0.26
Consensus pattern (131 bp):
GGCTTTCCCACTTACTTGTTGAGTGATAGAGAACAAGGGAGACTCTCGCGAGCCGCCGCCGCCGC
CGTCCGTCTCGTCTCGGGTCGGGTCGTGGTCGTGGTCGTGGTAATACGTGTATTCGACACGTCTT
G
Found at i:428542 original size:21 final size:21
Alignment explanation
Indices: 428516--428644 Score: 124
Period size: 21 Copynumber: 6.3 Consensus size: 21
428506 TTTGGAATAA
*
428516 ATCGCAACGCGGACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
428537 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
428556 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
428577 ATCGCAATGCGAA-TAT-GTA-A
1 ATCGCAACGCGAACT-TCG-ACT
*
428597 ATCGCAATGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
428618 ATCGCAACGCAAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
428639 ATCGCA
1 ATCGCA
428645 TTGCAATTTA
Statistics
Matches: 87, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
19 14 0.16
20 17 0.20
21 56 0.64
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:428611 original size:41 final size:40
Alignment explanation
Indices: 428513--428626 Score: 167
Period size: 41 Copynumber: 2.8 Consensus size: 40
428503 GAATTTGGAA
* *
428513 TAAATCGCAACGCGGACTTCGACTATCGCAACGAATTTGG
1 TAAATCGCAACGCGAACTTCGACTATCGCAACGAATATGG
*
428553 AAAATCGCAACGCGAACTTCGACTATCGCAATGCGAATAT-G
1 TAAATCGCAACGCGAACTTCGACTATCGCAA--CGAATATGG
*
428594 TAAATCGCAATGCGAACTTCGACTATCGCAACG
1 TAAATCGCAACGCGAACTTCGACTATCGCAACG
428627 CAAACTTCGA
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
39 2 0.03
40 29 0.43
41 30 0.45
42 6 0.09
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.21
Consensus pattern (40 bp):
TAAATCGCAACGCGAACTTCGACTATCGCAACGAATATGG
Found at i:428689 original size:21 final size:21
Alignment explanation
Indices: 428659--428836 Score: 170
Period size: 21 Copynumber: 8.6 Consensus size: 21
428649 AATTTACATA
428659 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* * *
428680 TTCACATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
428700 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
*
428721 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
428742 TTCGCGTTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
428763 TTCGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
428783 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
428804 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
428825 TTCGCGTTGCGA
1 TTCGCATTGCGA
428837 ATCTGGAAAC
Statistics
Matches: 128, Mismatches: 19, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
20 34 0.27
21 92 0.72
22 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:428699 original size:62 final size:62
Alignment explanation
Indices: 428633--428758 Score: 216
Period size: 62 Copynumber: 2.0 Consensus size: 62
428623 AACGCAAACT
428633 TCGACTATCGCATTGCAATTTACATATTCGCATTGCGATAGTCCAAGTTCACATTGCGATAG
1 TCGACTATCGCATTGCAATTTACATATTCGCATTGCGATAGTCCAAGTTCACATTGCGATAG
* * * *
428695 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAG
1 TCGACTATCGCATTGCAATTTACATATTCGCATTGCGATAGTCCAAGTTCACATTGCGATAG
428757 TC
1 TC
428759 CAAGTTCGCA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.33
Consensus pattern (62 bp):
TCGACTATCGCATTGCAATTTACATATTCGCATTGCGATAGTCCAAGTTCACATTGCGATAG
Found at i:428701 original size:83 final size:83
Alignment explanation
Indices: 428612--428836 Score: 235
Period size: 83 Copynumber: 2.7 Consensus size: 83
428602 AATGCGAACT
*
428612 TCGACTATCGCAACGCAAACTTCGAC-TA-TCGCATTGCAAT-TTAC-ATA-TTCGCATTGCGAT
1 TCGACTATCGCAACGC-AA-TT-GACATATTCGCATTGCAATAGT-CGA-AGTTCGCATTGCGAT
428672 AGTCCAAGTTCACATTGCGATAG
61 AGTCCAAGTTCACATTGCGATAG
** * * * *
428695 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCC
1 TCGACTATCGCAACGCAATTGACATATTCGCATTGCAATAGTCGAAGTTCGCATTGCGATAGTCC
*
428760 AAGTTCGCATTGCGATAG
66 AAGTTCACATTGCGATAG
** * * * * *
428778 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCGTTGCGA
1 TCGACTATCGCAACGCAATTGACATATTCGCATTGCAATAGTCGAAGTTCGCATTGCGA
428837 ATCTGGAAAC
Statistics
Matches: 128, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
80 2 0.02
81 4 0.03
82 14 0.11
83 108 0.84
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.31
Consensus pattern (83 bp):
TCGACTATCGCAACGCAATTGACATATTCGCATTGCAATAGTCGAAGTTCGCATTGCGATAGTCC
AAGTTCACATTGCGATAG
Found at i:428729 original size:41 final size:41
Alignment explanation
Indices: 428684--428820 Score: 197
Period size: 41 Copynumber: 3.3 Consensus size: 41
428674 TCCAAGTTCA
428684 CATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCG
1 CATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCG
* * * *
428725 CATTGCGATAGTCGAAGT-TCGCGTTGCGATAGTCCA-AGTTCG
1 CATTGCGATAGTCG-ACTATCGCATTGCGAT-TTACATA-TTCG
428767 CATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCG
1 CATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCG
428808 CATTGCGATAGTC
1 CATTGCGATAGTC
428821 CAAGTTCGCG
Statistics
Matches: 83, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
41 48 0.58
42 35 0.42
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (41 bp):
CATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCG
Found at i:428768 original size:62 final size:61
Alignment explanation
Indices: 428640--428836 Score: 215
Period size: 62 Copynumber: 3.2 Consensus size: 61
428630 ACTTCGACTA
* * * *
428640 TCGCATTGCAATTTACATATTCGCATTGCGATAGTCCAAGTTCACATTGCGATAGT-CGACT
1 TCGCATTGCGATTTACATATTCGCATTGCGATAGT-CAAGTTCGCATTGCGATAGTCCAAGT
*
428701 ATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAGT
1 -TCGCATTGCGATTTACATATTCGCATTGCGATAGTC-AAGTTCGCATTGCGATAGTCCAAGT
* *
428764 TCGCATTGCGATAGT-CGACTA-TCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTCCAAG
1 TCGCATTGCGAT-TTAC-A-TATTCGCATTGCGATAGT-CA-AGTTCGCATTGCGATAGTCCAAG
428825 T
61 T
*
428826 TCGCGTTGCGA
1 TCGCATTGCGA
428837 ATCTGGAAAC
Statistics
Matches: 119, Mismatches: 9, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
61 1 0.01
62 97 0.82
63 19 0.16
64 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (61 bp):
TCGCATTGCGATTTACATATTCGCATTGCGATAGTCAAGTTCGCATTGCGATAGTCCAAGT
Found at i:431696 original size:64 final size:64
Alignment explanation
Indices: 431622--431782 Score: 161
Period size: 64 Copynumber: 2.5 Consensus size: 64
431612 ATTGTTTGAA
* *
431622 AGTGTATCGATGCACAGGTAGTGCATCGATGCA-CTATTTTAA-AATAAAAACATCGAATGCA-A
1 AGTGAATCGATGCACAGGTAGTGCATCGATGCAGCCA--TTAATAAT-AAAACATCGAATGCATA
431684 TT
63 TT
* * * *
431686 AGTGCATCGATGCATAAGGCA-TGCATCGATGCATGCCATTAATAATAAAACATCGAATGCATTT
1 AGTGAATCGATGCA-CAGGTAGTGCATCGATGCA-GCCATTAATAATAAAACATCGAATGCATAT
431750 T
64 T
* * *
431751 A-TGAACCGATACACAAGTAGTGCATCGATGCA
1 AGTGAATCGATGCACAGGTAGTGCATCGATGCA
431783 TACCTTCATT
Statistics
Matches: 80, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
63 3 0.04
64 65 0.81
65 10 0.12
66 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (64 bp):
AGTGAATCGATGCACAGGTAGTGCATCGATGCAGCCATTAATAATAAAACATCGAATGCATATT
Found at i:434989 original size:64 final size:64
Alignment explanation
Indices: 434921--435077 Score: 169
Period size: 64 Copynumber: 2.5 Consensus size: 64
434911 TTGAAGGTGT
* ** *
434921 ATCGATGCACAGGTAGGGCATCGATGCA-CTCTTTTAA-AATAAAAACATCTAATGCA-ATTAGT
1 ATCGATGCACAGGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCATATTA-T
434983 GC
63 GC
* * *
434985 ATCGATGCATAAGGCA-TGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATTTTATGC
1 ATCGATGCA-CAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATGC
* *
435049 ACCGATGCACAAGTAGTGCATCGATGCAT
1 ATCGATGCACAGGTAGTGCATCGATGCAT
435078 ACCTTCATTA
Statistics
Matches: 77, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
63 3 0.04
64 63 0.82
65 11 0.14
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (64 bp):
ATCGATGCACAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATGC
Found at i:435622 original size:15 final size:15
Alignment explanation
Indices: 435604--435637 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
435594 GAGGGTATAA
435604 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
435619 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
435634 TAGT
1 TAGT
435638 GGTCCTACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.15, C:0.18, G:0.32, T:0.35
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:437378 original size:33 final size:33
Alignment explanation
Indices: 437304--437381 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 33
437294 AATTAGTACG
*
437304 ATATAAATATATATATGAAACGTATTAAAATTT
1 ATATAAATATAAATATGAAACGTATTAAAATTT
*
437337 A-AGT-AATATAAATTATTAAACTGT-TT-AAATTT
1 ATA-TAAATATAAA-TATGAAAC-GTATTAAAATTT
437369 ATATAAATATAAA
1 ATATAAATATAAA
437382 ACATATTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
32 16 0.42
33 20 0.53
34 2 0.05
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (33 bp):
ATATAAATATAAATATGAAACGTATTAAAATTT
Found at i:443372 original size:23 final size:21
Alignment explanation
Indices: 443318--443378 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
443308 GATTTCTGGG
*
443318 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGATACCCATT
*
443339 CAA-GGGAATCGATACCTATT
1 CAAGGGGAATCGATACCCATT
443359 CAATAGGGGAATCGATACCC
1 C-A-AGGGGAATCGATACCC
443379 CTTAAGCGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 16 0.47
21 4 0.12
22 1 0.03
23 13 0.38
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.20
Consensus pattern (21 bp):
CAAGGGGAATCGATACCCATT
Found at i:444304 original size:31 final size:31
Alignment explanation
Indices: 444266--444421 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
444256 AGGGTCGAGG
444266 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
444297 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
444328 GCTTACCTATGTTCTTCAGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
444359 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
444390 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
444421 G
1 G
444422 GTCCTTCGGG
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:444904 original size:21 final size:21
Alignment explanation
Indices: 444879--444921 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
444869 AAAGAATATA
444879 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
444900 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
444921 T
1 T
444922 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:447207 original size:16 final size:16
Alignment explanation
Indices: 447186--447228 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
447176 GGTAATTAAA
447186 GATTGATAAGGAATTT
1 GATTGATAAGGAATTT
* *
447202 GATTGATTAATGATTTT
1 GATTGA-TAAGGAATTT
*
447219 GAGTGATAAG
1 GATTGATAAG
447229 AACTGATGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.40
Consensus pattern (16 bp):
GATTGATAAGGAATTT
Found at i:448240 original size:23 final size:22
Alignment explanation
Indices: 448196--448240 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
448186 AATCTCATAG
*
448196 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
*
448218 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
448241 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:449087 original size:31 final size:31
Alignment explanation
Indices: 449049--449204 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
449039 AGGGTCGAGG
*
449049 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
449080 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
449111 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
449142 GTTTACCTATGTTCTTCGGGACATATAGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
449173 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
449204 G
1 G
449205 GTACTTCGGG
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:449685 original size:21 final size:21
Alignment explanation
Indices: 449660--449702 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
449650 AAAGAATATA
449660 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
449681 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
449702 T
1 T
449703 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:453524 original size:26 final size:25
Alignment explanation
Indices: 453493--453541 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
453483 AAAAATTAAA
453493 TGAATACATA-AAAACACTAAACTATC
1 TGAATA-ATACAAAACAC-AAACTATC
*
453519 TGAATAATACAAAAGACAAACTA
1 TGAATAATACAAAACACAAACTA
453542 ATCACAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.57, C:0.16, G:0.06, T:0.20
Consensus pattern (25 bp):
TGAATAATACAAAACACAAACTATC
Found at i:453694 original size:15 final size:15
Alignment explanation
Indices: 453674--453726 Score: 106
Period size: 15 Copynumber: 3.5 Consensus size: 15
453664 CAGAGACTAT
453674 GAAGGGAGTGAAGAG
1 GAAGGGAGTGAAGAG
453689 GAAGGGAGTGAAGAG
1 GAAGGGAGTGAAGAG
453704 GAAGGGAGTGAAGAG
1 GAAGGGAGTGAAGAG
453719 GAAGGGAG
1 GAAGGGAG
453727 ACATGGGGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.40, C:0.00, G:0.55, T:0.06
Consensus pattern (15 bp):
GAAGGGAGTGAAGAG
Found at i:462708 original size:12 final size:12
Alignment explanation
Indices: 462693--462719 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
462683 TGTTATTATT
462693 TTTGTTCACACA
1 TTTGTTCACACA
462705 TTTGTTCACACA
1 TTTGTTCACACA
462717 TTT
1 TTT
462720 TAGCGAGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.48
Consensus pattern (12 bp):
TTTGTTCACACA
Found at i:464633 original size:14 final size:14
Alignment explanation
Indices: 464614--464660 Score: 94
Period size: 14 Copynumber: 3.4 Consensus size: 14
464604 TGAATTGCAA
464614 ACATATATACATAG
1 ACATATATACATAG
464628 ACATATATACATAG
1 ACATATATACATAG
464642 ACATATATACATAG
1 ACATATATACATAG
464656 ACATA
1 ACATA
464661 GATTTTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (14 bp):
ACATATATACATAG
Found at i:464678 original size:2 final size:2
Alignment explanation
Indices: 464671--464710 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
464661 GATTTTATTA
464671 AT AT 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 AT AT
464711 TAATAAAATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:468493 original size:3 final size:3
Alignment explanation
Indices: 468485--468528 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
468475 CTAATTTCAT
468485 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
468529 GAGATCCTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:473446 original size:56 final size:55
Alignment explanation
Indices: 473366--473481 Score: 198
Period size: 56 Copynumber: 2.1 Consensus size: 55
473356 TTCCAGCCCG
*
473366 GCCACTCTTATGAGATGATTTCGGTTTCAGAAAACTGAGT-AGGGCAGGCGCAGCC
1 GCCACTCTTATGAGATGATTTCGGTTTCAGAAAACCGAGTCA-GGCAGGCGCAGCC
473421 GACCACTCTTATGAGATGATTTCGGTTTCAGAAAACCGAGTCAGGCAGGCGCAGCC
1 G-CCACTCTTATGAGATGATTTCGGTTTCAGAAAACCGAGTCAGGCAGGCGCAGCC
473477 GCCAC
1 GCCAC
473482 CGACGGGGAA
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
55 5 0.09
56 52 0.90
57 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.22
Consensus pattern (55 bp):
GCCACTCTTATGAGATGATTTCGGTTTCAGAAAACCGAGTCAGGCAGGCGCAGCC
Found at i:473858 original size:165 final size:165
Alignment explanation
Indices: 473661--473995 Score: 661
Period size: 165 Copynumber: 2.0 Consensus size: 165
473651 TTCATGGTAA
473661 AAATTTAAAATAAATCAATAGAACACATATCATTGTTCTGGTCGTAGAGTTTATTTTCACTACCA
1 AAATTTAAAATAAATCAATAGAACACATATCATTGTTCTGGTCGTAGAGTTTATTTTCACTACCA
473726 ATGTATTATATCCTAGGAATTATAAAATAATTTATGTTTTTACATTTAAACTAAATTAAAACTAG
66 ATGTATTATATCCTAGGAATTATAAAATAATTTATGTTTTTACATTTAAACTAAATTAAAACTAG
473791 CAAATTTATATATGATTTACCCAAGATAATGACTC
131 CAAATTTATATATGATTTACCCAAGATAATGACTC
473826 AAATTTAAAATAAATCAATAGAACACATATCATTGTTCTGGTCGTAGAGTTTATTTTCACTACCA
1 AAATTTAAAATAAATCAATAGAACACATATCATTGTTCTGGTCGTAGAGTTTATTTTCACTACCA
473891 ATGTATTATATCCTAGGAATTATAAAATAATTTATGTTTTTACATTTAAACTAAATTAAAACTAG
66 ATGTATTATATCCTAGGAATTATAAAATAATTTATGTTTTTACATTTAAACTAAATTAAAACTAG
*
473956 TAAATTTATATATGATTTACCCAAGATAATGACTC
131 CAAATTTATATATGATTTACCCAAGATAATGACTC
473991 AAATT
1 AAATT
473996 CAGATTTTAA
Statistics
Matches: 169, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
165 169 1.00
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (165 bp):
AAATTTAAAATAAATCAATAGAACACATATCATTGTTCTGGTCGTAGAGTTTATTTTCACTACCA
ATGTATTATATCCTAGGAATTATAAAATAATTTATGTTTTTACATTTAAACTAAATTAAAACTAG
CAAATTTATATATGATTTACCCAAGATAATGACTC
Found at i:477545 original size:10 final size:10
Alignment explanation
Indices: 477530--477558 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
477520 ACATTTCATC
477530 CTTATCCATA
1 CTTATCCATA
477540 CTTATCCATA
1 CTTATCCATA
477550 CTTATCCAT
1 CTTATCCAT
477559 TCCTTATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.31, G:0.00, T:0.41
Consensus pattern (10 bp):
CTTATCCATA
Found at i:482408 original size:23 final size:24
Alignment explanation
Indices: 482382--482426 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
482372 ATTAATCCCA
482382 TTAACCATTTTTA-ATTA-TTAAAT
1 TTAA-CATTTTTAGATTAGTTAAAT
*
482405 TTAATATTTTTAGATTAGTTAA
1 TTAACATTTTTAGATTAGTTAA
482427 TGTTACATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 8 0.42
24 4 0.21
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (24 bp):
TTAACATTTTTAGATTAGTTAAAT
Done.