Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005836.1 Hibiscus syriacus cultivar Beakdansim tig00013680_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: 991970
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:287641 original size:40 final size:42
Alignment explanation
Indices: 287597--287748 Score: 142
Period size: 40 Copynumber: 3.8 Consensus size: 42
287587 AATCTGTAAA
* *
287597 TCGCAATGCGAATTTGT-AAA-TCGCAACACAGAAGTCAAAT
1 TCGCAACGCGAATTTGTCAAATTCGCAACACAAAAGTCAAAT
*
287637 TCGCAACGCG-A-TAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACGCGAATTTGTCAAATTCGCAACACAAAAGTCAAAT
** **
287677 TCGCAACGCGGAA-TT-TCAAATTCGCAAC-TGAATTTCAAAT
1 TCGCAACGC-GAATTTGTCAAATTCGCAACACAAAAGTCAAAT
** *
287717 TCGCAACTAG-ATTT-TCGAATTCGCAACACAAA
1 TCGCAACGCGAATTTGTCAAATTCGCAACACAAA
287749 TTTAATTTCA
Statistics
Matches: 93, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
38 4 0.04
39 19 0.20
40 54 0.58
41 14 0.15
42 2 0.02
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (42 bp):
TCGCAACGCGAATTTGTCAAATTCGCAACACAAAAGTCAAAT
Found at i:287737 original size:20 final size:19
Alignment explanation
Indices: 287671--287743 Score: 92
Period size: 19 Copynumber: 3.7 Consensus size: 19
287661 AACACAAAAG
*
287671 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAA--CTGAATT
287692 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
287711 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACT-GAATT
*
287731 TCGAATTCGCAAC
1 TCAAATTCGCAAC
287744 ACAAATTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
19 20 0.42
20 16 0.33
21 12 0.25
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:287913 original size:16 final size:15
Alignment explanation
Indices: 287878--287916 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
287868 TCCCCGTCTC
*
287878 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
287893 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
287909 TAATTTTT
1 TAATTTTT
287917 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:288686 original size:24 final size:24
Alignment explanation
Indices: 288659--288712 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
288649 GTATTCGAAA
*
288659 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTTGGCCAATACTCGGAC
*
288683 TTTGATCTTGGCCAATACTCGGAT
1 TTTGATCTTGGCCAATACTCGGAC
288707 TTTGAT
1 TTTGAT
288713 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):
TTTGATCTTGGCCAATACTCGGAC
Found at i:291006 original size:18 final size:18
Alignment explanation
Indices: 290972--291007 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
290962 AAGCAAAAGG
**
290972 AAATCAAAATCGTAATCA
1 AAATCAAAATCCCAATCA
290990 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
291008 CTACTGGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:293382 original size:20 final size:20
Alignment explanation
Indices: 293334--293373 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
293324 ATTGTGTTTC
293334 GCGTTGCGAATTCGACTTCT
1 GCGTTGCGAATTCGACTTCT
* *
293354 GCATTGCGAATTTGACTTCT
1 GCGTTGCGAATTCGACTTCT
293374 TTGTTGCGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (20 bp):
GCGTTGCGAATTCGACTTCT
Found at i:293399 original size:20 final size:20
Alignment explanation
Indices: 293376--293463 Score: 77
Period size: 20 Copynumber: 4.3 Consensus size: 20
293366 TGACTTCTTT
293376 GTTGCGATTTACAAATTCAC
1 GTTGCGATTTACAAATTCAC
* *
293396 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAAATTCAC
* ** *
293416 GTTACGAATTTGGAAAATCAC
1 GTTGCG-ATTTACAAATTCAC
** * *
293437 AATGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCAC
293457 GTTGCGA
1 GTTGCGA
293464 AATTGGAGTT
Statistics
Matches: 49, Mismatches: 18, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
20 37 0.76
21 12 0.24
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCAC
Found at i:304782 original size:12 final size:12
Alignment explanation
Indices: 304767--304795 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
304757 TCCTCCACCT
304767 CCTCCTCTGCCG
1 CCTCCTCTGCCG
304779 CCTCCTCTGCCG
1 CCTCCTCTGCCG
304791 CCTCC
1 CCTCC
304796 ACGGCCCCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.62, G:0.14, T:0.24
Consensus pattern (12 bp):
CCTCCTCTGCCG
Found at i:305271 original size:11 final size:10
Alignment explanation
Indices: 305239--305276 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
305229 ATACTTATAT
305239 ATTCAA-TTA
1 ATTCAATTTA
305248 ATTCAATTCTA
1 ATTCAATT-TA
305259 ATTTCAATTTA
1 A-TTCAATTTA
305270 ATTCAAT
1 ATTCAAT
305277 AAATTTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 6 0.23
10 7 0.27
11 6 0.23
12 7 0.27
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.47
Consensus pattern (10 bp):
ATTCAATTTA
Found at i:306686 original size:25 final size:24
Alignment explanation
Indices: 306658--306717 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
306648 AATAGATAGT
*
306658 ATATATAATTTATTAATAATAAGTC
1 ATATATAATTTATTAATAA-AAGTA
* **
306683 ATATA-ACTTTATTAATAAATTTA
1 ATATATAATTTATTAATAAAAGTA
306706 ATATATAATTTA
1 ATATATAATTTA
306718 AAATTACATC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 7 0.24
24 17 0.59
25 5 0.17
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (24 bp):
ATATATAATTTATTAATAAAAGTA
Found at i:307208 original size:23 final size:23
Alignment explanation
Indices: 307167--307210 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
307157 CTTTATTTTA
*
307167 ATTTTATATTAATATTTCATTCG
1 ATTTTATAATAATATTTCATTCG
307190 ATTTATATAATAATA-TTCATT
1 ATTT-TATAATAATATTTCATT
307211 TATTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (23 bp):
ATTTTATAATAATATTTCATTCG
Found at i:307597 original size:21 final size:21
Alignment explanation
Indices: 307573--307644 Score: 126
Period size: 21 Copynumber: 3.4 Consensus size: 21
307563 ATTTTTTACT
307573 ATTTTATAATATGAACGGATC
1 ATTTTATAATATGAACGGATC
*
307594 ATTTTATAATGTGAACGGATC
1 ATTTTATAATATGAACGGATC
*
307615 ATTTTATAATATGAAAGGATC
1 ATTTTATAATATGAACGGATC
307636 ATTTTATAA
1 ATTTTATAA
307645 AATTCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (21 bp):
ATTTTATAATATGAACGGATC
Found at i:316365 original size:24 final size:24
Alignment explanation
Indices: 316338--316385 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
316328 GGCTCGATTT
*
316338 TCTTCCAACAGTCAGACCTTTTAA
1 TCTTCCAACAGTCAAACCTTTTAA
316362 TCTTCCAACAGTCAAACCTTTTAA
1 TCTTCCAACAGTCAAACCTTTTAA
316386 ATTCCAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.33
Consensus pattern (24 bp):
TCTTCCAACAGTCAAACCTTTTAA
Found at i:316757 original size:24 final size:26
Alignment explanation
Indices: 316730--316788 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 26
316720 TCCTACATGG
*
316730 TTAATTT-A-CTTCACTGTAATTTGT
1 TTAATTTCATCTTCAATGTAATTTGT
316754 TTAATTGCTTCATCTTCAATGTAATTTGT
1 TTAA-T--TTCATCTTCAATGTAATTTGT
316783 TTAATT
1 TTAATT
316789 GTTTATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
24 4 0.14
25 1 0.03
26 1 0.03
27 2 0.07
28 2 0.07
29 19 0.66
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.54
Consensus pattern (26 bp):
TTAATTTCATCTTCAATGTAATTTGT
Found at i:316946 original size:20 final size:20
Alignment explanation
Indices: 316886--316948 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 20
316876 ACTTGTTATT
316886 TTGTTAAGGTAATCTGTTTAA
1 TTGTT-AGGTAATCTGTTTAA
** *
316907 TTGTTTATCTATAATATGTTTAA
1 TTG-TTA--GGTAATCTGTTTAA
316930 TTGTTAGGTAATCTGTTTA
1 TTGTTAGGTAATCTGTTTA
316949 GAATTTAGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 10 0.30
21 4 0.12
22 5 0.15
23 14 0.42
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (20 bp):
TTGTTAGGTAATCTGTTTAA
Found at i:319156 original size:21 final size:21
Alignment explanation
Indices: 319118--319175 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
319108 TGAAGCAAGA
*
319118 GAAGCAGAGAGAGTAGCAGCG
1 GAAGCAGAGAGAGAAGCAGCG
*
319139 GAAGCAGAGAAAGAAGCAGCG
1 GAAGCAGAGAGAGAAGCAGCG
* *
319160 GCAGCACAGAGAGAAG
1 GAAGCAGAGAGAGAAG
319176 TAGTATATCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.43, C:0.16, G:0.40, T:0.02
Consensus pattern (21 bp):
GAAGCAGAGAGAGAAGCAGCG
Found at i:319566 original size:44 final size:42
Alignment explanation
Indices: 319513--319649 Score: 202
Period size: 44 Copynumber: 3.1 Consensus size: 42
319503 GTAAAAAAAT
319513 GCCGCAATATACCATACATTTAGCGGTACTTGTATACTAGAAAC
1 GCCGCAATATACCATACATTTAGCGGT--TTGTATACTAGAAAC
*
319557 GCCGCAATATACCATACATTTAGCAGCGTTTGTATATTAGAAAC
1 GCCGCAATATACCATACATTTAGC-G-GTTTGTATACTAGAAAC
*
319601 GCCGCAATATACCAAACATTTAGCGGCGTTTGTATACTAGAAAC
1 GCCGCAATATACCATACATTTAGC-G-GTTTGTATACTAGAAAC
319645 GCCGC
1 GCCGC
319650 TAAAAATCAT
Statistics
Matches: 87, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
44 84 0.97
45 1 0.01
46 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (42 bp):
GCCGCAATATACCATACATTTAGCGGTTTGTATACTAGAAAC
Found at i:319717 original size:43 final size:43
Alignment explanation
Indices: 319670--319758 Score: 106
Period size: 43 Copynumber: 2.1 Consensus size: 43
319660 CACATACTAC
* * * *
319670 GGCGTTTGTGGGAAAAACGCCACTAAACATCAACACCTATTGT
1 GGCGTTTGTCGGAAAAACACCACTAAACAACAAAACCTATTGT
* * * *
319713 GGCGTTTTTCTGACAAACACCACTAAATAACAAAACCTATTGT
1 GGCGTTTGTCGGAAAAACACCACTAAACAACAAAACCTATTGT
319756 GGC
1 GGC
319759 ATTTTTTTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.25
Consensus pattern (43 bp):
GGCGTTTGTCGGAAAAACACCACTAAACAACAAAACCTATTGT
Found at i:324713 original size:12 final size:13
Alignment explanation
Indices: 324696--324735 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
324686 TAAAAGGATT
324696 TTATATAT-TATA
1 TTATATATATATA
324708 TTATATATATATA
1 TTATATATATATA
*
324721 -TATATATATAAA
1 TTATATATATATA
324733 TTA
1 TTA
324736 GTAAATAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 19 0.76
13 6 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTATATATATATA
Found at i:324714 original size:2 final size:2
Alignment explanation
Indices: 324697--324730 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
324687 AAAAGGATTT
324697 TA TA TA T- TA TA T- 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
324731 AATTAGTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:326647 original size:17 final size:18
Alignment explanation
Indices: 326613--326645 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
326603 TTTTGTTTGT
326613 AATTTATTTAAGTATTTA
1 AATTTATTTAAGTATTTA
326631 AATTT-TTTAA-TATTT
1 AATTTATTTAAGTATTT
326646 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 (18 bp):
AATTTATTTAAGTATTTA
Found at i:333601 original size:17 final size:17
Alignment explanation
Indices: 333568--333602 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
333558 TGAGAGGTTC
**
333568 AATGAGAGTTTTTTTAA
1 AATGAGAGTTTAATTAA
333585 AATGAGAGTTTAATTAA
1 AATGAGAGTTTAATTAA
333602 A
1 A
333603 TTTAGACCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (17 bp):
AATGAGAGTTTAATTAA
Found at i:333906 original size:20 final size:20
Alignment explanation
Indices: 333881--333934 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
333871 GATCAACAAA
333881 TTCACAACGCGAATTCCAAT
1 TTCACAACGCGAATTCCAAT
*
333901 TTCACAACTC-AATTTCCAAT
1 TTCACAACGCGAA-TTCCAAT
*
333921 TTCGCAACGCGAAT
1 TTCACAACGCGAAT
333935 ATGTAAATCG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 2 0.07
20 25 0.86
21 2 0.07
ACGTcount: A:0.33, C:0.30, G:0.09, T:0.28
Consensus pattern (20 bp):
TTCACAACGCGAATTCCAAT
Found at i:333967 original size:20 final size:20
Alignment explanation
Indices: 333944--333984 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
333934 TATGTAAATC
333944 GCAACAC-AGAAGTCAAATTT
1 GCAACACGA-AAGTCAAATTT
*
333964 GCAACGCGAAAGTCAAATTT
1 GCAACACGAAAGTCAAATTT
333984 G
1 G
333985 TAAATCACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
GCAACACGAAAGTCAAATTT
Found at i:333990 original size:47 final size:47
Alignment explanation
Indices: 333936--334028 Score: 141
Period size: 47 Copynumber: 2.0 Consensus size: 47
333926 AACGCGAATA
* * *
333936 TGTAAATCGCAACACAGAAGTCAAATTTGCAACGCGAAAGTCAAATT
1 TGTAAATCACAACACAGAAGTCAAATTCGCAACACGAAAGTCAAATT
* *
333983 TGTAAATCACAACACATAAGTCATATTCGCAACACGAAAGTCAAAT
1 TGTAAATCACAACACAGAAGTCAAATTCGCAACACGAAAGTCAAAT
334029 ATTTTTACGC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.22
Consensus pattern (47 bp):
TGTAAATCACAACACAGAAGTCAAATTCGCAACACGAAAGTCAAATT
Found at i:336698 original size:42 final size:42
Alignment explanation
Indices: 336651--336750 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
336641 GCCCGATGCA
* * *
336651 CCTATCATCATTCAAGAGGCGCC-TCCTATCGTTCAAGAGGCC
1 CCTATCATCATTCAAGAAGC-CCATCCCACCGTTCAAGAGGCC
336693 CCTATCATCA-TCGAAGAAGCCCATCCCACCGTTCAAGAGGCC
1 CCTATCATCATTC-AAGAAGCCCATCCCACCGTTCAAGAGGCC
*
336735 CCTATCATCGTTCAAG
1 CCTATCATCATTCAAG
336751 TGTTCCCGCC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
41 4 0.08
42 45 0.88
43 2 0.04
ACGTcount: A:0.26, C:0.35, G:0.17, T:0.22
Consensus pattern (42 bp):
CCTATCATCATTCAAGAAGCCCATCCCACCGTTCAAGAGGCC
Found at i:336746 original size:21 final size:21
Alignment explanation
Indices: 336651--336750 Score: 87
Period size: 21 Copynumber: 4.8 Consensus size: 21
336641 GCCCGATGCA
* *
336651 CCTATCATCATTCAAGAGGCG
1 CCTATCATCGTTCAAGAGGCC
*
336672 CCT-CCTATCGTTCAAGAGGCC
1 CCTATC-ATCGTTCAAGAGGCC
* *
336693 CCTATCATC-ATCGAAGAAGCC
1 CCTATCATCGTTC-AAGAGGCC
* ** *
336714 CATCCCACCGTTCAAGAGGCC
1 CCTATCATCGTTCAAGAGGCC
336735 CCTATCATCGTTCAAG
1 CCTATCATCGTTCAAG
336751 TGTTCCCGCC
Statistics
Matches: 59, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
20 3 0.05
21 53 0.90
22 3 0.05
ACGTcount: A:0.26, C:0.35, G:0.17, T:0.22
Consensus pattern (21 bp):
CCTATCATCGTTCAAGAGGCC
Found at i:338197 original size:61 final size:66
Alignment explanation
Indices: 338114--338254 Score: 168
Period size: 66 Copynumber: 2.2 Consensus size: 66
338104 TTTTACATTG
338114 AAAGTTGATTTG-TTACAATTGATGAGGAAATAAG-A-T-TTATTTT-TTGATTAATTGATTTGT
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGT
338174 A
66 A
* * ** * * *
338175 AAAGTTAATTTGTTTA-ATTTGATTTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTG
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTT-CTTGATTAATTGATTTG
338239 TA
65 TA
338241 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
338255 GTTACTAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
61 25 0.38
62 4 0.06
63 1 0.02
64 6 0.09
66 30 0.45
ACGTcount: A:0.32, C:0.01, G:0.16, T:0.50
Consensus pattern (66 bp):
AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGT
A
Found at i:338619 original size:39 final size:39
Alignment explanation
Indices: 338565--338651 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
338555 TCAAGTTGTA
338565 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
338604 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
338643 GATTTTGAT
1 GATTTTGAT
338652 GAGCATCGGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:338976 original size:18 final size:18
Alignment explanation
Indices: 338955--338991 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
338945 CAAAATTTAT
338955 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
338973 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
338991 A
1 A
338992 CTCCAATTAC
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:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:339414 original size:24 final size:25
Alignment explanation
Indices: 339378--339426 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
339368 ATTATTTTTC
* *
339378 CAAATAATGTA-CCATAACAATGTT
1 CAAATAATATACCCACAACAATGTT
339402 CAAATAATATACCCACAACAATGTT
1 CAAATAATATACCCACAACAATGTT
339427 TAATTGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.47, C:0.20, G:0.06, T:0.27
Consensus pattern (25 bp):
CAAATAATATACCCACAACAATGTT
Found at i:339510 original size:20 final size:20
Alignment explanation
Indices: 339487--339528 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
339477 AGACCTGTTG
*
339487 AAGGTAAATTCGCAACGCGA
1 AAGGTAAATTCACAACGCGA
339507 AAGGTAAATTCACAACGCGA
1 AAGGTAAATTCACAACGCGA
339527 AA
1 AA
339529 TAAGCGTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.14
Consensus pattern (20 bp):
AAGGTAAATTCACAACGCGA
Found at i:340652 original size:20 final size:19
Alignment explanation
Indices: 340616--340686 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
340606 ACTAAAACCT
*
340616 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTC-C
*
340635 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCC
**
340654 GTTGCGAATTTGACTTTCAC
1 GTTGCGAATTTGAAATTC-C
340674 GTTGCGAATTTGA
1 GTTGCGAATTTGA
340687 CTTTTACGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 26 0.58
20 19 0.42
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCC
Found at i:340687 original size:20 final size:20
Alignment explanation
Indices: 340634--340708 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
340624 ATTAAATTCG
**
340634 CGTTGCGAATTTGAAATTCA
1 CGTTGCGAATTTGACTTTCA
340654 -GTTGCGAATTTGACTTTCA
1 CGTTGCGAATTTGACTTTCA
*
340673 CGTTGCGAATTTGACTTTTA
1 CGTTGCGAATTTGACTTTCA
*
340693 CGTTGAGAATTTGACT
1 CGTTGCGAATTTGACT
340709 ATCGCAACGT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.34
20 33 0.66
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (20 bp):
CGTTGCGAATTTGACTTTCA
Found at i:340734 original size:21 final size:21
Alignment explanation
Indices: 340699--340778 Score: 126
Period size: 21 Copynumber: 3.9 Consensus size: 21
340689 TTTACGTTGA
* *
340699 GAATTT-GACTATCGCAACGT
1 GAATTTGGAATATCGCAACGC
340719 GAATTTGGAATATCGCAACGC
1 GAATTTGGAATATCGCAACGC
340740 GAATTTGGAATATCGCAACGC
1 GAATTTGGAATATCGCAACGC
*
340761 GAATTTGGAAAATCGCAA
1 GAATTTGGAATATCGCAA
340779 TACGATTTAC
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 6 0.11
21 50 0.89
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (21 bp):
GAATTTGGAATATCGCAACGC
Found at i:342368 original size:3 final size:3
Alignment explanation
Indices: 342360--342400 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
342350 TATACTGTTT
*
342360 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
342401 GTGCTCACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:344185 original size:31 final size:31
Alignment explanation
Indices: 344056--344219 Score: 91
Period size: 31 Copynumber: 5.1 Consensus size: 31
344046 ATAACATGAC
* **
344056 ATATGATTCATGTCACATGTCAAAAGCGATG
1 ATATGATACATGTCACATGTCAAAATTGATG
** *
344087 ATATGATACATGTCATGTGTAAAAAATAATG-TG
1 ATATGATACATGTCACATGT-CAAAAT--TGATG
* * * * *
344120 ATAT-ATATCACGTATCAAAATTTTAAAAATGATG
1 ATATGATA-CA--TGTC-ACATGTCAAAATTGATG
*
344154 ATATGATACATGTCACGTGTCAAAATTGATG
1 ATATGATACATGTCACATGTCAAAATTGATG
* * **
344185 A-AGTGATACATGTCATATTTCAAAAGAGATG
1 ATA-TGATACATGTCACATGTCAAAATTGATG
344216 ATAT
1 ATAT
344220 AACAGTCTTA
Statistics
Matches: 99, Mismatches: 23, Indels: 22
0.69 0.16 0.15
Matches are distributed among these distances:
30 1 0.01
31 55 0.56
32 11 0.11
33 10 0.10
34 9 0.09
35 10 0.10
36 3 0.03
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.32
Consensus pattern (31 bp):
ATATGATACATGTCACATGTCAAAATTGATG
Found at i:352198 original size:21 final size:22
Alignment explanation
Indices: 352151--352205 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
352141 GGGTATATTA
352151 GTCATTCGGGACGTATACAGTG
1 GTCATTCGGGACGTATACAGTG
352173 GTCATTCGGGACGTAT-CTAG-G
1 GTCATTCGGGACGTATAC-AGTG
*
352194 GTCATTTGGGAC
1 GTCATTCGGGAC
352206 AAATACTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 13 0.42
22 18 0.58
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (22 bp):
GTCATTCGGGACGTATACAGTG
Found at i:353913 original size:361 final size:364
Alignment explanation
Indices: 353238--354210 Score: 1437
Period size: 361 Copynumber: 2.7 Consensus size: 364
353228 GGGGTGTTAC
* * * * *
353238 AAAACCTGTCACGAAAAGACAAAACCGGTAAAGCGCTACCGGATATATTGCACGTGTTGATGCTT
1 AAAACCGGTCACGAAAAGACAAAACCGGTAAAGCGCTACCAGATATATTGCAAGTGTCGATACTT
353303 TAATATAAGTATCG--ACA-TAGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCG
66 TAATATAAGTATCGACACATTA-TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCG
* * * *
353365 ATTCTTTATAAATATGTATCGATCCACAATGATATAAAAGGTAAAAATATGACAAAGCCGGTCAG
130 ATTCTTTATAAATATGTATCGATCCACAACGATATAAAAGGTAAAAATATGAAAAAACTGGTCAG
* * * *
353430 GAAAAGAC--AACTGGTAAAGAGATATCAGATATACTGCAAGTGTCGATATTTTAATATAAGTAT
195 GAAAAGACAAAACCGGTAAAGAGATACCAGATATATTGCAAGTGTCGATACTTTAATATAAGTAT
353493 CAACACATTGTGAATTTAAAGGAGAAGTAGTTTTAGCGCCTATAAAATGTCGATTCTTTATAAAT
260 CAACACATTGTGAATTTAAAGGAGAAGTAGTTTTAGCGCCTATAAAATGTCGATTCTTTATAAAT
**
353558 ATGTATCGATTTACAACGATATAACAAGTAAAAATATGAT
325 ATGTATCGATCCACAACGATATAACAAGTAAAAATATGAT
* * * * *
353598 AAAATCGGTCAGGAAAAGACAAAACCGGTAAAGAGATACCATATATATTGCAAGTGTCGATACTT
1 AAAACCGGTCACGAAAAGACAAAACCGGTAAAGCGCTACCAGATATATTGCAAGTGTCGATACTT
353663 TAATATAAGTATCGACACATTATGAATTT-AAAG-G-AGCAGTTTTAGCGCCTATAAAGTGTCGA
66 TAATATAAGTATCGACACATTATGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGA
*
353725 TTCTTTATAAATATGTATCGATCCACAACGATATAATAGGTAAAAATATGAAAAAACTGGTCAGG
131 TTCTTTATAAATATGTATCGATCCACAACGATATAAAAGGTAAAAATATGAAAAAACTGGTCAGG
353790 AAAAGACAAAACCGGTAAAGAGATACCAGATATATTGCAAGTGTCGATACTTTAATATAAGTATC
196 AAAAGACAAAACCGGTAAAGAGATACCAGATATATTGCAAGTGTCGATACTTTAATATAAGTATC
* * *
353855 GACACATTGTGAATTTAAAGGAGAAGTAGTTTTAGCGCCTATAAAGTGTTGATTCTTTATAAATA
261 AACACATTGTGAATTTAAAGGAGAAGTAGTTTTAGCGCCTATAAAATGTCGATTCTTTATAAATA
*
353920 TGTATCGATCCACAACGATATAACAGGTAAAAATATGAT
326 TGTATCGATCCACAACGATATAACAAGTAAAAATATGAT
* * * *
353959 AAAACCGGTCTCGAAAAGACAAAACCTGTAAAGCGCTACCAGATATATTGAAAGTGTCGATAATT
1 AAAACCGGTCACGAAAAGACAAAACCGGTAAAGCGCTACCAGATATATTGCAAGTGTCGATACTT
* *
354024 TAATATAAGTATCGACACTTTGTGAATTTAAAAGAGAAGCA-TATTTAGCGCCTATAAAGTGTCG
66 TAATATAAGTATCGACACATTATGAATTTAAAAGAGAAGCAGT-TTTAGCGCCTATAAAGTGTCG
* * * * * *
354088 ATACTTTATAAAAATGTATCGATCCATAACGATATAACAGGTAAAAATATGATAAAA-TCGGTCT
130 ATTCTTTATAAATATGTATCGATCCACAACGATATAAAAGGTAAAAATATGAAAAAACT-GGTCA
** * *** *
354152 CTAAATGACAAAACCGGTAAAGCCCTACCGGATATATTG-AACGTGTCGATACTTTAATA
194 GGAAAAGACAAAACCGGTAAAGAGATACCAGATATATTGCAA-GTGTCGATACTTTAATA
354211 AGTACGCATA
Statistics
Matches: 553, Mismatches: 49, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
359 95 0.17
360 70 0.13
361 237 0.43
362 14 0.03
363 7 0.01
364 130 0.24
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.28
Consensus pattern (364 bp):
AAAACCGGTCACGAAAAGACAAAACCGGTAAAGCGCTACCAGATATATTGCAAGTGTCGATACTT
TAATATAAGTATCGACACATTATGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGA
TTCTTTATAAATATGTATCGATCCACAACGATATAAAAGGTAAAAATATGAAAAAACTGGTCAGG
AAAAGACAAAACCGGTAAAGAGATACCAGATATATTGCAAGTGTCGATACTTTAATATAAGTATC
AACACATTGTGAATTTAAAGGAGAAGTAGTTTTAGCGCCTATAAAATGTCGATTCTTTATAAATA
TGTATCGATCCACAACGATATAACAAGTAAAAATATGAT
Found at i:354001 original size:182 final size:182
Alignment explanation
Indices: 353238--354210 Score: 1388
Period size: 182 Copynumber: 5.4 Consensus size: 182
353228 GGGGTGTTAC
* * * * * * *
353238 AAAACCTGTCACGAAAAGACAAAACCGGTAAAGCGCTACCGGATATATTGCACGTGTTGATGCTT
1 AAAACCGGTCACGAAAAGACAAAACCGGTAAAGAGATACCAGATATATTGCAAGTGTCGATACTT
*
353303 TAATATAAGTATCG--ACATAGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGA
66 TAATATAAGTATCGACACATTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGA
* * *
353366 TTCTTTATAAATATGTATCGATCCACAATGATATAAAAGGTAAAAATATGAC
131 TTCTTTATAAATATGTATCGATCCACAACGATATAACAGGTAAAAATATGAT
* * * * * *
353418 AAAGCCGGTCAGGAAAAGAC--AACTGGTAAAGAGATATCAGATATACTGCAAGTGTCGATATTT
1 AAAACCGGTCACGAAAAGACAAAACCGGTAAAGAGATACCAGATATATTGCAAGTGTCGATACTT
* * * *
353481 TAATATAAGTATCAACACATTGTGAATTTAAAGGAGAAGTAGTTTTAGCGCCTATAAAATGTCGA
66 TAATATAAGTATCGACACATTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGA
** *
353546 TTCTTTATAAATATGTATCGATTTACAACGATATAACAAGTAAAAATATGAT
131 TTCTTTATAAATATGTATCGATCCACAACGATATAACAGGTAAAAATATGAT
* * *
353598 AAAATCGGTCAGGAAAAGACAAAACCGGTAAAGAGATACCATATATATTGCAAGTGTCGATACTT
1 AAAACCGGTCACGAAAAGACAAAACCGGTAAAGAGATACCAGATATATTGCAAGTGTCGATACTT
*
353663 TAATATAAGTATCGACACATTATGAATTT-AAAG-G-AGCAGTTTTAGCGCCTATAAAGTGTCGA
66 TAATATAAGTATCGACACATTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGA
* *
353725 TTCTTTATAAATATGTATCGATCCACAACGATATAATAGGTAAAAATATGAA
131 TTCTTTATAAATATGTATCGATCCACAACGATATAACAGGTAAAAATATGAT
* *
353777 AAAACTGGTCAGGAAAAGACAAAACCGGTAAAGAGATACCAGATATATTGCAAGTGTCGATACTT
1 AAAACCGGTCACGAAAAGACAAAACCGGTAAAGAGATACCAGATATATTGCAAGTGTCGATACTT
* * *
353842 TAATATAAGTATCGACACATTGTGAATTTAAAGGAGAAGTAGTTTTAGCGCCTATAAAGTGTTGA
66 TAATATAAGTATCGACACATTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGA
353907 TTCTTTATAAATATGTATCGATCCACAACGATATAACAGGTAAAAATATGAT
131 TTCTTTATAAATATGTATCGATCCACAACGATATAACAGGTAAAAATATGAT
* * * * * *
353959 AAAACCGGTCTCGAAAAGACAAAACCTGTAAAGCGCTACCAGATATATTGAAAGTGTCGATAATT
1 AAAACCGGTCACGAAAAGACAAAACCGGTAAAGAGATACCAGATATATTGCAAGTGTCGATACTT
*
354024 TAATATAAGTATCGACACTTTGTGAATTTAAAAGAGAAGCA-TATTTAGCGCCTATAAAGTGTCG
66 TAATATAAGTATCGACACATTGTGAATTTAAAAGAGAAGCAGT-TTTAGCGCCTATAAAGTGTCG
* * *
354088 ATACTTTATAAAAATGTATCGATCCATAACGATATAACAGGTAAAAATATGAT
130 ATTCTTTATAAATATGTATCGATCCACAACGATATAACAGGTAAAAATATGAT
* * * * *** *
354141 AAAATCGGTCTCTAAATGACAAAACCGGTAAAGCCCTACCGGATATATTG-AACGTGTCGATACT
1 AAAACCGGTCACGAAAAGACAAAACCGGTAAAGAGATACCAGATATATTGCAA-GTGTCGATACT
354205 TTAATA
65 TTAATA
354211 AGTACGCATA
Statistics
Matches: 712, Mismatches: 72, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
178 46 0.06
179 163 0.23
180 130 0.18
181 7 0.01
182 366 0.51
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.28
Consensus pattern (182 bp):
AAAACCGGTCACGAAAAGACAAAACCGGTAAAGAGATACCAGATATATTGCAAGTGTCGATACTT
TAATATAAGTATCGACACATTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGA
TTCTTTATAAATATGTATCGATCCACAACGATATAACAGGTAAAAATATGAT
Found at i:356692 original size:33 final size:33
Alignment explanation
Indices: 356655--356721 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
356645 AAATAGATGG
356655 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
*
356688 AGTGGTGAAAGTAGTTGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
356721 A
1 A
356722 CTTAAGATGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.00, G:0.48, T:0.25
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
Found at i:356930 original size:18 final size:18
Alignment explanation
Indices: 356907--356980 Score: 121
Period size: 18 Copynumber: 4.1 Consensus size: 18
356897 AAAAAATATA
356907 AAGAAGAAAAGAGGGAGG
1 AAGAAGAAAAGAGGGAGG
*
356925 AAGAAGAAATGAGGGAGG
1 AAGAAGAAAAGAGGGAGG
*
356943 AAGAAAAAAAGAGGGAGG
1 AAGAAGAAAAGAGGGAGG
*
356961 AAGAAGAAAAGATGGAGG
1 AAGAAGAAAAGAGGGAGG
356979 AA
1 AA
356981 ATGAGGAGGA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 51 1.00
ACGTcount: A:0.57, C:0.00, G:0.41, T:0.03
Consensus pattern (18 bp):
AAGAAGAAAAGAGGGAGG
Found at i:358543 original size:19 final size:19
Alignment explanation
Indices: 358519--358566 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
358509 AATGTAAAGT
358519 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
358538 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
358557 TAATTTTGTA
1 TAATTTTGTA
358567 CGTGGATGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.54
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:359181 original size:200 final size:200
Alignment explanation
Indices: 358831--360215 Score: 2121
Period size: 200 Copynumber: 6.9 Consensus size: 200
358821 GTAAGCATAT
* * *
358831 GTGTCGATACATTTATAAAACGTGTCGATCCCAAAAATATCGAAACATATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACAAATAATTATAATGTAATA
* * *
358896 TGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATATGAGAATAGGTGTACATAATGT
66 GGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGT
* * *
358961 TTCGACACTTTTTAATTTTGTGTCGATACTTTTTGTCCAGAATAAATGCCAAAAATGATGAACGA
131 ATCGACACTTTTTTATTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAATGATGAACGA
359026 ATAAA
196 ATAAA
* *
359031 GTATCGATACATTTATAAAAAGTGTCGATCCCAAAAACAT-GAAAACAAATAACTATAATGTAAT
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCG-AAACAAATAATTATAATGTAAT
* *
359095 AGGTAATTTTGTATTATAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATG
65 AGGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATG
*
359160 TATCGACACTTTTTTATTTTGTGTCGATACTTTTTGTCCATAATGAATGCCAAAAATGATGAACG
130 TATCGACACTTTTTTATTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAATGATGAACG
*
359225 AATAAG
195 AATAAA
*
359231 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAATAAATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACAAATAATTATAATGTAATA
* * * * *
359296 GATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGTGAGAATAGTTTTATATAATGT
66 GGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGT
*
359361 ATCGACATTTTTTTATTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAATGATGAACGA
131 ATCGACACTTTTTTATTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAATGATGAACGA
359426 ATAAA
196 ATAAA
* * *
359431 GTGTCGATACATTTATAAAAAGTGTCGATCTCAAATACATCGAAACATATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACAAATAATTATAATGTAATA
* *
359496 GGTAATTTTGTAATATAACCGATATAAATATACCGGTTTTATGTGGGAATAGGTCTACATAATGT
66 GGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGT
* * *
359561 ATCGACACTATTTTATTTTGTGTCGATACTTTTTTTCCAGAATGAATGCCAGAAATGATGAACGA
131 ATCGACACTTTTTTATTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAATGATGAACGA
359626 ATAAA
196 ATAAA
*
359631 GTGTTGATACATTTATAAAAAGTGTCGA-CCCTAAAAACATCGAAACAAATAATTATAATGTAAT
1 GTGTCGATACATTTATAAAAAGTGTCGATCCC-AAAAACATCGAAACAAATAATTATAATGTAAT
* * * *
359695 AGGTAATTTTGTAATATAATCGATATAAATATACCGATTTTATGTAAGAATAGGTCTACATAATG
65 AGGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATG
* * * * *
359760 TATCGATACCTTTTTATTTTGTGTCGATACTTTTTGTCCAGAATGAATGCAAAAAAGGATGAATG
130 TATCGACACTTTTTTATTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAATGATGAACG
359825 AATAAA
195 AATAAA
* * * * * *
359831 GTGACGATACATTTATATAAAGTGTTGATCCCAAAAATATCAAAACAGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACAAATAATTATAATGTAATA
* * * * * *
359896 TGTAATTTTGTAATATAACCAGTATAAATATATCGGTTTTATATAAGAATAGGTCTATATAATGT
66 GGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGT
* * * * *
359961 ATCGATATTTTTTTATTTTGTGT-AATACTTTTTGTCCAGAATGAGTGCCAAAAAGGATGAACGA
131 ATCGACACTTTTTTATTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAATGATGAACGA
360025 ATAAA
196 ATAAA
* *
360030 GTGTCGATACATTTATAAAAAGTGTCGATCCCATAAACATCGAAACAGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACAAATAATTATAATGTAATA
* * * *
360095 GGTAATTTTATAATATAACCGATATAAATATACCGGTTTTATGTAAGAATATGTCTACATAATAG
66 GGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAAT-G
* *
360160 -ATCGACATTTTTTTTATTTTGTGTCGATAGTTTTTGTCCAGAATGAATGCCAAAAA
130 TATCGACA-CTTTTTTATTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAA
360216 CATCGAAACC
Statistics
Matches: 1082, Mismatches: 96, Indels: 13
0.91 0.08 0.01
Matches are distributed among these distances:
199 165 0.15
200 885 0.82
201 32 0.03
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (200 bp):
GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACAAATAATTATAATGTAATA
GGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGT
ATCGACACTTTTTTATTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAATGATGAACGA
ATAAA
Found at i:360239 original size:149 final size:148
Alignment explanation
Indices: 360064--360350 Score: 357
Period size: 149 Copynumber: 1.9 Consensus size: 148
360054 TCGATCCCAT
* * * * *
360064 AAACATCGAAACAGATAATTATAATGTAATAGGTAATTTTATAATATAACCGATATAA-ATATAC
1 AAACATCGAAACACATAAATATAATGTAATAAGTAAATTTACAATATAACCGATATAACA-ATAC
* * * ** *
360128 CGGTTTTATGTA-AGAATATGTCTACATA-ATAG-ATCGACATTTTTTTTATTTTGTGTCGATAG
65 CGGTTTTATG-AGAGAATAGGTCTACA-ACAT-GTATCGACA-CTTGTGGAATTTGTGTCGATAG
360190 TTTTTGTCCAGAATGAATGCCAA
126 TTTTTGTCCAGAATGAATGCCAA
* * * *
360213 AAACATCGAAACCCATAAATATAATGTAATAAGTAAATTTACAATGTAACCGGTATAACAATATC
1 AAACATCGAAACACATAAATATAATGTAATAAGTAAATTTACAATATAACCGATATAACAATACC
*
360278 GGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTGGAATTTGTGTCGATATTTTTT
66 GGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTGGAATTTGTGTCGATAGTTTTT
360343 GTCCAGAA
131 GTCCAGAA
360351 GGAAATCCAA
Statistics
Matches: 118, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
148 32 0.27
149 85 0.72
150 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (148 bp):
AAACATCGAAACACATAAATATAATGTAATAAGTAAATTTACAATATAACCGATATAACAATACC
GGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTGGAATTTGTGTCGATAGTTTTT
GTCCAGAATGAATGCCAA
Found at i:360513 original size:347 final size:348
Alignment explanation
Indices: 359861--360513 Score: 820
Period size: 347 Copynumber: 1.9 Consensus size: 348
359851 AGTGTTGATC
* * * * * **
359861 CCAAAAATATCAAAACAGATAATTATAATGTAATATGTAATTTTGTAATATAACCAGTATAAATA
1 CCAAAAACATCAAAACACATAAATATAATGTAATAAGTAAATTTACAATATAACCAGTATAAATA
* * * * ** *
359926 TATCGGTTTTATATAAGAATAGGTCTATATAATGTATCGATATTTTTTTATTTTGTGTAATACTT
66 TATCGGTTTTATATAAGAATAGGTCTACATAATGTATCGACACTTGTGGAATTTGTGTAATACTT
* * *
359991 TTTGTCCAGAATGAGTGCCAAAAAGGATGAACGAATAAAGTGTCGATACATTTATAAAAAGTGTC
131 TTTGTCCAGAAGGAATGCCAAAAAGGATGAACGAATAAAGTGTCGATACATTTATAAAAAGTATC
* * *
360056 GATCCCATAAACATCGAAACAGATAATTATAATGTAATAGGTAATTTTATAATATAACCGATATA
196 GATCCCATAAACATCGAAACAGATAATTATAATGTAATAGGTAAATTTACAATATAAACGATATA
* * * *
360121 AATATACCGGTTTTATGTAAGAATATGTCTACATAATAGATCGACATTTTTTTTATTTTGTGTCG
261 AATATACCGATTTTATGTAAAAATAGGTCTACATAAAAGATCGACATTTTTTTTATTTTGTGTCG
360186 ATAGTTTTTGTCCAGAATGAATG
326 ATAGTTTTTGTCCAGAATGAATG
* * * *
360209 CCAAAAACATCGAAACCCATAAATATAATGTAATAAGTAAATTTACAATGTAACCGGTATAACA-
1 CCAAAAACATCAAAACACATAAATATAATGTAATAAGTAAATTTACAATATAACCAGTATAA-AT
* *
360273 ATATCGGTTTTATGA-GAGAATAGGTCTACA-ACATGTATCGACACTTGTGGAATTTGTGTCGAT
65 ATATCGGTTTTAT-ATAAGAATAGGTCTACATA-ATGTATCGACACTTGTGGAATTTGTGT-AAT
* * * * *
360336 ATTTTTTGTCCAGAAGGAAAT-CC-AAAA-GTTGCACGCATAAAGTGTCGATACATTTTTAAAAA
127 ACTTTTTGTCCAGAAGG-AATGCCAAAAAGGATGAACGAATAAAGTGTCGATACATTTATAAAAA
* *
360398 GTATCGATCCCA-ATAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTCCAATATAAAC
191 GTATCGATCCCATA-AACATCGAAACAGATAATTATAATGTAATAGGTAAATTTACAATATAAAC
* *
360462 GGTATAAATATACCGATTTTATG-AGAAAATAGGTC-ATCATAAAATATCGACA
255 GATATAAATATACCGATTTTATGTA-AAAATAGGTCTA-CATAAAAGATCGACA
360514 ATTATTAAAT
Statistics
Matches: 258, Mismatches: 39, Indels: 17
0.82 0.12 0.05
Matches are distributed among these distances:
346 3 0.01
347 130 0.50
348 102 0.40
349 21 0.08
350 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (348 bp):
CCAAAAACATCAAAACACATAAATATAATGTAATAAGTAAATTTACAATATAACCAGTATAAATA
TATCGGTTTTATATAAGAATAGGTCTACATAATGTATCGACACTTGTGGAATTTGTGTAATACTT
TTTGTCCAGAAGGAATGCCAAAAAGGATGAACGAATAAAGTGTCGATACATTTATAAAAAGTATC
GATCCCATAAACATCGAAACAGATAATTATAATGTAATAGGTAAATTTACAATATAAACGATATA
AATATACCGATTTTATGTAAAAATAGGTCTACATAAAAGATCGACATTTTTTTTATTTTGTGTCG
ATAGTTTTTGTCCAGAATGAATG
Found at i:362053 original size:6 final size:6
Alignment explanation
Indices: 362013--362065 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
362003 CAAGAGTTCA
* * * * *
362013 ATGAAG ATGAAG ATGACG ATGAAG ATGATG ATGATG ATGATG ATTATG
1 ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG
362061 ATGAT
1 ATGAT
362066 CCAAACAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.40, C:0.02, G:0.30, T:0.28
Consensus pattern (6 bp):
ATGATG
Found at i:363061 original size:11 final size:11
Alignment explanation
Indices: 363045--363107 Score: 72
Period size: 11 Copynumber: 5.5 Consensus size: 11
363035 CGTTGTGGGT
363045 ACATTATTTGA
1 ACATTATTTGA
363056 ACATTATTTGA
1 ACATTATTTGA
*
363067 ACATTGTTATGTA
1 ACATTATT-TG-A
*
363080 TAAATTATTTGA
1 -ACATTATTTGA
*
363092 ACATTACTTGA
1 ACATTATTTGA
363103 ACATT
1 ACATT
363108 GTTATGTATA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
11 32 0.73
12 3 0.07
13 3 0.07
14 6 0.14
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.44
Consensus pattern (11 bp):
ACATTATTTGA
Found at i:363094 original size:36 final size:36
Alignment explanation
Indices: 363047--363121 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
363037 TTGTGGGTAC
*
363047 ATTATTTGAACATTATTTGAACATTGTTATGTATAA
1 ATTATTTGAACATTACTTGAACATTGTTATGTATAA
363083 ATTATTTGAACATTACTTGAACATTGTTATGTATAA
1 ATTATTTGAACATTACTTGAACATTGTTATGTATAA
363119 ATT
1 ATT
363122 TCTTGTGTAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.47
Consensus pattern (36 bp):
ATTATTTGAACATTACTTGAACATTGTTATGTATAA
Found at i:363399 original size:15 final size:15
Alignment explanation
Indices: 363379--363417 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
363369 TCTCCATAAC
* *
363379 AAAGTTTTCATACAT
1 AAAGTTTCCAAACAT
*
363394 AAAGTTTCCAAACTT
1 AAAGTTTCCAAACAT
363409 AAAGTTTCC
1 AAAGTTTCC
363418 CATAAAGTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (15 bp):
AAAGTTTCCAAACAT
Found at i:363760 original size:199 final size:198
Alignment explanation
Indices: 363418--364183 Score: 921
Period size: 199 Copynumber: 3.8 Consensus size: 198
363408 TAAAGTTTCC
* * * *
363418 CATAAAGTGTCGATACAGTTT-TAAAACGTATCGATCCCAGAAACATCGAAATCAATAAATATAA
1 CATAAAGTGTCGATACA-TTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAAATATAA
* ** * * * *
363482 TGTAATAGGTAATTTTGTATTATAACTGGTATAAATATACCGGTTTTAT-ATGAGAATAGATCTA
65 TGTAATAGGTAAATTTACAATATAACCGGTATAAATATACCGGTTTTATGA-GAAAATAGATATA
* *
363546 CATAATGTGTCGACACTTGTAAATGTTGTGTCGATACTTTTTGCCATTATGAATGCCCAAAAGGG
129 CATAATGTATCGACACTTGTAAAT-TTGTGTCGATACTTTTTGCCATAATGAATGCCCAAAAGGG
363611 TGAACG
193 TGAACG
* *
363617 CATAAAGTGTCGATACAATTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAAATATAAT
* * *
363682 GTAATAGGTAAATTTACAATGTAACCGGTATAAATAAACCGGTTTTTTGAGAAAATAGATATACA
66 GTAATAGGTAAATTTACAATATAACCGGTATAAATATACCGGTTTTATGAGAAAATAGATATACA
* * * * *
363747 TAATGTATCGACACTTGTAGAATTTGTGTTGATACTTTTGGTCCACAAGGAAAAT-CCAAAAAGG
131 TAATGTATCGACACTTGTA-AATTTGTGTCGATACTTTTTG-CCATAATG--AATGCCCAAAAGG
* *
363811 GTGCACC
192 GTGAACG
* * * * *
363818 CATAAAGTGTCGATACATTTTTCAACAGTATCGATCCCAGAAACATCGAAATTC-ATAAATATAA
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAA-CCGATAAATATAA
* * * ** ** * * * *
363882 TATAATATGTAATTTTGTAATATAATTGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTAC
65 TGTAATAGGTAAATTTACAATATAACCGGTATAAATATACCGGTTTTATGAGAAAATAGATATAC
* * ** *
363947 ATAATGTGTCGACACTTGTTAATGTTGTGTCGATACTTTTTGCTGTAATGAATGCCCAAAAGGTT
130 ATAATGTATCGACACTTGTAAAT-TTGTGTCGATACTTTTTGCCATAATGAATGCCCAAAAGGGT
364012 GAACG
194 GAACG
*
364017 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAAATATAAT
* * *
364082 GTAATAGGTAAATTTACAATGTAACCGGTATAAATGTACCGGTTTTATGAGAAAATAGGTGA-AC
66 GTAATAGGTAAATTTACAATATAACCGGTATAAATATACCGGTTTTATGAGAAAATAGAT-ATAC
* * *
364146 ATATTGTATCGACACATTTTAGATTTGTGTCGATACTT
130 ATAATGTATCGACAC-TTGTAAATTTGTGTCGATACTT
364184 GTAAATAACA
Statistics
Matches: 474, Mismatches: 81, Indels: 24
0.82 0.14 0.04
Matches are distributed among these distances:
198 6 0.01
199 290 0.61
200 21 0.04
201 153 0.32
202 4 0.01
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (198 bp):
CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAAATATAAT
GTAATAGGTAAATTTACAATATAACCGGTATAAATATACCGGTTTTATGAGAAAATAGATATACA
TAATGTATCGACACTTGTAAATTTGTGTCGATACTTTTTGCCATAATGAATGCCCAAAAGGGTGA
ACG
Found at i:364156 original size:400 final size:400
Alignment explanation
Indices: 363416--364183 Score: 1283
Period size: 400 Copynumber: 1.9 Consensus size: 400
363406 CTTAAAGTTT
363416 CCCATAAAGTGTCGATACAGTTTTAAAACGTATCGATCCCAGAAACATCGAAATCAATAAATATA
1 CCCATAAAGTGTCGATACAGTTTTAAAACGTATCGATCCCAGAAACATCGAAATCAATAAATATA
* *
363481 ATGTAATAGGTAATTTTGTATTATAACTGGTATAAATATACCGGTTTTATATGAGAATAGATCTA
66 ATATAATAGGTAATTTTGTAATATAACTGGTATAAATATACCGGTTTTATATGAGAATAGATCTA
*
363546 CATAATGTGTCGACACTTGTAAATGTTGTGTCGATACTTTTTGCCATTATGAATGCCCAAAAGGG
131 CATAATGTGTCGACACTTGTAAATGTTGTGTCGATACTTTTTGCCATAATGAATGCCCAAAAGGG
363611 TGAACGCATAAAGTGTCGATACAATTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAAT
196 TGAACGCATAAAGTGTCGATACAATTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAAT
*
363676 TATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATAAACCGGTTTTTTGAGAAAATAGA
261 TATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATAAACCGGTTTTATGAGAAAATAGA
*
363741 TATACATAATGTATCGACAC-TTGTAGAATTTGTGTTGATACTTTTGGTCCACAAGGAAAATCCA
326 TATACATAATGTATCGACACATTGTAG-ATTTGTGTCGATACTTTTGGTCCACAAGGAAAATCCA
363805 AAAAGGGTGCA
390 AAAAGGGTGCA
**
363816 CCCATAAAGTGTCGATACA-TTTTTCAACAGTATCGATCCCAGAAACATCGAAATTC-ATAAATA
1 CCCATAAAGTGTCGATACAGTTTTAAAAC-GTATCGATCCCAGAAACATCGAAA-TCAATAAATA
* * * *
363879 TAATATAATATGTAATTTTGTAATATAATTGGTATAAATATACCGGTTTTATGTGAGAATAGGTC
64 TAATATAATAGGTAATTTTGTAATATAACTGGTATAAATATACCGGTTTTATATGAGAATAGATC
* **
363944 TACATAATGTGTCGACACTTGTTAATGTTGTGTCGATACTTTTTGCTGTAATGAATGCCCAAAAG
129 TACATAATGTGTCGACACTTGTAAATGTTGTGTCGATACTTTTTGCCATAATGAATGCCCAAAAG
* *
364009 GTTGAACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATA
194 GGTGAACGCATAAAGTGTCGATACAATTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATA
**
364074 ATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATGTACCGGTTTTATGAGAAAATA
259 ATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATAAACCGGTTTTATGAGAAAATA
* * *
364139 GGTGA-ACATATTGTATCGACACATTTTAGATTTGTGTCGATACTT
324 GAT-ATACATAATGTATCGACACATTGTAGATTTGTGTCGATACTT
364184 GTAAATAACA
Statistics
Matches: 343, Mismatches: 21, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
399 7 0.02
400 328 0.96
401 8 0.02
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (400 bp):
CCCATAAAGTGTCGATACAGTTTTAAAACGTATCGATCCCAGAAACATCGAAATCAATAAATATA
ATATAATAGGTAATTTTGTAATATAACTGGTATAAATATACCGGTTTTATATGAGAATAGATCTA
CATAATGTGTCGACACTTGTAAATGTTGTGTCGATACTTTTTGCCATAATGAATGCCCAAAAGGG
TGAACGCATAAAGTGTCGATACAATTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAAT
TATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATAAACCGGTTTTATGAGAAAATAGA
TATACATAATGTATCGACACATTGTAGATTTGTGTCGATACTTTTGGTCCACAAGGAAAATCCAA
AAAGGGTGCA
Found at i:365027 original size:64 final size:64
Alignment explanation
Indices: 364821--365030 Score: 212
Period size: 65 Copynumber: 3.2 Consensus size: 64
364811 TTTTTCAGAG
* * ** *
364821 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGAATTAAATTG-AACATCGAATGGA
1 TGATGCATCGATGCACCAA-CCATGCATCGATGCACTC-TGGA-TATTTTGAAACATCGAATGCA
364884 TT
63 TT
* * * **
364886 TCATGCATCAATGCA-CATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACCA-ACCATGCATCGATGCACTCTGGATATTT-TG-AAACATCGAATGCA
364949 TT
63 TT
* * * *
364951 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCAAATGCACT
1 TGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATT
365015 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
365031 TCTTAGTGCA
Statistics
Matches: 119, Mismatches: 19, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
62 1 0.01
63 3 0.03
64 49 0.41
65 61 0.51
66 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (64 bp):
TGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATT
Found at i:365030 original size:17 final size:19
Alignment explanation
Indices: 365008--365050 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
364998 GAAACATCAA
*
365008 ATGCACT-TGA-TGCATCG
1 ATGCACTCTGAGTGCACCG
*
365025 ATGCACTCTTAGTGCACCG
1 ATGCACTCTGAGTGCACCG
365044 ATGCACT
1 ATGCACT
365051 GAGAGTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (19 bp):
ATGCACTCTGAGTGCACCG
Found at i:365046 original size:64 final size:63
Alignment explanation
Indices: 364908--365050 Score: 157
Period size: 64 Copynumber: 2.2 Consensus size: 63
364898 GCACATACCA
* * *
364908 TGCACCGATGCACTGAGGATTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCAGCC
1 TGCACCGATGCACTCAGGATTTTATGAAAACATCAAATGCACTTGATGCATCGATGCACCAG-C
* * *
364972 ATGCATCGATGCACTCTGGCTATTT-TG-AAACATCAAATGCACTTGATGCATCGATGCACTCTT
1 -TGCACCGATGCACTCAGGAT-TTTATGAAAACATCAAATGCACTTGATGCATCGATGCAC-C--
365035 AG-
61 AGC
365037 TGCACCGATGCACT
1 TGCACCGATGCACT
365051 GAGAGTCCAA
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
64 43 0.64
65 19 0.28
66 3 0.04
67 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.27
Consensus pattern (63 bp):
TGCACCGATGCACTCAGGATTTTATGAAAACATCAAATGCACTTGATGCATCGATGCACCAGC
Found at i:367856 original size:11 final size:11
Alignment explanation
Indices: 367840--367872 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
367830 ACTCTATTGA
367840 TATGACTAGTT
1 TATGACTAGTT
367851 TATGACTAGTT
1 TATGACTAGTT
*
367862 TATGCCTAGTT
1 TATGACTAGTT
367873 GCTAAGGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.45
Consensus pattern (11 bp):
TATGACTAGTT
Found at i:370712 original size:23 final size:25
Alignment explanation
Indices: 370666--370712 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
370656 TTAGGGGGAG
*
370666 TTTATGTTACATAGTGAAAATTAAT
1 TTTATGTTACATAATGAAAATTAAT
*
370691 TTTATGTT-CA-AATGAAATTTAA
1 TTTATGTTACATAATGAAAATTAA
370713 GGATTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 2 0.10
25 8 0.40
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (25 bp):
TTTATGTTACATAATGAAAATTAAT
Found at i:370921 original size:23 final size:23
Alignment explanation
Indices: 370852--370932 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 23
370842 ACACCTAACA
370852 GTGCATCGATGCATCA--TTGAAT
1 GTGCATCGATGCA-CACCTTGAAT
* *
370874 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
370895 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
370918 GTGCATCGATGCACA
1 GTGCATCGATGCACA
370933 AGGCCATGCA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
19 2 0.04
20 1 0.02
21 13 0.28
22 10 0.21
23 21 0.45
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:370925 original size:44 final size:42
Alignment explanation
Indices: 370833--370927 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 42
370823 TTGTGCTTCA
* *
370833 TGCATCGATACACCTAACAGTGCATCGATGCATCATTGAATG
1 TGCATCGATACACCTAACAGTGCACCGATGCAGCATTGAATG
* *
370875 TGCATCGATACACCATGAA-GGTGCACCGATGCACGCCTTGAATG
1 TGCATCGATACACC-T-AACAGTGCACCGATGCA-GCATTGAATG
370919 TGCATCGAT
1 TGCATCGAT
370928 GCACAAGGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 14 0.30
43 13 0.28
44 19 0.41
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.24
Consensus pattern (42 bp):
TGCATCGATACACCTAACAGTGCACCGATGCAGCATTGAATG
Found at i:370948 original size:43 final size:42
Alignment explanation
Indices: 370851--370950 Score: 103
Period size: 43 Copynumber: 2.3 Consensus size: 42
370841 TACACCTAAC
* * *
370851 AGTGCATCGATGCATCATTGAATGTGCATCGATACACCATGA
1 AGTGCATCGATGCAGCATTGAATGTGCATCGATACACAAGGA
* * * *
370893 AGGTGCACCGATGCACGCCTTGAATGTGCATCGATGCACAAGGCC
1 A-GTGCATCGATGCA-GCATTGAATGTGCATCGATACACAAGG-A
370938 A-TGCATCGATGCA
1 AGTGCATCGATGCA
370951 TCCATCGGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
42 1 0.02
43 23 0.49
44 22 0.47
45 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (42 bp):
AGTGCATCGATGCAGCATTGAATGTGCATCGATACACAAGGA
Found at i:372206 original size:65 final size:63
Alignment explanation
Indices: 372126--372279 Score: 175
Period size: 65 Copynumber: 2.4 Consensus size: 63
372116 ATTGAACAAT
* * *
372126 GAATGGATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACAT
1 GAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACAT
372190 C
63 C
* * * * *
372191 GAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATT
1 GAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGAAACATC
* *
372255 GAATGCACTTGATGCACCGATGCAC
1 GAATGCATTTGATGCATCGATGCAC
372280 TCTTAGTGCA
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
63 1 0.01
64 28 0.36
65 43 0.56
66 5 0.06
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (63 bp):
GAATGCATTTGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGAAACATC
Found at i:372291 original size:19 final size:19
Alignment explanation
Indices: 372267--372318 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
372257 ATGCACTTGA
372267 TGCACCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
*
372286 TGCACCGATGTACTCTTAG
1 TGCACCGATGCACTCTTAG
372305 TGCACCGATGCACT
1 TGCACCGATGCACT
372319 GAGAGTCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.27
Consensus pattern (19 bp):
TGCACCGATGCACTCTTAG
Found at i:372295 original size:64 final size:63
Alignment explanation
Indices: 372157--372301 Score: 143
Period size: 64 Copynumber: 2.3 Consensus size: 63
372147 GCACATACCA
** * *
372157 TGCACCGATGCACTGAGGATTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCAGCC
1 TGCACCGATGCACTCTGGATTTTATGAAAACATCGAATGCACTTGATGCACCGATGCACCAG-C
* * *
372221 ATGCATCGATGCACTCTGGCTATTT-TG-AAACATTGAATGCACTTGATGCACCGATGCACTCTT
1 -TGCACCGATGCACTCTGGAT-TTTATGAAAACATCGAATGCACTTGATGCACCGATGCAC-C--
372284 AG-
61 AGC
*
372286 TGCACCGATGTACTCT
1 TGCACCGATGCACTCT
372302 TAGTGCACCG
Statistics
Matches: 67, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
64 43 0.64
65 19 0.28
66 3 0.04
67 2 0.03
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (63 bp):
TGCACCGATGCACTCTGGATTTTATGAAAACATCGAATGCACTTGATGCACCGATGCACCAGC
Found at i:376066 original size:20 final size:19
Alignment explanation
Indices: 376028--376066 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
376018 CGAAACCAAT
*
376028 AATTATAATGTAATAGGTA
1 AATTATAATGTAACAGGTA
*
376047 AATTAATAATGTAACCGGTA
1 AATT-ATAATGTAACAGGTA
376067 TAAATATACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.33
Consensus pattern (19 bp):
AATTATAATGTAACAGGTA
Found at i:376223 original size:14 final size:14
Alignment explanation
Indices: 376199--376232 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
376189 TTACAATGCA
*
376199 ACCGATATAAATAT
1 ACCGGTATAAATAT
*
376213 ATCGGTATAAATAT
1 ACCGGTATAAATAT
376227 ACCGGT
1 ACCGGT
376233 TTTATAAGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (14 bp):
ACCGGTATAAATAT
Found at i:376484 original size:23 final size:23
Alignment explanation
Indices: 376451--376498 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
376441 TAATAGGTCA
*
376451 ATATAAACGCTACCTATTATATT
1 ATATAAACGCTACCTAATATATT
* *
376474 ATATAAGCGCTACCTAATATGTT
1 ATATAAACGCTACCTAATATATT
376497 AT
1 AT
376499 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATAAACGCTACCTAATATATT
Found at i:376542 original size:87 final size:87
Alignment explanation
Indices: 376451--376612 Score: 270
Period size: 87 Copynumber: 1.9 Consensus size: 87
376441 TAATAGGTCA
* *
376451 ATATAAACGCTACCTATTATATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAACGCTACCTATTACATTACATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
376516 TCGGTTAAATTCCTATTTTATT
66 TCGGTTAAATTCCTATTTTATT
* * * *
376538 ATATAAGCGCTACTTATTACATTACATAAGCGTTACCTAATATGTTATTGTATTTGATAATATTT
1 ATATAAACGCTACCTATTACATTACATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
376603 TCGGTTAAAT
66 TCGGTTAAAT
376613 AATATAACAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (87 bp):
ATATAAACGCTACCTATTACATTACATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
TCGGTTAAATTCCTATTTTATT
Found at i:376736 original size:3 final size:3
Alignment explanation
Indices: 376730--376776 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
376720 ATAAATTACA
* * *
376730 ATT ATT ATT ATT ATT ATT GTT GTT GTT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
376777 AAAATGTAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:381972 original size:46 final size:46
Alignment explanation
Indices: 381905--382005 Score: 166
Period size: 46 Copynumber: 2.2 Consensus size: 46
381895 GAGAAAAAAA
* * *
381905 AAAGGAGTTTATCAGATTAGCAATTTAATCTGAGTCTTCTGCAACG
1 AAAGGAGTTTATCAGATTAGCAAATTAATCTGAGTCCTCGGCAACG
*
381951 AAAGGAGTTTATCAGATTAGCAAATTAATCTGAGTCCTCGGGAACG
1 AAAGGAGTTTATCAGATTAGCAAATTAATCTGAGTCCTCGGCAACG
381997 AAAGGAGTT
1 AAAGGAGTT
382006 ATAGGTAACA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.29
Consensus pattern (46 bp):
AAAGGAGTTTATCAGATTAGCAAATTAATCTGAGTCCTCGGCAACG
Found at i:385645 original size:14 final size:14
Alignment explanation
Indices: 385626--385671 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
385616 AATGGGAAGT
385626 AATCCCTACAAAAA
1 AATCCCTACAAAAA
* *
385640 AATCCCTGCAAATA
1 AATCCCTACAAAAA
*
385654 AATCCCTACATAAA
1 AATCCCTACAAAAA
385668 AATC
1 AATC
385672 TCTGCAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.50, C:0.28, G:0.02, T:0.20
Consensus pattern (14 bp):
AATCCCTACAAAAA
Found at i:390228 original size:32 final size:32
Alignment explanation
Indices: 390187--390256 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
390177 GTTATGCACA
* *
390187 TCATCTTCAATCTCTTACATAACACACT-TCTT
1 TCATCTTCAATCTCTTACACAACAAACTCT-TT
390219 TCATCTTCAATCTCTTACACAACAAACTCTTT
1 TCATCTTCAATCTCTTACACAACAAACTCTTT
390251 TCATCT
1 TCATCT
390257 AACCAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 34 0.97
33 1 0.03
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.40
Consensus pattern (32 bp):
TCATCTTCAATCTCTTACACAACAAACTCTTT
Found at i:391085 original size:20 final size:19
Alignment explanation
Indices: 391008--391045 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
390998 GTGACGTTTC
391008 TATATATTATTATTATATT
1 TATATATTATTATTATATT
391027 TATATTATTATTATTATAT
1 TATA-TATTATTATTATAT
391046 ACATAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATATATTATTATTATATT
Found at i:392413 original size:18 final size:17
Alignment explanation
Indices: 392382--392421 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
392372 ATTTTAAGAC
*
392382 TAATTATAATATTATTA
1 TAATTATAATATTATGA
392399 TAATTATATATATTATGA
1 TAATTATA-ATATTATGA
392417 TAATT
1 TAATT
392422 TAAGTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TAATTATAATATTATGA
Found at i:394868 original size:3 final size:3
Alignment explanation
Indices: 394860--394892 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
394850 TTATAAATAT
*
394860 TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
394893 ATACAAACAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:395572 original size:16 final size:17
Alignment explanation
Indices: 395551--395586 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
395541 AGAGGATAGT
395551 TTTAGTTAAT-ATTAGG
1 TTTAGTTAATAATTAGG
*
395567 TTTAGTTTATAATTAGG
1 TTTAGTTAATAATTAGG
395584 TTT
1 TTT
395587 CTATATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.56
Consensus pattern (17 bp):
TTTAGTTAATAATTAGG
Found at i:396828 original size:11 final size:11
Alignment explanation
Indices: 396812--396874 Score: 67
Period size: 11 Copynumber: 5.9 Consensus size: 11
396802 GTATTATAGA
396812 ATTTTTAATAT
1 ATTTTTAATAT
396823 ATTTTTAATAT
1 ATTTTTAATAT
*
396834 -TTTATAAT-T
1 ATTTTTAATAT
*** *
396843 ATCAATAATGT
1 ATTTTTAATAT
396854 ATTTTTAATAT
1 ATTTTTAATAT
396865 ATTTTTAATA
1 ATTTTTAATA
396875 AAGTAATTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
9 1 0.02
10 13 0.30
11 29 0.67
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:407800 original size:37 final size:37
Alignment explanation
Indices: 407700--407800 Score: 136
Period size: 36 Copynumber: 2.8 Consensus size: 37
407690 TTCTCAAGTC
* *
407700 AATCAAGCCTTTACAAAATA-A-TAGTGAAGCAATGCA
1 AATCAAGCCTTCACAAAA-AGAGTAGTGAAACAATGCA
*
407736 AATCAAGCATTCAC-AAAAGAGTAGTGAAACAATGCA
1 AATCAAGCCTTCACAAAAAGAGTAGTGAAACAATGCA
*
407772 AATTAAGCCTTCACAAAAAGAGTAGTGAA
1 AATCAAGCCTTCACAAAAAGAGTAGTGAA
407801 GCAAGATCAA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
34 1 0.02
35 4 0.07
36 38 0.67
37 14 0.25
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.20
Consensus pattern (37 bp):
AATCAAGCCTTCACAAAAAGAGTAGTGAAACAATGCA
Found at i:413054 original size:65 final size:66
Alignment explanation
Indices: 412977--413184 Score: 274
Period size: 65 Copynumber: 3.0 Consensus size: 66
412967 TCCATTTCGC
*
412977 TTTTTTTTTTCAAATTTGTTAAAAATTTCTAAATGTTTGATATTATTTTTAACTTCGAAATTTTA
1 TTTTTTTTTTCAAATTTGTTAAAAATTTCTAAAAGTTTGATATTATTTTTAACTTCGAAATTTTA
413042 A
66 A
*
413043 -TTTTTTTTTCAAATTTGTTAAAAAATTCTAAAAGTTTGATATTATTTTTAACTTCGAAATTTTA
1 TTTTTTTTTTCAAATTTGTTAAAAATTTCTAAAAGTTTGATATTATTTTTAACTTCGAAATTTT-
413107 AAAA
65 --AA
* *
413111 TTTTAATATTTTAAAATTCAAATTTGTTAAAAATTTCTAAAAGTTTGATATTAATTTTAACTCCG
1 -TTT--T-TTTT----TTCAAATTTGTTAAAAATTTCTAAAAGTTTGATATTATTTTTAACTTCG
413176 AAATTTTAA
58 AAATTTTAA
413185 AAAATTTAAT
Statistics
Matches: 125, Mismatches: 5, Indels: 16
0.86 0.03 0.11
Matches are distributed among these distances:
65 61 0.49
68 2 0.02
70 2 0.02
72 1 0.01
73 4 0.03
74 2 0.02
77 53 0.42
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (66 bp):
TTTTTTTTTTCAAATTTGTTAAAAATTTCTAAAAGTTTGATATTATTTTTAACTTCGAAATTTTA
A
Found at i:413131 original size:77 final size:77
Alignment explanation
Indices: 413050--413199 Score: 255
Period size: 77 Copynumber: 1.9 Consensus size: 77
413040 TAATTTTTTT
* * *
413050 TTCAAATTTGTTAAAAAATTCTAAAAGTTTGATATTATTTTTAACTTCGAAATTTTAAAAATTTT
1 TTCAAATTTGTTAAAAAATTCTAAAAGTTTGATATTAATTTTAACTCCGAAATTTTAAAAAATTT
413115 AATATTTTAAAA
66 AATATTTTAAAA
*
413127 TTCAAATTTGTTAAAAATTTCTAAAAGTTTGATATTAATTTTAACTCCGAAATTTTAAAAAATTT
1 TTCAAATTTGTTAAAAAATTCTAAAAGTTTGATATTAATTTTAACTCCGAAATTTTAAAAAATTT
*
413192 AATTTTTT
66 AATATTTT
413200 TATTTTATTA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
77 68 1.00
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.47
Consensus pattern (77 bp):
TTCAAATTTGTTAAAAAATTCTAAAAGTTTGATATTAATTTTAACTCCGAAATTTTAAAAAATTT
AATATTTTAAAA
Found at i:415377 original size:2 final size:2
Alignment explanation
Indices: 415370--415430 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
415360 CCATTTTAAT
415370 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
415412 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
415431 TATTTAAATG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:416718 original size:36 final size:37
Alignment explanation
Indices: 416628--416767 Score: 174
Period size: 37 Copynumber: 3.8 Consensus size: 37
416618 CGAGATCAAT
* *
416628 TTGCTTCACTACTCTTTGGTGAAGGCTTAAAATAGAC
1 TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAGAC
** *
416665 TTGCTTCACTAGACTTCGGTGAAGGCTTAAGATTGA-
1 TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAGAC
* * * *
416701 TCGCTTCACAACTCTTCGGTGAAGGCTTAAGATGGAT
1 TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAGAC
* *
416738 TTACTTCACTACTCTTCAGTGAAGGCTTAA
1 TTGCTTCACTACTCTTCGGTGAAGGCTTAA
416768 AATGGCTCGA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
36 31 0.35
37 57 0.65
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (37 bp):
TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAGAC
Found at i:416760 original size:73 final size:73
Alignment explanation
Indices: 416630--416767 Score: 195
Period size: 73 Copynumber: 1.9 Consensus size: 73
416620 AGATCAATTT
* * * * *
416630 GCTTCACTACTCTTTGGTGAAGGCTTAAAATAGACTTGCTTCACTAGACTTCGGTGAAGGCTTAA
1 GCTTCACAACTCTTCGGTGAAGGCTTAAAATAGACTTACTTCACTACACTTCAGTGAAGGCTTAA
416695 GATTGATC
66 GATTGATC
* * * *
416703 GCTTCACAACTCTTCGGTGAAGGCTTAAGATGGATTTACTTCACTACTCTTCAGTGAAGGCTTAA
1 GCTTCACAACTCTTCGGTGAAGGCTTAAAATAGACTTACTTCACTACACTTCAGTGAAGGCTTAA
416768 AATGGCTCGA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
73 56 1.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (73 bp):
GCTTCACAACTCTTCGGTGAAGGCTTAAAATAGACTTACTTCACTACACTTCAGTGAAGGCTTAA
GATTGATC
Found at i:416861 original size:42 final size:42
Alignment explanation
Indices: 416814--416900 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 42
416804 ATCTTACCCG
* *
416814 AAGGTTTTATGGATGACCCGAAAGACTT-ATCATCTTGCTCAA
1 AAGG-TTTATAGATGACCCGAAAGACTTAATCATCATGCTCAA
* *
416856 AAGGTTTATAGATGACCCGAAAGATTTAATCATCATGCTCGA
1 AAGGTTTATAGATGACCCGAAAGACTTAATCATCATGCTCAA
416898 AAG
1 AAG
416901 ACTTACTGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 21 0.52
42 19 0.47
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (42 bp):
AAGGTTTATAGATGACCCGAAAGACTTAATCATCATGCTCAA
Found at i:416898 original size:22 final size:22
Alignment explanation
Indices: 416873--416943 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
416863 ATAGATGACC
416873 CGAAAGATTTAATCATCATGCT
1 CGAAAGATTTAATCATCATGCT
* * *
416895 CGAAAGACTTACTGAT-AT-C-
1 CGAAAGATTTAATCATCATGCT
* *
416914 CCAAAGGATTTCATCATCATGCT
1 CGAAA-GATTTAATCATCATGCT
416937 CGAAAGA
1 CGAAAGA
416944 CTTACTGATG
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
19 4 0.11
20 8 0.22
21 4 0.11
22 16 0.44
23 4 0.11
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (22 bp):
CGAAAGATTTAATCATCATGCT
Found at i:416924 original size:42 final size:42
Alignment explanation
Indices: 416878--417074 Score: 167
Period size: 42 Copynumber: 4.8 Consensus size: 42
416868 TGACCCGAAA
416878 GATTTAATCATCATGCTCGAAAGACTTACTGATATCCCAAAG
1 GATTTAATCATCATGCTCGAAAGACTTACTGATATCCCAAAG
* ** ***
416920 GATTTCATCATCATGCTCGAAAGACTTACTG--AT-GGATTT
1 GATTTAATCATCATGCTCGAAAGACTTACTGATATCCCAAAG
* * * * * ** *
416959 GCTTCACT-ACTC-TTC-CGTGAAGACTTACAAAT-TACCCGAAG
1 GATTTAATCA-TCATGCTCG-AAAGACTTACTGATAT-CCCAAAG
*
417000 GATTTAATCATCATGCTCGAAAGACTTACTGATGA-CCCGAAG
1 GATTTAATCATCATGCTCGAAAGACTTACTGAT-ATCCCAAAG
417042 GATTTAATCATCATGCTCGAAAGACTTACTGAT
1 GATTTAATCATCATGCTCGAAAGACTTACTGAT
417075 GGCCCGAAGG
Statistics
Matches: 117, Mismatches: 27, Indels: 22
0.70 0.16 0.13
Matches are distributed among these distances:
37 2 0.02
38 12 0.10
39 8 0.07
40 2 0.02
41 7 0.06
42 84 0.72
43 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (42 bp):
GATTTAATCATCATGCTCGAAAGACTTACTGATATCCCAAAG
Found at i:417075 original size:42 final size:42
Alignment explanation
Indices: 416978--417085 Score: 180
Period size: 42 Copynumber: 2.6 Consensus size: 42
416968 CTCTTCCGTG
** *
416978 AAGACTTACAAATTACCCGAAGGATTTAATCATCATGCTCGA
1 AAGACTTACTGATGACCCGAAGGATTTAATCATCATGCTCGA
417020 AAGACTTACTGATGACCCGAAGGATTTAATCATCATGCTCGA
1 AAGACTTACTGATGACCCGAAGGATTTAATCATCATGCTCGA
*
417062 AAGACTTACTGATGGCCCGAAGGA
1 AAGACTTACTGATGACCCGAAGGA
417086 CTTGCTAAGT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.24
Consensus pattern (42 bp):
AAGACTTACTGATGACCCGAAGGATTTAATCATCATGCTCGA
Found at i:417087 original size:20 final size:20
Alignment explanation
Indices: 417017--417088 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
417007 TCATCATGCT
*
417017 CGAAAGACTTACTGATGACC
1 CGAAAGACTTACTGATGGCC
* * * *
417037 CGAAGGATTTAATCATCAT-GCT
1 CGAAAGACTT-A-C-TGATGGCC
417059 CGAAAGACTTACTGATGGCC
1 CGAAAGACTTACTGATGGCC
*
417079 CGAAGGACTT
1 CGAAAGACTT
417089 GCTAAGTGTG
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
19 3 0.08
20 20 0.53
21 2 0.05
22 10 0.26
23 3 0.08
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (20 bp):
CGAAAGACTTACTGATGGCC
Found at i:417462 original size:216 final size:214
Alignment explanation
Indices: 416992--417509 Score: 586
Period size: 216 Copynumber: 2.4 Consensus size: 214
416982 CTTACAAATT
* * * *
416992 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTAATCATCATG
1 ACCCGAAGGATTT-ATCATCTTGCTCGAAAGGCTTACAGATGACCCGAAAGATTTAATCATCATG
*
417057 CTCGAAAGACTTACTGATGGCCCGAAGGACTTGCTAAGTGTGAAAATTTGGAAATCGCCTTCTTA
65 CTCGAAAGACTTACTGATGGCCCGAAGGACTT-CTAA--GTGAAAATTTGGAAATCACCTTCTTA
* * * * * *
417122 GTTTTCAAATATTTCATTTTTTTTAAAATATCACTTTCTCATTTTTCAACTTAATGTGAAAACAT
127 CTTTTCAAAAATTTAATTTTTTTTAAAATAGCACTTTCTCATATTTCAACTGAATGTGAAAACAT
* * *
417187 CCTACCCGAAGGTCTTATTGATG
192 CATACCCAAAGGTCTTATGGATG
* * * *
417210 GCCAGAAGGACTTATCATCTTGCTCGAAAGGCTTACAGATGACCCGAAAGATTTAATCATCATAC
1 ACCCGAAGGATTTATCATCTTGCTCGAAAGGCTTACAGATGACCCGAAAGATTTAATCATCATGC
* * *
417275 TCGAAAGACTTACTGATGGCCTGAAGGAC-T-T-A-T-AAATTTTGGAAATCACTTTCTTACTTT
66 TCGAAAGACTTACTGATGGCCCGAAGGACTTCTAAGTGAAAATTTGGAAATCACCTTCTTACTTT
* *
417335 TCAAAAATTTTGAATTTCATATTTATATGAGA-AGCA-TTTCTCATATTTCGA-TAGACATGTGA
131 TCAAAAA-TTT-AATTT--T-TTT-TA--AAATAGCACTTTCTCATATTTCAACT-GA-ATGTGA
*
417397 AAACATCATGCCCAAAGGTCTTATGGATG
186 AAACATCATACCCAAAGGTCTTATGGATG
* *
417426 ACCCGAAGGATTTATCATCTTGCTCGAAAGGCTTACAGATGACCC-AAAGGGTTTAAGCATCATG
1 ACCCGAAGGATTTATCATCTTGCTCGAAAGGCTTACAGATGACCCGAAA-GATTTAATCATCATG
**
417490 CTTAAAAGACTTACTGATGG
65 CTCGAAAGACTTACTGATGG
417510 ATTTGCTTCA
Statistics
Matches: 257, Mismatches: 32, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
209 29 0.11
210 4 0.02
211 4 0.02
213 2 0.01
214 5 0.02
215 19 0.07
216 107 0.42
217 77 0.30
218 10 0.04
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (214 bp):
ACCCGAAGGATTTATCATCTTGCTCGAAAGGCTTACAGATGACCCGAAAGATTTAATCATCATGC
TCGAAAGACTTACTGATGGCCCGAAGGACTTCTAAGTGAAAATTTGGAAATCACCTTCTTACTTT
TCAAAAATTTAATTTTTTTTAAAATAGCACTTTCTCATATTTCAACTGAATGTGAAAACATCATA
CCCAAAGGTCTTATGGATG
Found at i:417567 original size:80 final size:80
Alignment explanation
Indices: 417451--417662 Score: 280
Period size: 80 Copynumber: 2.6 Consensus size: 80
417441 CATCTTGCTC
* * * * * **
417451 GAAAGGCTTACAGATGACCCAAAGGGTTTAAGCATCATGCTTAAAAGACTTACTGATGGATTTGC
1 GAAA-GCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGC
417516 TTCACTACTCTTCCGT
65 TTCACTACTCTTCCGT
* ** * * *
417532 GAAGGCTTATGAATTACCCGGAGGATTTAATCATCATGCTCGAAAGACTTATTGATGGATTTGTT
1 GAAAGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCT
*
417597 TCACTACTCTTCTGT
66 TCACTACTCTTCCGT
*
417612 GAAAGCTTACAAATTACCTGAAGGATTTAATCATCATGCTCGAAAGACTTA
1 GAAAGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTA
417663 GGTGGTGTTT
Statistics
Matches: 112, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
80 109 0.97
81 3 0.03
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (80 bp):
GAAAGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCT
TCACTACTCTTCCGT
Found at i:417959 original size:27 final size:25
Alignment explanation
Indices: 417899--417969 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 25
417889 TTTTAATTTT
417899 AATATTAATTTTTTAA-A-TAAATTA
1 AATATTAA-TTTTTAATATTAAATTA
*
417923 AATATTAATTTTTAATATTATATTA
1 AATATTAATTTTTAATATTAAATTA
417948 TAGATATTAA-TTTTAATATTAA
1 -A-ATATTAATTTTTAATATTAA
417970 TTTTTTAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.17
24 9 0.22
25 6 0.15
26 12 0.29
27 7 0.17
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (25 bp):
AATATTAATTTTTAATATTAAATTA
Found at i:417966 original size:63 final size:64
Alignment explanation
Indices: 417876--418027 Score: 265
Period size: 63 Copynumber: 2.4 Consensus size: 64
417866 ATTTTATATT
*
417876 ATATTATATT-T-GATTTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAA-TTTTTA
1 ATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTTTTA
417937 ATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTTTTA
1 ATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTTTTA
418001 ATATTATATTATAGATATTTAATTTTA
1 ATATTATATTATAGATA-TTAATTTTA
418028 TATCATATAA
Statistics
Matches: 86, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
61 10 0.12
62 1 0.01
63 43 0.50
64 23 0.27
65 9 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (64 bp):
ATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTTTTA
Found at i:418064 original size:64 final size:61
Alignment explanation
Indices: 417857--418072 Score: 196
Period size: 63 Copynumber: 3.4 Consensus size: 61
417847 CAAAGAGGTT
* *
417857 TTATATT-TAATTTT-ATATTATATTATATTTGATTTTAATTTTAATATTAATTTTTTAAATAAA
1 TTATATTAAAATTTTAATATTATATTATA---GATATTAATTTTAATATTAATTTTTT-AATAAA
*
417920 TTAAATATT-AATTTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAA
1 TT--ATATTAAAATTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTT-AATAAA
**
417983 TTAAATATTAATTTTTTAATATTATATTATAGATATTTAATTTTATATCATATAAATTATTTT-A
1 TT--ATATTAAAATTTTAATATTATATTATAGATA-TTAATTTTA-AT-AT-T-AATT-TTTTAA
418047 TAAA
58 TAAA
418051 -T-TATTAAAATTTT-ATATT-TATT
1 TTATATTAAAATTTTAATATTATATT
418073 TTAATTATTT
Statistics
Matches: 137, Mismatches: 6, Indels: 21
0.84 0.04 0.13
Matches are distributed among these distances:
62 4 0.03
63 48 0.35
64 34 0.25
65 19 0.14
66 15 0.11
67 3 0.02
68 6 0.04
69 4 0.03
70 4 0.03
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (61 bp):
TTATATTAAAATTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAATAAA
Found at i:418574 original size:31 final size:31
Alignment explanation
Indices: 418537--418597 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
418527 GTAGTTGAAT
* * *
418537 AAATTATTTAAATTTTAGTATTGTAAAACTA
1 AAATTATTTAAATCTCAGTATTGCAAAACTA
418568 AAATTATTTAAATCTCAGTATTGCAAAACT
1 AAATTATTTAAATCTCAGTATTGCAAAACT
418598 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (31 bp):
AAATTATTTAAATCTCAGTATTGCAAAACTA
Found at i:419043 original size:41 final size:41
Alignment explanation
Indices: 418921--419105 Score: 190
Period size: 42 Copynumber: 4.5 Consensus size: 41
418911 AGATCTTATG
* *
418921 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGGCCCGAAGGACTTATCATCATGCTCTAAAGACTTACA
* * * * * *
418962 GATGACCTGAAGGATTTAAGCATCATGCTCAAAAGACTTACT
1 GATGGCCCGAAGGACTT-ATCATCATGCTCTAAAGACTTACA
* * *
419004 GATGGCCCGAATGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGGCCCGAAGGACTTATCATCATGCTCTAAAGACTTACA
* * * * * *
419045 AATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAGGACTT-ATCATCATGCTCTAAAGACTTACA
*
419087 GATGGCCCGAATGACTTAT
1 GATGGCCCGAAGGACTTAT
419106 AAATTGTGAA
Statistics
Matches: 111, Mismatches: 31, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
41 47 0.42
42 64 0.58
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTATCATCATGCTCTAAAGACTTACA
Found at i:419060 original size:83 final size:83
Alignment explanation
Indices: 418921--419105 Score: 334
Period size: 83 Copynumber: 2.2 Consensus size: 83
418911 AGATCTTATG
* * *
418921 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCTGAAGGATTTAAGCATC
1 GATGGCCCGAATGACTTATCATCTTGCTCTAAAGGCTTACAAATGACCCGAAGGATTTAAGCATC
418986 ATGCTCAAAAGACTTACT
66 ATGCTCAAAAGACTTACT
419004 GATGGCCCGAATGACTTATCATCTTGCTCTAAAGGCTTACAAATGACCCGAAGGATTTAAGCATC
1 GATGGCCCGAATGACTTATCATCTTGCTCTAAAGGCTTACAAATGACCCGAAGGATTTAAGCATC
*
419069 ATGCTCGAAAGACTTACT
66 ATGCTCAAAAGACTTACT
419087 GATGGCCCGAATGACTTAT
1 GATGGCCCGAATGACTTAT
419106 AAATTGTGAA
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 98 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (83 bp):
GATGGCCCGAATGACTTATCATCTTGCTCTAAAGGCTTACAAATGACCCGAAGGATTTAAGCATC
ATGCTCAAAAGACTTACT
Found at i:419309 original size:36 final size:36
Alignment explanation
Indices: 419251--419444 Score: 182
Period size: 36 Copynumber: 5.4 Consensus size: 36
419241 TCTTGCTCTA
419251 AAGGCTTACAGA-TGATTTGCTTCACTACTCTTCTGTG
1 AAGGCTTA-AGATTG-TTTGCTTCACTACTCTTCTGTG
* *
419288 AAGGCTTAAGATTGTTTGCTTCACCATTCTT-TGGTG
1 AAGGCTTAAGATTGTTTGCTTCACTACTCTTCT-GTG
* *
419324 AAGGCTTAAGA-TGATTGCTTCACTAATCTT-TGGTG
1 AAGGCTTAAGATTGTTTGCTTCACTACTCTTCT-GTG
* * * * * *
419359 AAGGCTTCAA-ATGGATCGCTTTACTACTCTCCAGTG
1 AAGGCTT-AAGATTGTTTGCTTCACTACTCTTCTGTG
* * * *
419395 AAGGCTTAAAATTATTTGCTTCACTACTCTCCAGTG
1 AAGGCTTAAGATTGTTTGCTTCACTACTCTTCTGTG
419431 AAGGCTTAAGATTG
1 AAGGCTTAAGATTG
419445 ACTTGCCCCA
Statistics
Matches: 133, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
35 32 0.24
36 91 0.68
37 10 0.08
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (36 bp):
AAGGCTTAAGATTGTTTGCTTCACTACTCTTCTGTG
Found at i:419396 original size:71 final size:72
Alignment explanation
Indices: 419251--419442 Score: 201
Period size: 71 Copynumber: 2.7 Consensus size: 72
419241 TCTTGCTCTA
* * * * *
419251 AAGGCTTACAGATGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAGATTGTTTGCTTCACCATT
1 AAGGCTTA-AGATGATTTGCTTCACTAATCTTCTGTGAAGGCTTAAGATGGATCGCTTCACCACT
***
419316 CTTTGGTG
65 CTCCAGTG
* *
419324 AAGGCTTAAGATGA-TTGCTTCACTAATCTT-TGGTGAAGGCTTCAA-ATGGATCGCTTTACTAC
1 AAGGCTTAAGATGATTTGCTTCACTAATCTTCT-GTGAAGGCTT-AAGATGGATCGCTTCACCAC
419386 TCTCCAGTG
64 TCTCCAGTG
* * * * *
419395 AAGGCTTAAAATTATTTGCTTCACTACTCTCCAGTGAAGGCTTAAGAT
1 AAGGCTTAAGATGATTTGCTTCACTAATCTTCTGTGAAGGCTTAAGAT
419443 TGACTTGCCC
Statistics
Matches: 99, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
70 1 0.01
71 56 0.57
72 34 0.34
73 8 0.08
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (72 bp):
AAGGCTTAAGATGATTTGCTTCACTAATCTTCTGTGAAGGCTTAAGATGGATCGCTTCACCACTC
TCCAGTG
Found at i:420393 original size:125 final size:125
Alignment explanation
Indices: 420206--420488 Score: 415
Period size: 125 Copynumber: 2.3 Consensus size: 125
420196 AATCTTGTTT
* * * * * *
420206 TCTCATCATGACGTGGGTTCAATTGTGCCCCAACCTTATCTTATACTGGTACAAGCCTTCAAAAT
1 TCTCAACATGATGTGGGTTCAGTCGTGCCCCAACATTATCTTATACTAGTACAAGCCTTCAAAAT
* *
420271 GCCTCATCACCTCAAATTGTAATGATCATTCTTCATGCCTCCTTGGTCTGAACA-TTGTCA
66 GCCCCATCACCTCAAATTGTAAGGATCATTCTTCATGCCTCCTTGGTCTGAA-AGTTGTCA
* * * **
420331 TCTCAACATGATGTGGGATCAGTCGTGCCCCCACATTTTCTTATACTAGTACGGGCCTTCAAAAT
1 TCTCAACATGATGTGGGTTCAGTCGTGCCCCAACATTATCTTATACTAGTACAAGCCTTCAAAAT
*
420396 GCCCCATCACCTCAAATTGTAAGGCTCATTCTTCATGCCTCCTTGGTCTGAAAGTTGTCA
66 GCCCCATCACCTCAAATTGTAAGGATCATTCTTCATGCCTCCTTGGTCTGAAAGTTGTCA
*
420456 TCTCAACATAATGTGGGTTCAGTCGTGCCCCAA
1 TCTCAACATGATGTGGGTTCAGTCGTGCCCCAA
420489 TATATCCTAA
Statistics
Matches: 140, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
124 1 0.01
125 139 0.99
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.32
Consensus pattern (125 bp):
TCTCAACATGATGTGGGTTCAGTCGTGCCCCAACATTATCTTATACTAGTACAAGCCTTCAAAAT
GCCCCATCACCTCAAATTGTAAGGATCATTCTTCATGCCTCCTTGGTCTGAAAGTTGTCA
Found at i:423630 original size:18 final size:18
Alignment explanation
Indices: 423607--423643 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
423597 GATTGCTCTA
423607 TTTCTTCTATTTGTTTGT
1 TTTCTTCTATTTGTTTGT
423625 TTTCTTCTATTTGTTTGT
1 TTTCTTCTATTTGTTTGT
423643 T
1 T
423644 CATGATGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.11, G:0.11, T:0.73
Consensus pattern (18 bp):
TTTCTTCTATTTGTTTGT
Found at i:428430 original size:2 final size:2
Alignment explanation
Indices: 428423--428472 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
428413 ATTTTAATTA
428423 AT 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 AT
428465 AT AT AT AT
1 AT AT AT AT
428473 TATTTAAATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:429415 original size:18 final size:18
Alignment explanation
Indices: 429369--429416 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
429359 AACCAACATC
* *
429369 TTGTAATTAGGTTGATAT
1 TTGTAATTGGGTTAATAT
*
429387 TTGTAACTGGGTTAATAT
1 TTGTAATTGGGTTAATAT
429405 TTGTAATTGGGT
1 TTGTAATTGGGT
429417 CCAGTTGGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (18 bp):
TTGTAATTGGGTTAATAT
Found at i:432531 original size:20 final size:20
Alignment explanation
Indices: 432506--432545 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
432496 AAACTAATGA
432506 TAAAAGAACACTAAACGAAC
1 TAAAAGAACACTAAACGAAC
*
432526 TAAAAGAACACTTAACGAAC
1 TAAAAGAACACTAAACGAAC
432546 ATGTTTGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.20, G:0.10, T:0.12
Consensus pattern (20 bp):
TAAAAGAACACTAAACGAAC
Found at i:432560 original size:23 final size:23
Alignment explanation
Indices: 432531--432581 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
432521 CGAACTAAAA
* * *
432531 GAACACTTAACGAACATGTTTGT
1 GAACACTAAACGAACAAGTTCGT
*
432554 GAACACTAAATGAACAAGTTCGT
1 GAACACTAAACGAACAAGTTCGT
432577 GAACA
1 GAACA
432582 TATAAATGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (23 bp):
GAACACTAAACGAACAAGTTCGT
Found at i:432614 original size:23 final size:23
Alignment explanation
Indices: 432542--432616 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
432532 AACACTTAAC
* *
432542 GAACATGTTTGTGAACACTAAAT
1 GAACAAGTTTGTGAACATTAAAT
*
432565 GAACAAGTTCGTGAACATATAAAT
1 GAACAAGTTTGTGAACAT-TAAAT
* * *
432589 GAACACGTTTGCGATCATTAAAT
1 GAACAAGTTTGTGAACATTAAAT
432612 GAACA
1 GAACA
432617 TGTTCAAAGA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 25 0.57
24 19 0.43
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (23 bp):
GAACAAGTTTGTGAACATTAAAT
Found at i:442152 original size:21 final size:21
Alignment explanation
Indices: 442125--442171 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
442115 TGAAATCTAA
442125 ATTTTGTTTAGTTAATTACTT
1 ATTTTGTTTAGTTAATTACTT
* *
442146 GTTTTGTTTGGTTAATTACTT
1 ATTTTGTTTAGTTAATTACTT
442167 ATTTT
1 ATTTT
442172 ATTGATTGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.19, C:0.04, G:0.13, T:0.64
Consensus pattern (21 bp):
ATTTTGTTTAGTTAATTACTT
Found at i:465482 original size:10 final size:10
Alignment explanation
Indices: 465467--465494 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
465457 GTTAGATTGT
465467 AAAAAAATGA
1 AAAAAAATGA
465477 AAAAAAATGA
1 AAAAAAATGA
465487 AAAAAAAT
1 AAAAAAAT
465495 ATTAATATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.11
Consensus pattern (10 bp):
AAAAAAATGA
Found at i:465515 original size:6 final size:6
Alignment explanation
Indices: 465506--465582 Score: 61
Period size: 6 Copynumber: 12.2 Consensus size: 6
465496 TTAATATAGT
465506 AATAAA AAT-AA AATAAA TGAA-AAA GAA-AAA AATAAA AATAAAA AATAAAA
1 AATAAA AATAAA AATAAA --AATAAA -AATAAA AATAAA AAT-AAA AAT-AAA
*
465556 AATTAAA AATAAA AGGTAAA AATAAA A
1 AA-TAAA AATAAA A-ATAAA AATAAA A
465583 GAAATAGAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
5 7 0.11
6 27 0.44
7 25 0.40
8 3 0.05
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:465542 original size:7 final size:7
Alignment explanation
Indices: 465509--465582 Score: 64
Period size: 7 Copynumber: 10.4 Consensus size: 7
465499 ATATAGTAAT
465509 AAAAATAA
1 AAAAAT-A
465517 AATAAATGA
1 AA-AAAT-A
465526 AAAAGA-A
1 AAAA-ATA
465533 AAAAAT-
1 AAAAATA
465539 AAAAATA
1 AAAAATA
465546 AAAAATA
1 AAAAATA
*
465553 AAAAATT
1 AAAAATA
465560 AAAAATA
1 AAAAATA
**
465567 AAAGGT-
1 AAAAATA
465573 AAAAATA
1 AAAAATA
465580 AAA
1 AAA
465583 GAAATAGAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
6 11 0.20
7 31 0.57
8 4 0.07
9 8 0.15
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (7 bp):
AAAAATA
Found at i:465583 original size:13 final size:13
Alignment explanation
Indices: 465559--465583 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
465549 AATAAAAAAT
465559 TAAAAATAAAAGG
1 TAAAAATAAAAGG
465572 TAAAAATAAAAG
1 TAAAAATAAAAG
465584 AAATAGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (13 bp):
TAAAAATAAAAGG
Found at i:465695 original size:26 final size:24
Alignment explanation
Indices: 465642--465697 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 24
465632 AAAAAACATG
*
465642 AAATAAAAAAAAACTAATAAAGGA
1 AAATAAAAAAAAACTAATAAAGAA
*
465666 AAATAAAAAGAAAGACTAA-AAATAA
1 AAATAAAAA-AAA-ACTAATAAAGAA
465691 CAAATAA
1 -AAATAA
465698 TAATAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 9 0.33
25 7 0.26
26 11 0.41
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.12
Consensus pattern (24 bp):
AAATAAAAAAAAACTAATAAAGAA
Found at i:465856 original size:18 final size:18
Alignment explanation
Indices: 465835--465886 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
465825 AAAATTAAAG
465835 AAAAAAAGAAACAAAAAT
1 AAAAAAAGAAACAAAAAT
* *
465853 -AAAATAGAAAAATAAAAT
1 AAAAAAAGAAACA-AAAAT
465871 AAAATAAA-AAACAAAA
1 AAAA-AAAGAAACAAAA
465887 CAAAACAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
17 10 0.37
18 8 0.30
19 7 0.26
20 2 0.07
ACGTcount: A:0.83, C:0.04, G:0.04, T:0.10
Consensus pattern (18 bp):
AAAAAAAGAAACAAAAAT
Found at i:465863 original size:13 final size:13
Alignment explanation
Indices: 465847--465871 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
465837 AAAAAGAAAC
465847 AAAAATAAAATAG
1 AAAAATAAAATAG
465860 AAAAATAAAATA
1 AAAAATAAAATA
465872 AAATAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAATAAAATAG
Found at i:465863 original size:23 final size:22
Alignment explanation
Indices: 465837--465908 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 22
465827 AATTAAAGAA
*
465837 AAAAAGAAACAAAAATAAAATAG
1 AAAAA-AAACAAAAATAAAATAC
*
465860 AAAAATAAA-ATAAAATAAAAAAC
1 AAAAA-AAACA-AAAATAAAATAC
465883 AAAACAAAACAAAAATAAGAATAC
1 AAAA-AAAACAAAAATAA-AATAC
465907 AA
1 AA
465909 TACATTTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
22 1 0.02
23 32 0.78
24 8 0.20
ACGTcount: A:0.79, C:0.07, G:0.04, T:0.10
Consensus pattern (22 bp):
AAAAAAAACAAAAATAAAATAC
Found at i:465866 original size:41 final size:41
Alignment explanation
Indices: 465821--465899 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 41
465811 TAATGGAAAC
*
465821 AAATAAAATTAAAGAAAAAA-AGAAACAAAA-ATAAAATAGAA
1 AAATAAAATAAAAGAAAAAACA-AAACAAAACA-AAAATAGAA
*
465862 AAATAAAATAAAATAAAAAACAAAACAAAACAAAAATA
1 AAATAAAATAAAAGAAAAAACAAAACAAAACAAAAATA
465900 AGAATACAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 32 0.94
42 2 0.06
ACGTcount: A:0.80, C:0.05, G:0.04, T:0.11
Consensus pattern (41 bp):
AAATAAAATAAAAGAAAAAACAAAACAAAACAAAAATAGAA
Found at i:467728 original size:85 final size:85
Alignment explanation
Indices: 467522--468544 Score: 1441
Period size: 85 Copynumber: 12.1 Consensus size: 85
467512 AATTGAATTA
* * * *
467522 AACTCAAAGGTATTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTTGATATGC
1 AACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
* *
467587 CTTT-AACTGAGTGTAATCG
66 CTTTGAGCTGAATGTAATCG
* * * * * *
467606 AACTCGAAGGTCTTGGTTGACAGATATCCTTTCTCGCCTTGAGTTATGCTGTAAATTTGACATTC
1 AACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
* *
467671 CTTTGAGCTGAGTGTAATAG
66 CTTTGAGCTGAATGTAATCG
* * * * * * *
467691 AACTCGAAGGTATTGGTTGACAAAAAACCCTTTTCGCCTTGAGCTATGTTGTAAATTTGACATGC
1 AACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
467756 CTTTGAGCTGAATGTAATCG
66 CTTTGAGCTGAATGTAATCG
* *
467776 AACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATTTGA-AGTG
1 AACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATA-TG
467840 CCTTTGAGCTGAATGTAATCG
65 CCTTTGAGCTGAATGTAATCG
*
467861 AACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTATAAATTTGATATG
1 AACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATG
467926 CCTTTGAGCTGAATGTAATCG
65 CCTTTGAGCTGAATGTAATCG
* * * *
467947 AACTCGAAGGTCTTTGTTGACACATATCCCTTCTCGCCTTGAGCTATGCTGCAAATTTGATGTGC
1 AACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
*
468012 CTTTGAGCTGAACGTAATCG
66 CTTTGAGCTGAATGTAATCG
* * * *
468032 AACTCGAAGGTTTTTAGTTGACAGATAGCCCTTTTTGCCTTGAGCTATGCTGTAAATTTGATATG
1 AACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATG
* *
468097 CCTTTGAGCTTAGTGTAATCG
65 CCTTTGAGCTGAATGTAATCG
* * * * *
468118 AACTCGAAGGTATTTGTTGACAGATAGCCCTTTTCGCCTTGAGCTATGCTGCAAATTTGATGTGC
1 AACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
*
468183 TTTTGAGCTGAATGTAATCG
66 CTTTGAGCTGAATGTAATCG
468203 AACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
1 AACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
*
468268 CTTTGAGCTGAATATAATCG
66 CTTTGAGCTGAATGTAATCG
* * * *
468288 AACTCGAAGGTCTTTGCTGACAGATAACCCTTCTCACCTTGAGTTATGCTATAAATTTGATATGC
1 AACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
*
468353 CTTTGAGCTAAATGTAATCG
66 CTTTGAGCTGAATGTAATCG
* *
468373 AACTCGAAGGT-TTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTAATGTG
1 AACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATG
* *
468437 CCTTTGAGCTGAGTGTAATCA
65 CCTTTGAGCTGAATGTAATCG
* * * * *
468458 AACTCGAAGGTCTTGGTTGACAGATAACCATTCTCGCCTTGAGTTTTACTGT-AA----ATATGC
1 AACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
*
468518 CTTTGAGCTTAATGTAATCG
66 CTTTGAGCTGAATGTAATCG
468538 AACTCGA
1 AACTCGA
468545 TTCTTTCTGA
Statistics
Matches: 846, Mismatches: 86, Indels: 18
0.89 0.09 0.02
Matches are distributed among these distances:
80 29 0.03
84 67 0.08
85 592 0.70
86 157 0.19
87 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (85 bp):
AACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
CTTTGAGCTGAATGTAATCG
Found at i:472166 original size:17 final size:17
Alignment explanation
Indices: 472140--472173 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
472130 ACCTCTTTTG
* *
472140 AATGATGTAAATGAAAA
1 AATGAAGTAAAAGAAAA
472157 AATGAAGTAAAAGAAAA
1 AATGAAGTAAAAGAAAA
472174 TAAAAATTAA
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:0.65, C:0.00, G:0.18, T:0.18
Consensus pattern (17 bp):
AATGAAGTAAAAGAAAA
Found at i:473155 original size:6 final size:6
Alignment explanation
Indices: 473144--473184 Score: 73
Period size: 6 Copynumber: 6.7 Consensus size: 6
473134 TTTACTTGCG
473144 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATTT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAA-TT AAAA
473185 AATTCAACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 28 0.82
7 6 0.18
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:473318 original size:19 final size:20
Alignment explanation
Indices: 473274--473319 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
473264 TATTAATATC
* *
473274 GTAATAACAATAAAATAAAT
1 GTAAAAACAATAAAATAAAA
*
473294 GAAAAAACAA-AAAATAAAA
1 GTAAAAACAATAAAATAAAA
473313 GTAAAAA
1 GTAAAAA
473320 GGTAAAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (20 bp):
GTAAAAACAATAAAATAAAA
Found at i:473318 original size:20 final size:20
Alignment explanation
Indices: 473279--473319 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
473269 ATATCGTAAT
*
473279 AACAATAAAATAAATGAAAA
1 AACAATAAAATAAAAGAAAA
473299 AACAA-AAAATAAAAGTAAAA
1 AACAATAAAATAAAAG-AAAA
473319 A
1 A
473320 GGTAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.12
Consensus pattern (20 bp):
AACAATAAAATAAAAGAAAA
Found at i:473517 original size:17 final size:18
Alignment explanation
Indices: 473491--473537 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
473481 ACAATTTTAA
*
473491 AAAAAGAAAAAA-GGAAT
1 AAAAAGAAAAAATGAAAT
*
473508 AAAAATAAAAAATGAAAT
1 AAAAAGAAAAAATGAAAT
*
473526 AAAAGGAAAAAA
1 AAAAAGAAAAAA
473538 AGGCACGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.09
Consensus pattern (18 bp):
AAAAAGAAAAAATGAAAT
Done.