Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397268.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_81.0, 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: 6219335
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 77647 characters in sequence are not A, C, G, or T
File 11 of 13
Found at i:5176440 original size:13 final size:11
Alignment explanation
Indices: 5176413--5176444 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
5176403 CAACTTGTTT
5176413 ACACACAATTA
1 ACACACAATTA
5176424 ACACACAATTA
1 ACACACAATTA
5176435 ACACACAATT
1 ACACACAATT
5176445 GATACAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (11 bp):
ACACACAATTA
Found at i:5185560 original size:30 final size:31
Alignment explanation
Indices: 5185525--5185588 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
5185515 AGGGGTGAAG
5185525 TTGTAA-TTATGAACAAG-TTAAAGGATCAAA
1 TTGTAATTTATGAA-AAGCTTAAAGGATCAAA
* *
5185555 TTGTAATTTATGAAATGCTTGAAGGATCAAA
1 TTGTAATTTATGAAAAGCTTAAAGGATCAAA
5185586 TTG
1 TTG
5185589 AAAAGGATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 8 0.27
31 22 0.73
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (31 bp):
TTGTAATTTATGAAAAGCTTAAAGGATCAAA
Found at i:5188070 original size:25 final size:26
Alignment explanation
Indices: 5188042--5188090 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
5188032 AAGGCCATGG
*
5188042 GTTGGTATATGTGGCTAGG-CCACAA
1 GTTGGTATAGGTGGCTAGGACCACAA
* *
5188067 GTTGTTATAGGTGGTTAGGACCAC
1 GTTGGTATAGGTGGCTAGGACCAC
5188091 TTGATTTCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.22, C:0.14, G:0.33, T:0.31
Consensus pattern (26 bp):
GTTGGTATAGGTGGCTAGGACCACAA
Found at i:5192815 original size:77 final size:79
Alignment explanation
Indices: 5192652--5192818 Score: 216
Period size: 77 Copynumber: 2.2 Consensus size: 79
5192642 TAAATACTAT
* * **
5192652 ATATTTTAATTTTGGGTGATTCATAAAAAAATAAAAAATGATTTCCTCCTTTAAAAGTAATTCCT
1 ATATTTTAATTTTGGGTGATTCATAAAAAAATAAAAAATGACTTCCTACTTTAAAAAAAATTCCT
5192717 AAAATTAAGGATAG
66 AAAATTAAGGATAG
* ** * *
5192731 A-AGTTTAATTTTGGGTGATTCAT-AAAGGATAGGAAATTG-CTTCCTACTTTAAAAAAAATTCC
1 ATATTTTAATTTTGGGTGATTCATAAAAAAATA-AAAAATGACTTCCTACTTTAAAAAAAATTCC
5192793 TAAAATTAAGGATA-
65 TAAAATTAAGGATAG
5192807 ATATTTTAATTT
1 ATATTTTAATTT
5192819 GAGAAATTCA
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
76 1 0.01
77 48 0.63
78 26 0.34
79 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (79 bp):
ATATTTTAATTTTGGGTGATTCATAAAAAAATAAAAAATGACTTCCTACTTTAAAAAAAATTCCT
AAAATTAAGGATAG
Found at i:5210445 original size:10 final size:10
Alignment explanation
Indices: 5210432--5210465 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
5210422 TAATTTAAAA
5210432 TAAAATAACT
1 TAAAATAACT
5210442 TAAAATTAAC-
1 TAAAA-TAACT
5210452 TAAAATAACT
1 TAAAATAACT
5210462 TAAA
1 TAAA
5210466 TTGATCACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 4 0.18
10 14 0.64
11 4 0.18
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (10 bp):
TAAAATAACT
Found at i:5215583 original size:16 final size:15
Alignment explanation
Indices: 5215564--5215594 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
5215554 TTGATTTTTA
5215564 AACATTTGCATTACAT
1 AACATTTGCA-TACAT
5215580 AACATTTGCATACAT
1 AACATTTGCATACAT
5215595 TTTGTTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (15 bp):
AACATTTGCATACAT
Found at i:5220039 original size:23 final size:24
Alignment explanation
Indices: 5220004--5220058 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
5219994 AATTGAGACC
*
5220004 CAAAAAATTTGAAATTAAGTTAA-TT
1 CAAAAAA-TTGAAATTAA-CTAATTT
*
5220029 CAAAAAA-TGAATTTAACTAATTT
1 CAAAAAATTGAAATTAACTAATTT
5220052 CAAAAAA
1 CAAAAAA
5220059 ATCACGTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 3 0.11
23 17 0.63
25 7 0.26
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.31
Consensus pattern (24 bp):
CAAAAAATTGAAATTAACTAATTT
Found at i:5231770 original size:14 final size:14
Alignment explanation
Indices: 5231753--5231791 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
5231743 AAAACTTCAC
5231753 AATAAAATAATATT
1 AATAAAATAATATT
* **
5231767 AATAATATTTTATT
1 AATAAAATAATATT
5231781 AATAAAATAAT
1 AATAAAATAAT
5231792 TCTAAAATAT
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATAAAATAATATT
Found at i:5231808 original size:28 final size:28
Alignment explanation
Indices: 5231753--5231808 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
5231743 AAAACTTCAC
*
5231753 AATAAAATAATATTAATAATATTTTATT
1 AATAAAATAATATTAATAATATTATATT
5231781 AATAAAATAAT-TCTAA-AATATTAATATT
1 AATAAAATAATAT-TAATAATATT-ATATT
5231809 TTAACCGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (28 bp):
AATAAAATAATATTAATAATATTATATT
Found at i:5238782 original size:20 final size:20
Alignment explanation
Indices: 5238754--5238791 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5238744 GTTTTGGAGG
5238754 AAATCTATCGATACATTTAT
1 AAATCTATCGATACATTTAT
* *
5238774 AAATGTATCGATAGATTT
1 AAATCTATCGATACATTT
5238792 GGAAATTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (20 bp):
AAATCTATCGATACATTTAT
Found at i:5238797 original size:20 final size:20
Alignment explanation
Indices: 5238752--5238797 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
5238742 GTGTTTTGGA
5238752 GGAAATCTATCGATACATTT
1 GGAAATCTATCGATACATTT
** * *
5238772 ATAAATGTATCGATAGATTT
1 GGAAATCTATCGATACATTT
5238792 GGAAAT
1 GGAAAT
5238798 TAATGAACAT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (20 bp):
GGAAATCTATCGATACATTT
Found at i:5241629 original size:56 final size:55
Alignment explanation
Indices: 5241519--5241642 Score: 162
Period size: 56 Copynumber: 2.2 Consensus size: 55
5241509 GTAAGATGGT
5241519 CAAATAAAATAAGAAGAATAAGAATGCATGTATTGTGATTGGTTTCAAAAGGTGGC
1 CAAAT-AAATAAGAAGAATAAGAATGCATGTATTGTGATTGGTTTCAAAAGGTGGC
* * *
5241575 CAAATGAAATAAGAAGAATAAGAATGCATGTGTT-TGGATTGG-TTCATGAGGGTGGC
1 CAAAT-AAATAAGAAGAATAAGAATGCATGTATTGT-GATTGGTTTCA-AAAGGTGGC
*
5241631 CAAGTAAATAAG
1 CAAATAAATAAG
5241643 TAAAAGAGCA
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
55 12 0.20
56 49 0.80
ACGTcount: A:0.41, C:0.07, G:0.26, T:0.26
Consensus pattern (55 bp):
CAAATAAATAAGAAGAATAAGAATGCATGTATTGTGATTGGTTTCAAAAGGTGGC
Found at i:5257660 original size:31 final size:29
Alignment explanation
Indices: 5257587--5257663 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
5257577 TGATGAGTGG
* *
5257587 AATTGCAAATAATGAAAAGTAAAGGGATTA
1 AATTGC-AATTATGAAAAGTAAAGGGATCA
* *
5257617 AGTTGTAATTATGAACAAGTTAAA-GGATCA
1 AATTGCAATTATGAA-AAG-TAAAGGGATCA
5257647 AATTGCAATTTATGAAA
1 AATTGCAA-TTATGAAA
5257664 TGTTTGAAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
29 8 0.21
30 19 0.50
31 11 0.29
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (29 bp):
AATTGCAATTATGAAAAGTAAAGGGATCA
Found at i:5260165 original size:28 final size:24
Alignment explanation
Indices: 5260130--5260202 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 24
5260120 TTAGACGTGT
5260130 CAAGGCCACGGTATGTTATTATACATGG
1 CAAGGCCACGGT-TGTTA-TAT--ATGG
*
5260158 CAAGGCCACGGGTTGTTATATGTGG
1 CAAGGCCAC-GGTTGTTATATATGG
*
5260183 CAAGGCCACGAGTTGATATA
1 CAAGGCCACG-GTTGTTATA
5260203 CGTGGTTACC
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
24 1 0.02
25 20 0.49
27 3 0.07
28 14 0.34
29 3 0.07
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (24 bp):
CAAGGCCACGGTTGTTATATATGG
Found at i:5260183 original size:25 final size:25
Alignment explanation
Indices: 5260149--5260207 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
5260139 GGTATGTTAT
* * *
5260149 TATACATGGCAAGGCCACGGGTTGT
1 TATACGTGGCAAGGCCACGAGTTGA
*
5260174 TATATGTGGCAAGGCCACGAGTTGA
1 TATACGTGGCAAGGCCACGAGTTGA
5260199 TATACGTGG
1 TATACGTGG
5260208 TTACCACCAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.25
Consensus pattern (25 bp):
TATACGTGGCAAGGCCACGAGTTGA
Found at i:5265315 original size:11 final size:12
Alignment explanation
Indices: 5265281--5265318 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5265271 GGAAAGAGAG
*
5265281 GAAAGAAAGAAA
1 GAAAGAGAGAAA
*
5265293 GGAAGAGAGAAA
1 GAAAGAGAGAAA
5265305 GAAAG-GAGAAA
1 GAAAGAGAGAAA
5265316 GAA
1 GAA
5265319 GAAAAAGACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (12 bp):
GAAAGAGAGAAA
Found at i:5272506 original size:19 final size:19
Alignment explanation
Indices: 5272482--5272530 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
5272472 AAAATTTTAA
5272482 AATAAAATAATATTTTATT
1 AATAAAATAATATTTTATT
*
5272501 AATAAAATAACATTTTATT
1 AATAAAATAATATTTTATT
5272520 AATAAAATAAT
1 AATAAAATAAT
5272531 TTAAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
AATAAAATAATATTTTATT
Found at i:5281389 original size:35 final size:35
Alignment explanation
Indices: 5281350--5281457 Score: 132
Period size: 35 Copynumber: 3.2 Consensus size: 35
5281340 TTTAATTGTC
5281350 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* * * * *
5281385 TAATTTAGTTAATTAAGCCTAATGACTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
*
5281420 TAATTTAATGAATTAGG--C-ATAACTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
*
5281452 CAATTT
1 TAATTT
5281458 TANNNNNNNN
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
32 18 0.29
35 44 0.71
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.38
Consensus pattern (35 bp):
TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
Found at i:5290097 original size:6 final size:6
Alignment explanation
Indices: 5290086--5290111 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5290076 ATTGGTGATA
5290086 ATGAAG ATGAAG ATGAAG ATGAAG AT
1 ATGAAG ATGAAG ATGAAG ATGAAG AT
5290112 TAGAGCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (6 bp):
ATGAAG
Found at i:5291799 original size:16 final size:16
Alignment explanation
Indices: 5291778--5291814 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
5291768 TTTTAATTGG
5291778 ACTAGGAGAGTGCATT
1 ACTAGGAGAGTGCATT
5291794 ACTAGGAGAGTGCATT
1 ACTAGGAGAGTGCATT
5291810 -CTAGG
1 ACTAGG
5291815 TGCAAACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.30, C:0.14, G:0.32, T:0.24
Consensus pattern (16 bp):
ACTAGGAGAGTGCATT
Found at i:5292892 original size:16 final size:18
Alignment explanation
Indices: 5292866--5292906 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
5292856 TTCTTGTTAA
5292866 TTAGATTTAGTTAATT-T
1 TTAGATTTAGTTAATTAT
5292883 TTAG-TTTAGTTAATTAT
1 TTAGATTTAGTTAATTAT
5292900 TTA-ATTT
1 TTAGATTT
5292907 TGATTGGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (18 bp):
TTAGATTTAGTTAATTAT
Found at i:5303576 original size:21 final size:21
Alignment explanation
Indices: 5303517--5303578 Score: 56
Period size: 22 Copynumber: 3.0 Consensus size: 21
5303507 GTTTATTCTA
* *
5303517 AAAGTATTGATACA-TT-CAT
1 AAAGTATCGATACATTTGAAT
* *
5303536 ATAAGTATCAATATCTTTTGAAT
1 A-AAGTATCGATA-CATTTGAAT
5303559 AAAGTATCGATACATTTGAA
1 AAAGTATCGATACATTTGAA
5303579 ACAAAAAGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
19 1 0.03
20 9 0.27
21 8 0.24
22 12 0.36
23 3 0.09
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (21 bp):
AAAGTATCGATACATTTGAAT
Found at i:5306025 original size:21 final size:22
Alignment explanation
Indices: 5305990--5306033 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
5305980 CTCTTAAAGT
5305990 AATTTAAAATAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
*
5306012 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
5306033 A
1 A
5306034 TTAATCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (22 bp):
AATTTAAAATAAAATAACTTAA
Found at i:5306037 original size:26 final size:27
Alignment explanation
Indices: 5305994--5306046 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
5305984 TAAAGTAATT
*
5305994 TAAAATAAAATAACTTAA-AATTTAAC
1 TAAAATAAAATAAATTAATAATTTAAC
** *
5306020 TAAAATAACTTAAATTAATCATTTAAC
1 TAAAATAAAATAAATTAATAATTTAAC
5306047 AAGTAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (27 bp):
TAAAATAAAATAAATTAATAATTTAAC
Found at i:5313028 original size:68 final size:68
Alignment explanation
Indices: 5312910--5313232 Score: 319
Period size: 68 Copynumber: 4.8 Consensus size: 68
5312900 TGATGAATGT
* * * *
5312910 GATTTTGTATATGATGTAAATTCCATATACCATGTGAGATGATAAAGTATGCATGATGT-ATAG-
1 GATTTTGTATATGATGTAAATTCCATATACTATATAAGATGATTAAGTATGCATGAT-TAAT-GC
* *
5312973 TATAA
64 CATGA
* * * * * *
5312978 GATTGTGTATGTGATGTAAATTCCATATACTGTATAAGGTGATTAGGTATGCATTATTAATGCCA
1 GATTTTGTATATGATGTAAATTCCATATACTATATAAGATGATTAAGTATGCATGATTAATGCCA
5313043 TGA
66 TGA
* * * *
5313046 GATTATGTATATGATGTATATTCCATATACTACATAAGATGATTAAATATGCATGATTAATGCCA
1 GATTTTGTATATGATGTAAATTCCATATACTATATAAGATGATTAAGTATGCATGATTAATGCCA
5313111 TGA
66 TGA
* * * * * * * *
5313114 GATTTTGTATATGATGTATATTCCATATACTACATGAGATGATTGAGCAAGCTTGATAAATGCCA
1 GATTTTGTATATGATGTAAATTCCATATACTATATAAGATGATTAAGTATGCATGATTAATGCCA
*
5313179 TAA
66 TGA
* ** * * *
5313182 GATTATGCGTATGATGTAAATTCCGTATACCT-TATGAGATGAGTAAGTATG
1 GATTTTGTATATGATGTAAATTCCATATA-CTATATAAGATGATTAAGTATG
5313233 TATGTGAAGG
Statistics
Matches: 212, Mismatches: 40, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
67 2 0.01
68 208 0.98
69 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.37
Consensus pattern (68 bp):
GATTTTGTATATGATGTAAATTCCATATACTATATAAGATGATTAAGTATGCATGATTAATGCCA
TGA
Found at i:5329675 original size:28 final size:29
Alignment explanation
Indices: 5329599--5329677 Score: 74
Period size: 28 Copynumber: 2.8 Consensus size: 29
5329589 ACATCAACCT
*
5329599 TTTC-AAGGATCAAGCAAAA-CTTCAGCC
1 TTTCTAAGGATCAGGCAAAACCTTCAGCC
* * *** *
5329626 TTTTTGAGGATCAGGTTGAACCTT-GGCC
1 TTTCTAAGGATCAGGCAAAACCTTCAGCC
5329654 TTTCTAAGGATCAGGCAAAACCTT
1 TTTCTAAGGATCAGGCAAAACCTT
5329678 TACATCATTG
Statistics
Matches: 38, Mismatches: 12, Indels: 3
0.72 0.23 0.06
Matches are distributed among these distances:
27 3 0.08
28 32 0.84
29 3 0.08
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (29 bp):
TTTCTAAGGATCAGGCAAAACCTTCAGCC
Found at i:5330266 original size:21 final size:21
Alignment explanation
Indices: 5330223--5330275 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
5330213 TGCCAGGTAC
*
5330223 CAAGGCTTTGAAACCAAGCAT
1 CAAGACTTTGAAACCAAGCAT
* *
5330244 CAAGATTTTGAAACC-AGATAT
1 CAAGACTTTGAAACCAAG-CAT
5330265 CAAGACTTTGA
1 CAAGACTTTGA
5330276 CTCTAGGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.25
Consensus pattern (21 bp):
CAAGACTTTGAAACCAAGCAT
Found at i:5331557 original size:69 final size:68
Alignment explanation
Indices: 5331403--5331557 Score: 188
Period size: 68 Copynumber: 2.3 Consensus size: 68
5331393 CTAACTCAGA
* *
5331403 CCTGTGGTATTCTTACCCCCACATCAGGACTCATAAGAAGGGGAAAAGTGGTAGATGCCTAACTT
1 CCTGTGGTATTCTTACCCCCACACCAGGACTCATAAGAAGGGAAAAAGTGGTAGATGCCTAACTT
5331468 AAC
66 AAC
* * * * * * *
5331471 CTTATGGTATTCGTACCCCCACACCTA-GATTTATAAGGAGGGAAAAAGTGGTATGATGCCCT-T
1 CCTGTGGTATTCTTACCCCCACACC-AGGACTCATAAGAAGGGAAAAAGTGGTA-GATG-CCTAA
5331534 CTTAAC
63 CTTAAC
5331540 CCTGTGGTATTCTTACCC
1 CCTGTGGTATTCTTACCC
5331558 TACATTGAGA
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
68 43 0.60
69 26 0.36
70 3 0.04
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (68 bp):
CCTGTGGTATTCTTACCCCCACACCAGGACTCATAAGAAGGGAAAAAGTGGTAGATGCCTAACTT
AAC
Found at i:5332775 original size:50 final size:49
Alignment explanation
Indices: 5332672--5332786 Score: 133
Period size: 50 Copynumber: 2.3 Consensus size: 49
5332662 AATTGATGAA
* * *
5332672 ATGTATCGATATATTTGGTTCTGGAAAGATTGTATTGATACATTTGGCCC
1 ATGTATCGATACATTTAGTTCTGGAAAAATTGTATTGATACATTTGG-CC
* * *
5332722 ATGTATCGATGCATTTAGTTTTGGAAAAATTGTTTTGATACATTATGAG-C
1 ATGTATCGATACATTTAGTTCTGGAAAAATTGTATTGATACATT-TG-GCC
*
5332772 ATGTATCAATACATT
1 ATGTATCGATACATT
5332787 ATGAATATGT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
50 52 0.95
51 2 0.04
52 1 0.02
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (49 bp):
ATGTATCGATACATTTAGTTCTGGAAAAATTGTATTGATACATTTGGCC
Found at i:5332804 original size:21 final size:20
Alignment explanation
Indices: 5332757--5332812 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
5332747 AAAATTGTTT
**
5332757 TGATACATTATGAGCATGTA
1 TGATACATTATGAATATGTA
*
5332777 TCAATACATTATGAATATGTAA
1 T-GATACATTATGAATATGT-A
5332799 TGATACATT-TGAAT
1 TGATACATTATGAAT
5332813 CAGAATACAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.20
21 22 0.73
22 2 0.07
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (20 bp):
TGATACATTATGAATATGTA
Found at i:5333008 original size:16 final size:15
Alignment explanation
Indices: 5332984--5333014 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
5332974 ATAAAAATAT
5332984 CAAAAAATCAAAATC
1 CAAAAAATCAAAATC
5332999 CAAAAGAATCAAAATC
1 CAAAA-AATCAAAATC
5333015 TGAATTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.65, C:0.19, G:0.03, T:0.13
Consensus pattern (15 bp):
CAAAAAATCAAAATC
Found at i:5339219 original size:45 final size:45
Alignment explanation
Indices: 5339151--5339347 Score: 215
Period size: 45 Copynumber: 4.5 Consensus size: 45
5339141 CATGCCAGAA
* * * * * *
5339151 TGTTACACACCGTGTACAGAAACATGTTACATGCCATGGTTAGGT
1 TGTTACACGCCATGTACAAAAACATGTTACACGCCATGATTAAGT
5339196 TGTTACACGCCATGTACAAAAACATGTTACACGCCATGATT-AG-
1 TGTTACACGCCATGTACAAAAACATGTTACACGCCATGATTAAGT
* * * * * *
5339239 -GTTACACGCCATGTACAAAAACGTATGACACGTCGTGGTTAAGT
1 TGTTACACGCCATGTACAAAAACATGTTACACGCCATGATTAAGT
* * *
5339283 TGTTACACGCTATGTAC--AAACATGTTACACACTATGATTAAGT
1 TGTTACACGCCATGTACAAAAACATGTTACACGCCATGATTAAGT
*
5339326 TGTTACACGCCATATACAAAAA
1 TGTTACACGCCATGTACAAAAA
5339348 GATACTGTTG
Statistics
Matches: 124, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
42 34 0.27
43 35 0.28
44 1 0.01
45 54 0.44
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (45 bp):
TGTTACACGCCATGTACAAAAACATGTTACACGCCATGATTAAGT
Found at i:5339298 original size:87 final size:87
Alignment explanation
Indices: 5339187--5339347 Score: 236
Period size: 87 Copynumber: 1.8 Consensus size: 87
5339177 TTACATGCCA
* *
5339187 TGGTTAGGTTGTTACACGCCATGTACAAAAACATGTTACACGCCATGATT-AG-GTTACACGCCA
1 TGGTTAAGTTGTTACACGCCATGTAC--AAACATGTTACACACCATGATTAAGTGTTACACGCCA
*
5339250 TGTACAAAAACGTATGACACGTCG
64 TATACAAAAACGTATGACACGTCG
* *
5339274 TGGTTAAGTTGTTACACGCTATGTACAAACATGTTACACACTATGATTAAGTTGTTACACGCCAT
1 TGGTTAAGTTGTTACACGCCATGTACAAACATGTTACACACCATGATTAAG-TGTTACACGCCAT
5339339 ATACAAAAA
65 ATACAAAAA
5339348 GATACTGTTG
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
85 20 0.30
86 2 0.03
87 24 0.36
88 20 0.30
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (87 bp):
TGGTTAAGTTGTTACACGCCATGTACAAACATGTTACACACCATGATTAAGTGTTACACGCCATA
TACAAAAACGTATGACACGTCG
Found at i:5339331 original size:21 final size:22
Alignment explanation
Indices: 5339277--5339333 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
5339267 CACGTCGTGG
*
5339277 TTAAGTTGTTACACGCTATGTA
1 TTAAGTTGTTACACACTATGTA
** **
5339299 CAAACATGTTACACACTATG-A
1 TTAAGTTGTTACACACTATGTA
5339320 TTAAGTTGTTACAC
1 TTAAGTTGTTACAC
5339334 GCCATATACA
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (22 bp):
TTAAGTTGTTACACACTATGTA
Found at i:5344598 original size:26 final size:26
Alignment explanation
Indices: 5344569--5344622 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
5344559 TCACCTCCCT
* * *
5344569 CTCTATTAATGTAGGCTATCACTTAA
1 CTCTATTAATATAGGCCAGCACTTAA
5344595 CTCTATTAATATAGGCCAGCACTTAA
1 CTCTATTAATATAGGCCAGCACTTAA
5344621 CT
1 CT
5344623 AAAGATCCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.35
Consensus pattern (26 bp):
CTCTATTAATATAGGCCAGCACTTAA
Found at i:5358158 original size:12 final size:13
Alignment explanation
Indices: 5358140--5358175 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
5358130 CTTTTTCTAA
5358140 AGAAAAAAAAAAG
1 AGAAAAAAAAAAG
*
5358153 -GAAAAACAAAAG
1 AGAAAAAAAAAAG
5358165 AGAAAAAAAAA
1 AGAAAAAAAAA
5358176 GGTTTTTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAAAG
Found at i:5361230 original size:36 final size:36
Alignment explanation
Indices: 5361190--5361261 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
5361180 TGCAAATCTG
*
5361190 GACTTAAGAAGTCGACCCCAGCACAAAAAGGGTCAA
1 GACTTAAGAAGTCGACCCCAGCACAAAAAAGGTCAA
*
5361226 GACTTAAGAAGTCGACCCGAGCACAAAAAAGGTCAA
1 GACTTAAGAAGTCGACCCCAGCACAAAAAAGGTCAA
5361262 TCTCGTGTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.43, C:0.24, G:0.22, T:0.11
Consensus pattern (36 bp):
GACTTAAGAAGTCGACCCCAGCACAAAAAAGGTCAA
Found at i:5370819 original size:29 final size:29
Alignment explanation
Indices: 5370777--5370834 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
5370767 GCACCTTTAA
5370777 TCAAGGGCTTCACCTACCAAGCTCGTGCC
1 TCAAGGGCTTCACCTACCAAGCTCGTGCC
*
5370806 TCAAGGGCTTCACCTGCCAAGCTCGTGCC
1 TCAAGGGCTTCACCTACCAAGCTCGTGCC
5370835 CCAATCATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.19, C:0.38, G:0.22, T:0.21
Consensus pattern (29 bp):
TCAAGGGCTTCACCTACCAAGCTCGTGCC
Found at i:5380728 original size:49 final size:49
Alignment explanation
Indices: 5380662--5380770 Score: 182
Period size: 49 Copynumber: 2.2 Consensus size: 49
5380652 GTTGAGGAAC
5380662 ATGTTCCATCCGGGGATGATTCTAGACAATGATATGATGTGAGATATGT
1 ATGTTCCATCCGGGGATGATTCTAGACAATGATATGATGTGAGATATGT
* * **
5380711 ATGTTCCTTCCGTGGATGATTCTAGATGATGATATGATGTGAGATATGT
1 ATGTTCCATCCGGGGATGATTCTAGACAATGATATGATGTGAGATATGT
5380760 ATGTTCCATCC
1 ATGTTCCATCC
5380771 ATAGAGGATT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 55 1.00
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.36
Consensus pattern (49 bp):
ATGTTCCATCCGGGGATGATTCTAGACAATGATATGATGTGAGATATGT
Found at i:5380786 original size:49 final size:49
Alignment explanation
Indices: 5380679--5380795 Score: 162
Period size: 49 Copynumber: 2.4 Consensus size: 49
5380669 ATCCGGGGAT
** * * * *
5380679 GATTCTAGACAATGATATGATGTGAGATATGTATGTTCCTTCCGTGGAT
1 GATTCTAGATGATGATATGATGTGAGATATGTATGTTCCATCCATAGAG
5380728 GATTCTAGATGATGATATGATGTGAGATATGTATGTTCCATCCATAGAG
1 GATTCTAGATGATGATATGATGTGAGATATGTATGTTCCATCCATAGAG
*
5380777 GATTTTAGATGATGGATAT
1 GATTCTAGATGAT-GATAT
5380796 TATGAGGTTG
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
49 55 0.92
50 5 0.08
ACGTcount: A:0.29, C:0.09, G:0.25, T:0.37
Consensus pattern (49 bp):
GATTCTAGATGATGATATGATGTGAGATATGTATGTTCCATCCATAGAG
Found at i:5393614 original size:21 final size:20
Alignment explanation
Indices: 5393590--5393657 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 20
5393580 TTCTCTTGCT
5393590 TTTCTTCTTTATTCTTTTTCC
1 TTTCTTCTTT-TTCTTTTTCC
*
5393611 TTTCCTTCTTTTTATTTTATCC
1 TTT-CTTCTTTTTCTTTT-TCC
* *
5393633 TTTCTTCCTTTCTCTTTTTAC
1 TTTCTT-CTTTTTCTTTTTCC
5393654 TTTC
1 TTTC
5393658 AAAATCGACT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 18 0.45
22 22 0.55
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTCTTCTTTTTCTTTTTCC
Found at i:5397363 original size:216 final size:217
Alignment explanation
Indices: 5396978--5397412 Score: 534
Period size: 216 Copynumber: 2.0 Consensus size: 217
5396968 TTTTAGATGA
* *
5396978 GTTTGAATGCAAACACTAGTATTGGATAAATGTTTAATTTAATTATTTAAACAATAATAAATATT
1 GTTTGAATGCAAACACTAGTATTAGATAAATATTTAATTTAATTATTTAAACAATAATAAATATT
* * * *
5397043 TATAAATGGGTATCGTGTTCGAGGTAGGTTCTCAAGGAACTTAAATAACAACATAATTGGATTCA
66 TATAAATGGGTATCGGGTTCGAGGCAGATTCTCAAGGAACCTAAATAACAACATAATTGGATTCA
* **
5397108 GTTATCACTATCTAAACCCATCCCAAGCTTGGTTATAGGATA-CCTCAACCCTATATAACTGTCA
131 GGTATCACTATCTAAACCCATCCCAAGCTTGGTTATAGGATACCCT-AACCCTATATAACCATCA
5397172 AATATCAACATAATTGGGTTCAG
195 AATATCAACATAATTGGGTTCAG
* * * *
5397195 GTTTGAAT-CCAACACTAGTATTAGATAAATATTTAATTTAATTATTTAAATAGTAATAAATGTT
1 GTTTGAATGCAAACACTAGTATTAGATAAATATTTAATTTAATTATTTAAACAATAATAAATATT
* * * * ** * * *
5397259 TATGAATGGGTATTGGGTTCTAGGCA-ATTATTTGAGGAACCTGAATATCAACATAATTGGGTTC
66 TATAAATGGGTATCGGGTTCGAGGCAGATT-CTCAAGGAACCTAAATAACAACATAATTGGATTC
* * * * * * * * *
5397323 AGGTATCACTCTTTGAACTCATCTCAAGCTTTGTTATAGGATACCCTAATCTTATATAACCATCG
130 AGGTATCACTATCTAAACCCATCCCAAGCTTGGTTATAGGATACCCTAACCCTATATAACCATCA
* *
5397388 AATATCAATATAATTGGGTTTAG
195 AATATCAACATAATTGGGTTCAG
5397411 GT
1 GT
5397413 ATCACTATCT
Statistics
Matches: 183, Mismatches: 33, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
215 2 0.01
216 170 0.93
217 11 0.06
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (217 bp):
GTTTGAATGCAAACACTAGTATTAGATAAATATTTAATTTAATTATTTAAACAATAATAAATATT
TATAAATGGGTATCGGGTTCGAGGCAGATTCTCAAGGAACCTAAATAACAACATAATTGGATTCA
GGTATCACTATCTAAACCCATCCCAAGCTTGGTTATAGGATACCCTAACCCTATATAACCATCAA
ATATCAACATAATTGGGTTCAG
Found at i:5397446 original size:86 final size:86
Alignment explanation
Indices: 5397301--5397468 Score: 237
Period size: 86 Copynumber: 2.0 Consensus size: 86
5397291 TGAGGAACCT
* * * * **
5397301 GAATATCAACATAATTGGGTTCAGGTATCACTCTTTGAACTCATCTCAAGCTTTGTTATAGGATA
1 GAATATCAACATAATTGGGTTCAGGTATCACTATCTAAACTCATCCCAAGCTCAGTTATAGGATA
*
5397366 CCCTAATCTTATATAACCATC
66 CCCTAACCTTATATAACCATC
* * * *
5397387 GAATATCAATATAATTGGGTTTAGGTATCACTATCTAAACTCGTCCCAAGCTCAGTTATAGGGTA
1 GAATATCAACATAATTGGGTTCAGGTATCACTATCTAAACTCATCCCAAGCTCAGTTATAGGATA
5397452 CCCTAACCTTATATAAC
66 CCCTAACCTTATATAAC
5397469 TAGATAAAGT
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
86 71 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (86 bp):
GAATATCAACATAATTGGGTTCAGGTATCACTATCTAAACTCATCCCAAGCTCAGTTATAGGATA
CCCTAACCTTATATAACCATC
Found at i:5403726 original size:33 final size:36
Alignment explanation
Indices: 5403689--5403759 Score: 85
Period size: 33 Copynumber: 2.1 Consensus size: 36
5403679 AATATTATAA
*
5403689 CCTTATCACTTAATTAAACCA-TTT-TAA-TTAAGT
1 CCTTATCACTTAACTAAACCAGTTTATAATTTAAGT
* * *
5403722 CCTTATTAGTTAACTAAACTAGTTTATAATTTAAGT
1 CCTTATCACTTAACTAAACCAGTTTATAATTTAAGT
5403758 CC
1 CC
5403760 AACTTAAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
33 17 0.55
34 3 0.10
35 3 0.10
36 8 0.26
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (36 bp):
CCTTATCACTTAACTAAACCAGTTTATAATTTAAGT
Found at i:5403907 original size:19 final size:20
Alignment explanation
Indices: 5403871--5403908 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5403861 TTATTGATTA
5403871 ATTAAATGAATCCAATTCAT
1 ATTAAATGAATCCAATTCAT
*
5403891 ATTAAATTAAT-CAATTCA
1 ATTAAATGAATCCAATTCA
5403909 ATTCCATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (20 bp):
ATTAAATGAATCCAATTCAT
Found at i:5408124 original size:4 final size:4
Alignment explanation
Indices: 5408115--5408162 Score: 69
Period size: 4 Copynumber: 12.0 Consensus size: 4
5408105 CACCCATAAC
***
5408115 AAAG AAAG AAAG AAAG GGGG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
5408163 GAGGAAGAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:5408139 original size:16 final size:16
Alignment explanation
Indices: 5408118--5408188 Score: 76
Period size: 16 Copynumber: 4.6 Consensus size: 16
5408108 CCATAACAAA
*
5408118 GAAAGAAAGAAAGGGG
1 GAAAGAAAGAAAGGAG
* *
5408134 GAAAGAAAGAAAGAAA
1 GAAAGAAAGAAAGGAG
5408150 GAAAGAAAGAAAGGAG
1 GAAAGAAAGAAAGGAG
*
5408166 G-AAG-AAGAAA-AAG
1 GAAAGAAAGAAAGGAG
5408179 GAAAGGAAAG
1 GAAA-GAAAG
5408189 TCCGGGTTGG
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
13 3 0.07
14 8 0.17
15 4 0.09
16 31 0.67
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (16 bp):
GAAAGAAAGAAAGGAG
Found at i:5409636 original size:27 final size:25
Alignment explanation
Indices: 5409593--5409648 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 25
5409583 CATGGCTGGT
5409593 GCCATAGTCTGTGATATACGTGGCAAG
1 GCCATAGTCTGTGATAT--GTGGCAAG
* *
5409620 GCCATAGAT-TGTTATATGTGGCTAG
1 GCCATAG-TCTGTGATATGTGGCAAG
5409645 GCCA
1 GCCA
5409649 CAAGTGATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 11 0.42
27 14 0.54
28 1 0.04
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.29
Consensus pattern (25 bp):
GCCATAGTCTGTGATATGTGGCAAG
Found at i:5411627 original size:11 final size:11
Alignment explanation
Indices: 5411611--5411635 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5411601 AAACTGTGAT
5411611 AAGAAAAAAAG
1 AAGAAAAAAAG
5411622 AAGAAAAAAAG
1 AAGAAAAAAAG
5411633 AAG
1 AAG
5411636 TGTTGAACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAG
Found at i:5420071 original size:11 final size:11
Alignment explanation
Indices: 5420055--5420081 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5420045 AAAAACTCTA
5420055 TATCATAGAGT
1 TATCATAGAGT
5420066 TATCATAGAGT
1 TATCATAGAGT
5420077 TATCA
1 TATCA
5420082 AAAAACTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (11 bp):
TATCATAGAGT
Found at i:5421493 original size:21 final size:20
Alignment explanation
Indices: 5421454--5421493 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5421444 AAGTGAGCTA
* *
5421454 TTTTAATTTTATGTTATTTC
1 TTTTAATTTGATATTATTTC
5421474 TTTTAATTTGATTATTATTT
1 TTTTAATTTGA-TATTATTT
5421494 ATTAGTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.70
Consensus pattern (20 bp):
TTTTAATTTGATATTATTTC
Found at i:5421610 original size:24 final size:24
Alignment explanation
Indices: 5421578--5421625 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
5421568 AAAGTCTGCT
5421578 TACATATGCTTCAATGTTTTAGCC
1 TACATATGCTTCAATGTTTTAGCC
*
5421602 TACATATGCTTCAGTGTTTTAGCC
1 TACATATGCTTCAATGTTTTAGCC
5421626 ATAACTCGCA
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:0.23, C:0.21, G:0.15, T:0.42
Consensus pattern (24 bp):
TACATATGCTTCAATGTTTTAGCC
Found at i:5439149 original size:30 final size:29
Alignment explanation
Indices: 5439115--5439174 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
5439105 ACATGGCATG
*
5439115 TAACAACATTTTAAGCATAGCGTGTAACAA
1 TAACAACATTTTAA-CATAGCGTATAACAA
**
5439145 TAACAATTTTTTAACATAGCGTATAACAA
1 TAACAACATTTTAACATAGCGTATAACAA
5439174 T
1 T
5439175 TTTTTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (29 bp):
TAACAACATTTTAACATAGCGTATAACAA
Found at i:5439194 original size:28 final size:27
Alignment explanation
Indices: 5439151--5439208 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 27
5439141 ACAATAACAA
*
5439151 TTTTTTAACATAGCGTATAACAATTTT
1 TTTTTTAACATAGCGTATAACAACTTT
*
5439178 TTTTTTCAACATGGCGTATAACAACTTT
1 TTTTTT-AACATAGCGTATAACAACTTT
5439206 TTT
1 TTT
5439209 CAACATGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 6 0.21
28 22 0.79
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.48
Consensus pattern (27 bp):
TTTTTTAACATAGCGTATAACAACTTT
Found at i:5439206 original size:27 final size:27
Alignment explanation
Indices: 5439013--5439221 Score: 126
Period size: 27 Copynumber: 7.7 Consensus size: 27
5439003 GATTGCAACA
* *
5439013 TTTTTTCAACAAGGTGTGTTAACAACTTT
1 TTTTTTCAACATGGCGTG-TAACAAC-TT
* *
5439042 TTTTTTGCAGCATGGCATGTAACAACTT
1 TTTTTT-CAACATGGCGTGTAACAACTT
* ** * *
5439070 TTTTTCCAACATAACATGCAACAACTT
1 TTTTTTCAACATGGCGTGTAACAACTT
*
5439097 TTTTTTCAACATGGCATGTAACAAC--
1 TTTTTTCAACATGGCGTGTAACAACTT
* * **
5439122 -ATTTT-AAGCATAGCGTGTAACAATAACAA
1 TTTTTTCAA-CATGGCGTGTAAC---AACTT
* * *
5439151 TTTTTT-AACATAGCGTATAACAATTTT
1 TTTTTTCAACATGGCGTGTAACAA-CTT
*
5439178 TTTTTTCAACATGGCGTATAACAAC--
1 TTTTTTCAACATGGCGTGTAACAACTT
*
5439203 TTTTTTCAACATGGTGTGT
1 TTTTTTCAACATGGCGTGT
5439222 GTAATGACCG
Statistics
Matches: 145, Mismatches: 25, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
23 2 0.01
24 15 0.10
25 17 0.12
26 2 0.01
27 47 0.32
28 23 0.16
29 25 0.17
30 14 0.10
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (27 bp):
TTTTTTCAACATGGCGTGTAACAACTT
Found at i:5439212 original size:25 final size:24
Alignment explanation
Indices: 5439144--5439216 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 24
5439134 GCGTGTAACA
*
5439144 ATAACAATTTTTT-AACATAGCGT
1 ATAACAATTTTTTCAACATGGCGT
5439167 ATAACAATTTTTTTTTTCAACATGGCGT
1 ATAACAA----TTTTTTCAACATGGCGT
5439195 ATAACAACTTTTTTCAACATGG
1 ATAACAA-TTTTTTCAACATGG
5439217 TGTGTGTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
23 7 0.16
25 14 0.33
27 6 0.14
28 16 0.37
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (24 bp):
ATAACAATTTTTTCAACATGGCGT
Found at i:5439705 original size:26 final size:26
Alignment explanation
Indices: 5439627--5439794 Score: 97
Period size: 27 Copynumber: 6.2 Consensus size: 26
5439617 CATAGGCTTA
*
5439627 TAACAATTTTTTTTCAACATGGCGTG
1 TAACAATTTTTTTTCAACATGACGTG
* * *
5439653 TAATAACTATTTTTTCAATAT-AGCGTG
1 TAACAA-TTTTTTTTCAACATGA-CGTG
*
5439680 TAACAATTTTTTTTGAACATGACGTG
1 TAACAATTTTTTTTCAACATGACGTG
* * *
5439706 TGAA-AATAATATTTTTTCAATATAACATG
1 T-AACAAT--T-TTTTTTCAACATGACGTG
* * * *
5439735 TAACAGCTTTTTTTTTAAAATGACATG
1 TAACA-ATTTTTTTTCAACATGACGTG
* * * * *
5439762 CAATAGCTTCTTTTTCAACATGACATG
1 TAACA-ATTTTTTTTCAACATGACGTG
5439789 TAACAA
1 TAACAA
5439795 CATTTTATTC
Statistics
Matches: 109, Mismatches: 24, Indels: 18
0.72 0.16 0.12
Matches are distributed among these distances:
26 24 0.22
27 64 0.59
28 4 0.04
29 16 0.15
30 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (26 bp):
TAACAATTTTTTTTCAACATGACGTG
Found at i:5439725 original size:55 final size:53
Alignment explanation
Indices: 5439627--5439794 Score: 169
Period size: 53 Copynumber: 3.1 Consensus size: 53
5439617 CATAGGCTTA
* * *
5439627 TAACAATTTTTTTTCAACATGGCGTGTAATAACTATTTTTTCAATATAGCGTG
1 TAACAATTTTTTTTCAACATGACGTGTAATAACTATTTTTTCAATATAACATG
*
5439680 TAACAATTTTTTTTGAACATGACGTGTGAAAATAA-TATTTTTTCAATATAACATG
1 TAACAATTTTTTTTCAACATGACGTGT---AATAACTATTTTTTCAATATAACATG
* * * * * * * *
5439735 TAACAGCTTTTTTTTTAAAATGACATGCAATAGCT-TCTTTTTCAACATGACATG
1 TAACA-ATTTTTTTTCAACATGACGTGTAATAACTAT-TTTTTCAATATAACATG
5439789 TAACAA
1 TAACAA
5439795 CATTTTATTC
Statistics
Matches: 96, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
53 30 0.31
54 21 0.22
55 23 0.24
56 22 0.23
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (53 bp):
TAACAATTTTTTTTCAACATGACGTGTAATAACTATTTTTTCAATATAACATG
Found at i:5441181 original size:2 final size:2
Alignment explanation
Indices: 5441174--5441199 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5441164 TCGATAGATT
5441174 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
5441200 TTGAGTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5442296 original size:18 final size:18
Alignment explanation
Indices: 5442275--5442314 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5442265 AGTTTCACAA
* *
5442275 ATAATTTATAACTAACAC
1 ATAATTCATAAATAACAC
*
5442293 ATAATTCATAAATAACTC
1 ATAATTCATAAATAACAC
5442311 ATAA
1 ATAA
5442315 ATGAACGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAATTCATAAATAACAC
Found at i:5446361 original size:29 final size:28
Alignment explanation
Indices: 5446213--5446414 Score: 165
Period size: 28 Copynumber: 7.0 Consensus size: 28
5446203 TTAAGACAAC
* * *
5446213 TCTTGTCTTTAATTAAGACAAAAATATGTTA
1 TCTTGTC-TAAATTAAGAC--AAACATGTTT
* * *
5446244 TCTTGCCTAAATTGAGACAAATATG-TT
1 TCTTGTCTAAATTAAGACAAACATGTTT
* * *
5446271 TCTTG-CTTAGATTAATACAAAACATATTTT
1 TCTTGTC-TAAATTAAGAC-AAACAT-GTTT
* *
5446301 TCTTATCTCAAATTAAGACAAACATATTT
1 TCTTGTCT-AAATTAAGACAAACATGTTT
* *
5446330 TTTTGTCTAAATTAAGACCAAATATGTTT
1 TCTTGTCTAAATTAAGA-CAAACATGTTT
* *
5446359 TTTTGTCTAAATTAAGACAAGCATGTTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
* *
5446387 TCTTATCTAAATTAAGGCAAACATGTTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
5446415 AAGCTGTCAT
Statistics
Matches: 141, Mismatches: 23, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
26 1 0.01
27 14 0.10
28 54 0.38
29 35 0.25
30 22 0.16
31 15 0.11
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATGTTT
Found at i:5446376 original size:57 final size:57
Alignment explanation
Indices: 5446213--5446407 Score: 171
Period size: 57 Copynumber: 3.4 Consensus size: 57
5446203 TTAAGACAAC
* * * * *
5446213 TCTTGTCTTTAATTAAGACAAAAATATGTTATCTTGCCTAAATTGAGAC-AA-ATATGTT
1 TCTTGTC-TAAATTAAGAC-AAAATATGTTTTTTTGTCTAAATTAAGACAAACATAT-TT
* * * * *
5446271 TCTTG-CTTAGATTAATACAAAACATATTTTTCTTATCTCAAATTAAGACAAACATATTT
1 TCTTGTC-TAAATTAAGACAAAATATGTTTTT-TTGTCT-AAATTAAGACAAACATATTT
* * * *
5446330 TTTTGTCTAAATTAAGACCAAATATGTTTTTTTGTCTAAATTAAGACAAGCATGTTT
1 TCTTGTCTAAATTAAGACAAAATATGTTTTTTTGTCTAAATTAAGACAAACATATTT
* *
5446387 TCTTATCTAAATTAAGGCAAA
1 TCTTGTCTAAATTAAGACAAA
5446408 CATGTTTAAG
Statistics
Matches: 109, Mismatches: 23, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
56 9 0.08
57 49 0.45
58 19 0.17
59 27 0.25
60 5 0.05
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.41
Consensus pattern (57 bp):
TCTTGTCTAAATTAAGACAAAATATGTTTTTTTGTCTAAATTAAGACAAACATATTT
Found at i:5455366 original size:26 final size:25
Alignment explanation
Indices: 5455336--5455384 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
5455326 ATGTGACTGG
*
5455336 GGCCACAGTTTGTGATTATGTGGCAA
1 GGCCACAGGTTGTGA-TATGTGGCAA
* *
5455362 GGCCACGGGTTGTTATATGTGGC
1 GGCCACAGGTTGTGATATGTGGC
5455385 TAGTCCACCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.18, C:0.16, G:0.35, T:0.31
Consensus pattern (25 bp):
GGCCACAGGTTGTGATATGTGGCAA
Found at i:5461793 original size:26 final size:28
Alignment explanation
Indices: 5461737--5461793 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 28
5461727 ATTAAGATAA
* *
5461737 AAATATGTTATCCTGTCTAAATTGAGAC
1 AAATATGTTATCCTATCTAAATTAAGAC
* *
5461765 AAATATGTT-TCTTATC-AAATTAAGGC
1 AAATATGTTATCCTATCTAAATTAAGAC
5461791 AAA
1 AAA
5461794 ACATATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 11 0.44
27 5 0.20
28 9 0.36
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (28 bp):
AAATATGTTATCCTATCTAAATTAAGAC
Found at i:5461805 original size:29 final size:30
Alignment explanation
Indices: 5461716--5461913 Score: 162
Period size: 29 Copynumber: 6.7 Consensus size: 30
5461706 TTAAGACAAC
* * *
5461716 TCTTGTCTTTAATTAAGATAAAA-ATATGTTA
1 TCTTGTC-TAAATTAAGACAAAACATAT-TTT
* * *
5461747 TCCTGTCTAAATTGAGAC--AA-ATATGTT
1 TCTTGTCTAAATTAAGACAAAACATATTTT
* *
5461774 TCTTATC-AAATTAAGGCAAAACATATTTT
1 TCTTGTCTAAATTAAGACAAAACATATTTT
*
5461803 TCTTGTCTAAATTAAGAC-TAACATATTTT
1 TCTTGTCTAAATTAAGACAAAACATATTTT
*
5461832 T-TTGTC-AAATTAAGACCAAACA-ATTTT
1 TCTTGTCTAAATTAAGACAAAACATATTTT
* * *
5461859 TCTTCTCTAAATTAAGTCAAAGACAAACATGTTT
1 TCTTGTCTAAATTAAGACAAA-AC--ATAT-TTT
5461893 TCTTGTCTAAATTAAGACAAA
1 TCTTGTCTAAATTAAGACAAA
5461914 TATGTTTAAG
Statistics
Matches: 135, Mismatches: 20, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
26 8 0.06
27 22 0.16
28 21 0.16
29 34 0.25
30 19 0.14
31 6 0.04
32 1 0.01
33 2 0.01
34 22 0.16
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (30 bp):
TCTTGTCTAAATTAAGACAAAACATATTTT
Found at i:5461810 original size:56 final size:56
Alignment explanation
Indices: 5461750--5461874 Score: 164
Period size: 56 Copynumber: 2.2 Consensus size: 56
5461740 TATGTTATCC
* *
5461750 TGTCTAAATTGAGAC-AA-ATATGTTTCTTATCAAATTAAGGCAAAACATATTTTTCT
1 TGTCTAAATTAAGACTAACATAT-TTTCTTATCAAATTAAGACAAAACA-ATTTTTCT
* * *
5461806 TGTCTAAATTAAGACTAACATATTTTTTTGTCAAATTAAGACCAAACAATTTTTCT
1 TGTCTAAATTAAGACTAACATATTTTCTTATCAAATTAAGACAAAACAATTTTTCT
*
5461862 TCTCTAAATTAAG
1 TGTCTAAATTAAG
5461875 TCAAAGACAA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
56 34 0.56
57 23 0.38
58 4 0.07
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.40
Consensus pattern (56 bp):
TGTCTAAATTAAGACTAACATATTTTCTTATCAAATTAAGACAAAACAATTTTTCT
Found at i:5461887 original size:34 final size:35
Alignment explanation
Indices: 5461843--5461913 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 35
5461833 TTGTCAAATT
*
5461843 AAGACCAAACAAT-TTTTCTTCTCTAAATTAAGTCA
1 AAGACCAAAC-ATGTTTTCTTCTCTAAATTAAGACA
*
5461878 AAGA-CAAACATGTTTTCTTGTCTAAATTAAGACA
1 AAGACCAAACATGTTTTCTTCTCTAAATTAAGACA
5461912 AA
1 AA
5461914 TATGTTTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 2 0.06
34 27 0.82
35 4 0.12
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.32
Consensus pattern (35 bp):
AAGACCAAACATGTTTTCTTCTCTAAATTAAGACA
Found at i:5461918 original size:28 final size:28
Alignment explanation
Indices: 5461737--5461920 Score: 130
Period size: 28 Copynumber: 6.4 Consensus size: 28
5461727 ATTAAGATAA
* * *
5461737 AAATATGTTATCCTGTCTAAATTGAGAC
1 AAATATGTTTTCTTGTCTAAATTAAGAC
* *
5461765 AAATATG-TTTCTTATC-AAATTAAGGCAA
1 AAATATGTTTTCTTGTCTAAATTAA-G-AC
5461793 AACATAT-TTTTCTTGTCTAAATTAAGAC
1 AA-ATATGTTTTCTTGTCTAAATTAAGAC
5461821 TAACATAT-TTTT-TTGTC-AAATTAAGACC
1 -AA-ATATGTTTTCTTGTCTAAATTAAGA-C
* *
5461849 AAACAAT-TTTTCTTCTCTAAATTAAGTCAAAGAC
1 AAA-TATGTTTTCTTGTCTAAA-T---T--AAGAC
*
5461883 AAACATGTTTTCTTGTCTAAATTAAGAC
1 AAATATGTTTTCTTGTCTAAATTAAGAC
5461911 AAATATGTTT
1 AAATATGTTT
5461921 AAGCTGTCAT
Statistics
Matches: 127, Mismatches: 12, Indels: 34
0.73 0.07 0.20
Matches are distributed among these distances:
26 7 0.06
27 24 0.19
28 35 0.28
29 27 0.21
30 9 0.07
33 4 0.03
34 17 0.13
35 4 0.03
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (28 bp):
AAATATGTTTTCTTGTCTAAATTAAGAC
Found at i:5464579 original size:16 final size:17
Alignment explanation
Indices: 5464553--5464589 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
5464543 CTAAATCTTC
5464553 TGAACTTATTTTCAACA
1 TGAACTTATTTTCAACA
*
5464570 TGAA-TTATTTTTAACA
1 TGAACTTATTTTCAACA
5464586 TGAA
1 TGAA
5464590 ATATCTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (17 bp):
TGAACTTATTTTCAACA
Found at i:5466310 original size:29 final size:29
Alignment explanation
Indices: 5466268--5466330 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
5466258 TACCATGATC
* * *
5466268 ATGAAATATGCCATGATAATGTTAGTGTG
1 ATGAAACATGCCATGATAATATTAGTATG
*
5466297 ATGAAACATGCCATGATAATATTTGTATG
1 ATGAAACATGCCATGATAATATTAGTATG
5466326 ATGAA
1 ATGAA
5466331 GTACACCATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (29 bp):
ATGAAACATGCCATGATAATATTAGTATG
Found at i:5466865 original size:17 final size:17
Alignment explanation
Indices: 5466835--5466875 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
5466825 AGCTCCACCC
*
5466835 AAGAGGAAA-AAAAAAG
1 AAGAGGAAAGAAAAAAA
5466851 AA-AGGAAAGAAAAAAA
1 AAGAGGAAAGAAAAAAA
5466867 AAGAGGAAA
1 AAGAGGAAA
5466876 TGAAGGCTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 6 0.27
16 10 0.45
17 6 0.27
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAGAGGAAAGAAAAAAA
Found at i:5474701 original size:19 final size:19
Alignment explanation
Indices: 5474661--5474701 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
5474651 AGAATTTTAA
** *
5474661 AATAAAATAATATTTTATT
1 AATAAAATAATATTAAAAT
5474680 AATAAAATAATATTAAAAT
1 AATAAAATAATATTAAAAT
5474699 AAT
1 AAT
5474702 CTGATGCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATAAAATAATATTAAAAT
Found at i:5487697 original size:20 final size:19
Alignment explanation
Indices: 5487668--5487715 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
5487658 TAAATGTTTA
*
5487668 TTTTAAGTTACTAAAGTTAG
1 TTTTATGTTACTAAAGTT-G
* * *
5487688 TTTTATGTTATTTAAGTTT
1 TTTTATGTTACTAAAGTTG
5487707 TTTTATGTT
1 TTTTATGTT
5487716 TTTTTAGGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.25, C:0.02, G:0.12, T:0.60
Consensus pattern (19 bp):
TTTTATGTTACTAAAGTTG
Found at i:5495724 original size:14 final size:14
Alignment explanation
Indices: 5495695--5495773 Score: 70
Period size: 14 Copynumber: 5.5 Consensus size: 14
5495685 TTTTTCTTCT
* *
5495695 TCTTTCTTCCTCTC
1 TCTTTTTTCCTTTC
*
5495709 TCTTTTTTTCTTTC
1 TCTTTTTTCCTTTC
*
5495723 TCCTTTCTTCCTTTC
1 T-CTTTTTTCCTTTC
*
5495738 TCTTTTCTT-CTTTG
1 TCTTTT-TTCCTTTC
*
5495752 TCCTTTCTTCCTTTC
1 T-CTTTTTTCCTTTC
5495767 TCTTTTT
1 TCTTTTT
5495774 GCTTCCAAAC
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
14 28 0.55
15 23 0.45
ACGTcount: A:0.00, C:0.32, G:0.01, T:0.67
Consensus pattern (14 bp):
TCTTTTTTCCTTTC
Found at i:5495728 original size:29 final size:29
Alignment explanation
Indices: 5495685--5495773 Score: 135
Period size: 29 Copynumber: 3.1 Consensus size: 29
5495675 TCTCCTTTCG
* *
5495685 TTTTTC-TTCTTCTTTCTTCCTCTCTCTT
1 TTTTTCTTTCTCCTTTCTTCCTTTCTCTT
5495713 TTTTTCTTTCTCCTTTCTTCCTTTCTCTT
1 TTTTTCTTTCTCCTTTCTTCCTTTCTCTT
* *
5495742 TTCTTCTTTGTCCTTTCTTCCTTTCTCTT
1 TTTTTCTTTCTCCTTTCTTCCTTTCTCTT
5495771 TTT
1 TTT
5495774 GCTTCCAAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 6 0.11
29 49 0.89
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.69
Consensus pattern (29 bp):
TTTTTCTTTCTCCTTTCTTCCTTTCTCTT
Found at i:5495736 original size:15 final size:15
Alignment explanation
Indices: 5495691--5495768 Score: 88
Period size: 15 Copynumber: 5.3 Consensus size: 15
5495681 TTCGTTTTTC
*
5495691 TTCTTCTTTCTTCCT
1 TTCTCCTTTCTTCCT
* * *
5495706 CTCT-CTTTTTTTCT
1 TTCTCCTTTCTTCCT
5495720 TTCTCCTTTCTTCCT
1 TTCTCCTTTCTTCCT
*
5495735 TTCTCTTTTCTT-CT
1 TTCTCCTTTCTTCCT
*
5495749 TTGTCCTTTCTTCCT
1 TTCTCCTTTCTTCCT
5495764 TTCTC
1 TTCTC
5495769 TTTTTGCTTC
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
14 23 0.45
15 28 0.55
ACGTcount: A:0.00, C:0.33, G:0.01, T:0.65
Consensus pattern (15 bp):
TTCTCCTTTCTTCCT
Found at i:5495770 original size:21 final size:21
Alignment explanation
Indices: 5495731--5495771 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5495721 TCTCCTTTCT
*
5495731 TCCTTTCTCTTTTCTTCTTTG
1 TCCTTTCTCCTTTCTTCTTTG
5495752 TCCTTTCTTCCTTTC-TCTTT
1 TCCTTTC-TCCTTTCTTCTTT
5495772 TTGCTTCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66
Consensus pattern (21 bp):
TCCTTTCTCCTTTCTTCTTTG
Found at i:5496691 original size:40 final size:40
Alignment explanation
Indices: 5496633--5496711 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
5496623 AATTAGTCAT
* ** *
5496633 ATAATCTTCCTTTGTGACTAATTTCAACTATAGATAAAAC
1 ATAATCCTCCTTCATGACTAATTTCAACAATAGATAAAAC
5496673 ATAATCCTCCTTCATGACTAATTTCAACAATAGATAAAA
1 ATAATCCTCCTTCATGACTAATTTCAACAATAGATAAAA
5496712 TATTAATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (40 bp):
ATAATCCTCCTTCATGACTAATTTCAACAATAGATAAAAC
Found at i:5500004 original size:45 final size:45
Alignment explanation
Indices: 5499910--5500014 Score: 111
Period size: 45 Copynumber: 2.3 Consensus size: 45
5499900 CAGGTCTCGT
** ** * * *
5499910 ACCTTCTCCATTCTGTTTTGCTGCAGATCGCACCGCCGCACTCGT
1 ACCTTCTCCATTCTGGATTGCCACAGATCGCACCACCGCACCCGC
* * *
5499955 ACCTTCTCCATTTTGGATTGCCACAGATCGCATCACTGCACCCGC
1 ACCTTCTCCATTCTGGATTGCCACAGATCGCACCACCGCACCCGC
*
5500000 ACCTTCTCCGTTCTG
1 ACCTTCTCCATTCTG
5500015 CTTAGCCTCA
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.15, C:0.38, G:0.16, T:0.30
Consensus pattern (45 bp):
ACCTTCTCCATTCTGGATTGCCACAGATCGCACCACCGCACCCGC
Found at i:5502896 original size:28 final size:28
Alignment explanation
Indices: 5502865--5502919 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
5502855 ATTTGAAATT
5502865 TTATTTATATTTGATATAATGTATTTGC
1 TTATTTATATTTGATATAATGTATTTGC
* * * *
5502893 TTATTTATGTTTGGTGTAATTTATTTG
1 TTATTTATATTTGATATAATGTATTTG
5502920 TTTGTAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.24, C:0.02, G:0.15, T:0.60
Consensus pattern (28 bp):
TTATTTATATTTGATATAATGTATTTGC
Found at i:5508778 original size:13 final size:13
Alignment explanation
Indices: 5508760--5508787 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5508750 ACATACCGCC
5508760 TCTAAACATAACA
1 TCTAAACATAACA
5508773 TCTAAACATAACA
1 TCTAAACATAACA
5508786 TC
1 TC
5508788 AGTTTCCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (13 bp):
TCTAAACATAACA
Found at i:5514283 original size:105 final size:105
Alignment explanation
Indices: 5514127--5514343 Score: 242
Period size: 106 Copynumber: 2.1 Consensus size: 105
5514117 TGTGTATCAT
* * * *
5514127 ATACACTTTGATATCTTATATCAAATAGGTATAAACTCCTACTAATAAAAAA-ATATATTGAGTG
1 ATACAATTTGATATCTTATATCAAATAGGCATAAACTCCTACTAACAAAAAATATATATTAAGTG
** *
5514191 CGTATAGTTTTAACATGTTATCTCATAACAAGATGATTATA
66 CGTATAAATCTAACATGTTATCTCATAACAAGATGATTA-A
* * * * * *
5514232 ATACAATTTGATGTCTTATATCAAATATGCATAAGCTTCC-ATTAACCAAAAATATATTTTAAGT
1 ATACAATTTGATATCTTATATCAAATAGGCATAAAC-TCCTACTAACAAAAAATATATATTAAGT
* * * *
5514296 GTGTATAAATCTAACATGTTTTCTTATAACAAGATTATTAA
65 GCGTATAAATCTAACATGTTATCTCATAACAAGATGATTAA
5514337 A-ACAATT
1 ATACAATT
5514344 ATAGTTAATA
Statistics
Matches: 93, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
104 6 0.06
105 42 0.45
106 45 0.48
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.37
Consensus pattern (105 bp):
ATACAATTTGATATCTTATATCAAATAGGCATAAACTCCTACTAACAAAAAATATATATTAAGTG
CGTATAAATCTAACATGTTATCTCATAACAAGATGATTAA
Found at i:5516429 original size:30 final size:30
Alignment explanation
Indices: 5516387--5516451 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
5516377 CTCCCAAGAG
*
5516387 TGCTCCCTTCCCTTAGGACCACCATATCAA
1 TGCTCCCTTCCCTTAAGACCACCATATCAA
*
5516417 TGCTCGCC-TCCCTTAAGACCACCATATTAA
1 TGCTC-CCTTCCCTTAAGACCACCATATCAA
5516447 TGCTC
1 TGCTC
5516452 TTTTCCTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 30 0.94
31 2 0.06
ACGTcount: A:0.23, C:0.38, G:0.11, T:0.28
Consensus pattern (30 bp):
TGCTCCCTTCCCTTAAGACCACCATATCAA
Found at i:5521078 original size:57 final size:58
Alignment explanation
Indices: 5521002--5521110 Score: 202
Period size: 57 Copynumber: 1.9 Consensus size: 58
5520992 TTAAGTAATG
5521002 AAACTATATTTCACCAACAAACATTCGATAATTAGTTCAAACTAACCTGTAATCAATA
1 AAACTATATTTCACCAACAAACATTCGATAATTAGTTCAAACTAACCTGTAATCAATA
*
5521060 AAACTAT-TTTCACCAACAAACATTCGTTAATTAGTTCAAACTAACCTGTAA
1 AAACTATATTTCACCAACAAACATTCGATAATTAGTTCAAACTAACCTGTAA
5521111 CCTTGCAATT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
57 43 0.86
58 7 0.14
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.30
Consensus pattern (58 bp):
AAACTATATTTCACCAACAAACATTCGATAATTAGTTCAAACTAACCTGTAATCAATA
Found at i:5525780 original size:35 final size:36
Alignment explanation
Indices: 5525697--5525781 Score: 86
Period size: 35 Copynumber: 2.3 Consensus size: 36
5525687 GGAAATGAGA
*
5525697 TTTTTAATGAGATCAAGCATTAAACCCTTACAATCGC
1 TTTTT-ATGAGATAAAGCATTAAACCCTTACAATCGC
* *
5525734 TTTTTATTGAGATAAAGC--TATAACCCTTATAA-CGT
1 TTTTTA-TGAGATAAAGCATTA-AACCCTTACAATCGC
5525769 TTTTTCATGAGAT
1 TTTTT-ATGAGAT
5525782 CAAGTAGAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
35 15 0.36
36 12 0.29
37 15 0.36
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (36 bp):
TTTTTATGAGATAAAGCATTAAACCCTTACAATCGC
Found at i:5527863 original size:28 final size:28
Alignment explanation
Indices: 5527809--5527863 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
5527799 ATAAACAGGA
*
5527809 AATAAAGAAATGAAAAAAGAAAGAATGG
1 AATAAAGAAATCAAAAAAGAAAGAATGG
*
5527837 AATAAAGAAATCAAGAAAATAAA-AATG
1 AATAAAGAAATCAA-AAAAGAAAGAATG
5527864 AAAAAGGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.69, C:0.02, G:0.16, T:0.13
Consensus pattern (28 bp):
AATAAAGAAATCAAAAAAGAAAGAATGG
Found at i:5530583 original size:20 final size:20
Alignment explanation
Indices: 5530558--5530609 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
5530548 TTTATGTTTA
5530558 AATGTTTATTTTAAGTTAAT
1 AATGTTTATTTTAAGTTAAT
*
5530578 AATG-TTAGTTTTAAGTTATT
1 AATGTTTA-TTTTAAGTTAAT
*
5530598 TATGTTTATTTT
1 AATGTTTATTTT
5530610 TAATTTTCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 3 0.11
20 22 0.79
21 3 0.11
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.60
Consensus pattern (20 bp):
AATGTTTATTTTAAGTTAAT
Found at i:5532711 original size:73 final size:73
Alignment explanation
Indices: 5532620--5532787 Score: 239
Period size: 73 Copynumber: 2.3 Consensus size: 73
5532610 AAGGAGGTGA
* *
5532620 ATGTGGATGGTAAAATGCCCACAAGCATAAATTATGAGAGTGGGTGAATAAGTCTCCACCACTTG
1 ATGTGGATGGTAAAATGCCCACAAACATAAATTATGAGAGTGGATGAATAAGTCTCCACCACTTG
*
5532685 ATTGTTAT
66 ATTGATAT
* * * *
5532693 ATGTGGATGGTAATATGCCCACAAATATACATTATGAGAGTGGATGAGTAAGTCTCCACCACTTG
1 ATGTGGATGGTAAAATGCCCACAAACATAAATTATGAGAGTGGATGAATAAGTCTCCACCACTTG
5532758 ATTGATAT
66 ATTGATAT
* *
5532766 ATGTGAAT-ATAAAAATGCCCAC
1 ATGTGGATGGT-AAAATGCCCAC
5532788 TGATGAAATT
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
72 1 0.01
73 83 0.99
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (73 bp):
ATGTGGATGGTAAAATGCCCACAAACATAAATTATGAGAGTGGATGAATAAGTCTCCACCACTTG
ATTGATAT
Found at i:5533023 original size:35 final size:35
Alignment explanation
Indices: 5532978--5533044 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
5532968 ACATGTGTAA
* *
5532978 AAAGGCTAGATGTGAGGCATTATACCATACAAGAT
1 AAAGGCTAGATATGAGGCATTATACCAAACAAGAT
* *
5533013 AAAGGCTAGATATGGGGCATTGTACCAAACAA
1 AAAGGCTAGATATGAGGCATTATACCAAACAA
5533045 TTACCCAGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (35 bp):
AAAGGCTAGATATGAGGCATTATACCAAACAAGAT
Found at i:5535853 original size:20 final size:20
Alignment explanation
Indices: 5535828--5535865 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5535818 AATAAGACAA
*
5535828 ATCTATTGATAGATGCATTC
1 ATCTATCGATAGATGCATTC
5535848 ATCTATCGATAGATGCAT
1 ATCTATCGATAGATGCAT
5535866 GGAAAATGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (20 bp):
ATCTATCGATAGATGCATTC
Found at i:5538799 original size:17 final size:17
Alignment explanation
Indices: 5538777--5538810 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5538767 AGAGATTTTA
5538777 ATGGAATTGTGCATATG
1 ATGGAATTGTGCATATG
5538794 ATGGAATTGTGCATATG
1 ATGGAATTGTGCATATG
5538811 TTTGGCACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.35
Consensus pattern (17 bp):
ATGGAATTGTGCATATG
Found at i:5558623 original size:16 final size:16
Alignment explanation
Indices: 5558593--5558631 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5558583 ACCCATAACA
*
5558593 AAGAGAGAAAAAAAGG
1 AAGAAAGAAAAAAAGG
* *
5558609 GAGAAAGAAAGAAAGG
1 AAGAAAGAAAAAAAGG
5558625 AAGAAAG
1 AAGAAAG
5558632 GAGGAAGAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (16 bp):
AAGAAAGAAAAAAAGG
Found at i:5574457 original size:21 final size:21
Alignment explanation
Indices: 5574419--5574470 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
5574409 ATTATGTTTT
* *
5574419 GATACATATTCATGATGTATC
1 GATACATATTTATAATGTATC
5574440 GATACATATTTATAATGTATC
1 GATACATATTTATAATGTATC
*
5574461 AATACA-ATTT
1 GATACATATTT
5574471 TTCCAAAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (21 bp):
GATACATATTTATAATGTATC
Found at i:5575600 original size:80 final size:77
Alignment explanation
Indices: 5575497--5575661 Score: 215
Period size: 80 Copynumber: 2.1 Consensus size: 77
5575487 TGAGTTCCAC
* * * * *
5575497 TTATGAAATTATGACATGTATGCCATGAGATGTATGTGTTAAGCATA-TCATGTACATTATTGGC
1 TTATGAAATTATGAAATGCATGCCATGAGATGTATGTGCTAAG-ATAGTCA--CACATTATAGGC
5575561 TAAGCATGTGAGTGAT
63 TAAGCATGTGA-TGAT
* * *
5575577 TTATGAGATTATGAAATGCATGCCATGAGATGTATGTGCTGAGATAGTCACACATTATAGGCTGA
1 TTATGAAATTATGAAATGCATGCCATGAGATGTATGTGCTAAGATAGTCACACATTATAGGCTAA
5575642 GCATGTGATGAT
66 GCATGTGATGAT
5575654 TTATGAAA
1 TTATGAAA
5575662 AAAATTTTAT
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
77 11 0.15
78 20 0.27
79 3 0.04
80 41 0.55
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (77 bp):
TTATGAAATTATGAAATGCATGCCATGAGATGTATGTGCTAAGATAGTCACACATTATAGGCTAA
GCATGTGATGAT
Found at i:5582805 original size:21 final size:20
Alignment explanation
Indices: 5582773--5582833 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
5582763 TGCATTCTCT
* *
5582773 TTCAAATCTATCGATACATG
1 TTCAAATGTATCGATACATA
*
5582793 TTCATAATGTATCGATACTTA
1 TTCA-AATGTATCGATACATA
*
5582814 TTCAAAATGTATCGACACAT
1 TTC-AAATGTATCGATACAT
5582834 TTTTTTCAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 4 0.12
21 29 0.85
22 1 0.03
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (20 bp):
TTCAAATGTATCGATACATA
Found at i:5593538 original size:21 final size:21
Alignment explanation
Indices: 5593512--5593554 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5593502 CTCTTAAAGT
5593512 AATTTAAATAAAATAACTTAA
1 AATTTAAATAAAATAACTTAA
*
5593533 AATTTAACTAAAATAACTTAA
1 AATTTAAATAAAATAACTTAA
5593554 A
1 A
5593555 TTAATCACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTTAAATAAAATAACTTAA
Found at i:5601068 original size:13 final size:13
Alignment explanation
Indices: 5601050--5601074 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5601040 AAAACCAGAG
5601050 CAAGTGATTTTCT
1 CAAGTGATTTTCT
5601063 CAAGTGATTTTC
1 CAAGTGATTTTC
5601075 AACAATAAAC
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:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (13 bp):
CAAGTGATTTTCT
Found at i:5603076 original size:41 final size:41
Alignment explanation
Indices: 5603000--5603077 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
5602990 AAAATATTAG
*
5603000 TATCAACAAGCAAAATGAAAATCGATTGATGGCAAAACTGA
1 TATCAACAAGCAAAATGAAAATCGATTGATAGCAAAACTGA
* * *
5603041 TATCGACAAGCAAAGTGAAAATTGGA-TGATAGCAAAA
1 TATCAACAAGCAAAATGAAAA-TCGATTGATAGCAAAA
5603078 AAAGACATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 29 0.91
42 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.19, T:0.19
Consensus pattern (41 bp):
TATCAACAAGCAAAATGAAAATCGATTGATAGCAAAACTGA
Found at i:5616714 original size:20 final size:19
Alignment explanation
Indices: 5616685--5616722 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5616675 TCTTCCTACT
*
5616685 AAGAATGTATTGATACATG
1 AAGAATGTATAGATACATG
5616704 AAGAGATGTATAGATACAT
1 AAGA-ATGTATAGATACAT
5616723 CTTTCCCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (19 bp):
AAGAATGTATAGATACATG
Found at i:5624335 original size:17 final size:18
Alignment explanation
Indices: 5624305--5624340 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
5624295 TACCTCTTTA
*
5624305 TCTCTTTCTTTTTTGCTT
1 TCTCTTTCTCTTTTGCTT
5624323 TCTC-TTCTCTTTTGCTT
1 TCTCTTTCTCTTTTGCTT
5624340 T
1 T
5624341 TTATTTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.00, C:0.25, G:0.06, T:0.69
Consensus pattern (18 bp):
TCTCTTTCTCTTTTGCTT
Found at i:5628738 original size:19 final size:19
Alignment explanation
Indices: 5628693--5628738 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5628683 AAACTTTAAA
*
5628693 TATTTAAATATTTAATTTAT
1 TATTT-AATATATAATTTAT
* *
5628713 TAATTAATATATAATTTTT
1 TATTTAATATATAATTTAT
5628732 TATTTAA
1 TATTTAA
5628739 AAAATAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTTAATATATAATTTAT
Found at i:5628981 original size:21 final size:21
Alignment explanation
Indices: 5628955--5629030 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 21
5628945 TTTATCATTA
*
5628955 TATATAGTACAATATTAATAT
1 TATATAATACAATATTAATAT
* *
5628976 TATATATTGAC-ATATTATTAT
1 TATATAAT-ACAATATTAATAT
*
5628997 ATATAATAATAAAATATTTTAATAT
1 -TAT-ATAATACAATA--TTAATAT
5629022 TATATAATA
1 TATATAATA
5629031 ATAAGAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
21 16 0.36
22 6 0.14
23 13 0.30
24 3 0.07
25 6 0.14
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (21 bp):
TATATAATACAATATTAATAT
Found at i:5629028 original size:23 final size:24
Alignment explanation
Indices: 5628925--5629031 Score: 80
Period size: 23 Copynumber: 4.5 Consensus size: 24
5628915 ATTAAATAAT
*
5628925 TATTAT-TAATTAAAATATTATTTA
1 TATTATATAA-TAAAATATTATTAA
** * *
5628949 TCATTATAT-ATAGTACAATATTAA
1 T-ATTATATAATAAAATATTATTAA
* * *
5628973 TATTATATATTGACATATTATT-A
1 TATTATATAATAAAATATTATTAA
5628996 TA-TATAATAATAAAATATT-TTAA
1 TATTAT-ATAATAAAATATTATTAA
5629019 TATTATATAATAA
1 TATTATATAATAA
5629032 TAAGAATATA
Statistics
Matches: 63, Mismatches: 14, Indels: 13
0.70 0.16 0.14
Matches are distributed among these distances:
22 5 0.08
23 30 0.48
24 21 0.33
25 6 0.10
26 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (24 bp):
TATTATATAATAAAATATTATTAA
Found at i:5629032 original size:26 final size:26
Alignment explanation
Indices: 5628996--5629048 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
5628986 CATATTATTA
*
5628996 TATATAATAATAA-AATATTTTAATAT
1 TATATAATAATAAGAATA-TATAATAT
5629022 TATATAATAATAAGAATATATAATAT
1 TATATAATAATAAGAATATATAATAT
5629048 T
1 T
5629049 TTTATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
TATATAATAATAAGAATATATAATAT
Found at i:5629163 original size:28 final size:26
Alignment explanation
Indices: 5629127--5629199 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 26
5629117 TTATTAATTT
*
5629127 TAAAAATTTATTTAATTTAAAATAAAAT
1 TAAAAATTTATTTAATTT--AATAAAAA
* *
5629155 TATAAATTTAATTAAATTTAATAAAAA
1 TAAAAATTT-ATTTAATTTAATAAAAA
5629182 TAAAAAGTTT-TTTAATTT
1 TAAAAA-TTTATTTAATTT
5629200 TTTAAAATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 7 0.18
27 12 0.32
28 11 0.29
29 8 0.21
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (26 bp):
TAAAAATTTATTTAATTTAATAAAAA
Found at i:5629218 original size:20 final size:20
Alignment explanation
Indices: 5629195--5629248 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
5629185 AAAGTTTTTT
*
5629195 AATTTTTTAAAATAATTTAA
1 AATTTTTTTAAATAATTTAA
5629215 AATTTTTTTAAATAATTTAA
1 AATTTTTTTAAATAATTTAA
*
5629235 ATTTTTTTTAAATA
1 AATTTTTTTAAATA
5629249 TTATACTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AATTTTTTTAAATAATTTAA
Found at i:5630526 original size:45 final size:46
Alignment explanation
Indices: 5630396--5630526 Score: 115
Period size: 45 Copynumber: 2.9 Consensus size: 46
5630386 TTCATGACTG
* * * *
5630396 CTCGTTGGGACTATGATATCCTCCTTTC-ATGTGAGATTCATAGCTC
1 CTCGTTGGGACCATGACATCCTCC-TTCGATGTAAGATTAATAGCTC
** * * ** * *
5630442 CTCACTGAGACCATAACATTTTCCTTAGA-GTAAGGTTAATAGCTC
1 CTCGTTGGGACCATGACATCCTCCTTCGATGTAAGATTAATAGCTC
*
5630487 CTCGTTGGGACCATGACATCCTCC-TCGATGTTAGATTAAT
1 CTCGTTGGGACCATGACATCCTCCTTCGATGTAAGATTAAT
5630527 GGTTCCCCAC
Statistics
Matches: 62, Mismatches: 21, Indels: 5
0.70 0.24 0.06
Matches are distributed among these distances:
44 3 0.05
45 42 0.68
46 17 0.27
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (46 bp):
CTCGTTGGGACCATGACATCCTCCTTCGATGTAAGATTAATAGCTC
Found at i:5636958 original size:31 final size:31
Alignment explanation
Indices: 5636923--5636992 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
5636913 CTATTGTGTT
*
5636923 TTATACCTCCACAT-AAAAGGTAGTG-TAAAGG
1 TTATACCTCC-CATGAAAAGGTAATGCT-AAGG
*
5636954 TTATACCT-CCTTGAAAAGGTAATGCTAAGG
1 TTATACCTCCCATGAAAAGGTAATGCTAAGG
5636984 TTATACCTC
1 TTATACCTC
5636993 TTCTAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 2 0.06
30 23 0.68
31 9 0.26
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (31 bp):
TTATACCTCCCATGAAAAGGTAATGCTAAGG
Found at i:5640852 original size:26 final size:26
Alignment explanation
Indices: 5640823--5640877 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
5640813 ATAAATATAA
5640823 ATTCTTAATTGAATTAATTTATATTT
1 ATTCTTAATTGAATTAATTTATATTT
* *
5640849 ATTCTTAGTTTAATTAATTTATATTT
1 ATTCTTAATTGAATTAATTTATATTT
5640875 ATT
1 ATT
5640878 GGTAACATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (26 bp):
ATTCTTAATTGAATTAATTTATATTT
Found at i:5642772 original size:6 final size:6
Alignment explanation
Indices: 5642753--5642798 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
5642743 AAGATTTCAC
* * * *
5642753 TATATA TATGCA TATACA TATACA TATACA TACACA TACACA TATA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATA
5642799 TTTGTATGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.48, C:0.17, G:0.02, T:0.33
Consensus pattern (6 bp):
TATACA
Found at i:5642839 original size:18 final size:18
Alignment explanation
Indices: 5642818--5642942 Score: 69
Period size: 18 Copynumber: 7.0 Consensus size: 18
5642808 GTGTGTGTAC
5642818 ATGTATATATATGTATAT
1 ATGTATATATATGTATAT
* * * * *
5642836 ATGTGTCTGTGTGTGTAT
1 ATGTATATATATGTATAT
*
5642854 A-GATATATATATGCA-A-
1 ATG-TATATATATGTATAT
*
5642870 ATGTATGTATATATGTACAT
1 ATGTA--TATATATGTATAT
* * *
5642890 -TATATATGTATGTGTAT
1 ATGTATATATATGTATAT
* *
5642907 GTGTATGTATATGTATAT
1 ATGTATATATATGTATAT
* *
5642925 GTGTATGTATATGTATAT
1 ATGTATATATATGTATAT
5642943 GTGTGCGTGT
Statistics
Matches: 80, Mismatches: 20, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
16 3 0.04
17 13 0.16
18 60 0.75
19 4 0.05
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.47
Consensus pattern (18 bp):
ATGTATATATATGTATAT
Found at i:5642907 original size:6 final size:6
Alignment explanation
Indices: 5642896--5642946 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
5642886 ACATTATATA
* * * *
5642896 TGTATG TGTATG TGTATG TATATG TATATG TGTATG TATATG TATATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
5642944 TGT
1 TGT
5642947 GCGTGTATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (6 bp):
TGTATG
Found at i:5642913 original size:12 final size:12
Alignment explanation
Indices: 5642871--5642946 Score: 73
Period size: 12 Copynumber: 6.2 Consensus size: 12
5642861 TATATGCAAA
*
5642871 TGTATGTATATA
1 TGTATGTATATG
*
5642883 TGTACAT-TATATA
1 TGT--ATGTATATG
*
5642896 TGTATGTGTATG
1 TGTATGTATATG
5642908 TGTATGTATATG
1 TGTATGTATATG
* *
5642920 TATATGTGTATG
1 TGTATGTATATG
*
5642932 TATATGTATATG
1 TGTATGTATATG
5642944 TGT
1 TGT
5642947 GCGTGTATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
11 2 0.04
12 41 0.76
13 9 0.17
14 2 0.04
ACGTcount: A:0.28, C:0.01, G:0.21, T:0.50
Consensus pattern (12 bp):
TGTATGTATATG
Found at i:5642943 original size:18 final size:18
Alignment explanation
Indices: 5642898--5642946 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
5642888 ATTATATATG
*
5642898 TATGTGTATGTGTATGTA
1 TATGTATATGTGTATGTA
5642916 TATGTATATGTGTATGTA
1 TATGTATATGTGTATGTA
5642934 TATGTATATGTGT
1 TATGTATATGTGT
5642947 GCGTGTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (18 bp):
TATGTATATGTGTATGTA
Found at i:5642952 original size:24 final size:24
Alignment explanation
Indices: 5642892--5642960 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
5642882 ATGTACATTA
*
5642892 TATATGTAT--GTGTATGTGTATG
1 TATATGTATACGTGTATGTATATG
*
5642914 TATATGTATATGTGTATGTATATG
1 TATATGTATACGTGTATGTATATG
* * *
5642938 TATATGTGTGCGTGTATTTATAT
1 TATATGTATACGTGTATGTATAT
5642961 ATACATATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 9 0.22
24 31 0.77
ACGTcount: A:0.25, C:0.01, G:0.23, T:0.51
Consensus pattern (24 bp):
TATATGTATACGTGTATGTATATG
Found at i:5644478 original size:19 final size:20
Alignment explanation
Indices: 5644445--5644498 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
5644435 GCGCTATCCT
*
5644445 CATAATGCACATGTTATT-A
1 CATAATGAACATGTTATTCA
* *
5644464 CATAATGAACGTGTTCTTCA
1 CATAATGAACATGTTATTCA
* *
5644484 CATTATGAATATGTT
1 CATAATGAACATGTT
5644499 CATCTATAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (20 bp):
CATAATGAACATGTTATTCA
Found at i:5653289 original size:27 final size:28
Alignment explanation
Indices: 5653239--5653297 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
5653229 ATCTCCTCAC
* *
5653239 TATTCATCAACTTCTAATGGGTT-AAAG
1 TATTAATCAACTTCTAATGAGTTAAAAG
**
5653266 TATTAATCAACTTCTGGTGAGTTAAAAG
1 TATTAATCAACTTCTAATGAGTTAAAAG
5653294 TATT
1 TATT
5653298 CTTATTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (28 bp):
TATTAATCAACTTCTAATGAGTTAAAAG
Found at i:5655622 original size:14 final size:15
Alignment explanation
Indices: 5655598--5655627 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5655588 AAAAAAAAAT
5655598 GAAAACAAAAATTAA
1 GAAAACAAAAATTAA
5655613 GAAAAC-AAAATTAA
1 GAAAACAAAAATTAA
5655627 G
1 G
5655628 TAAAGGGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.70, C:0.07, G:0.10, T:0.13
Consensus pattern (15 bp):
GAAAACAAAAATTAA
Found at i:5656274 original size:20 final size:20
Alignment explanation
Indices: 5656251--5656295 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5656241 AAAAATATAA
*
5656251 TATTTAAAAAACTTCTAAAT
1 TATTTAAAAAAATTCTAAAT
*
5656271 TATTTAAAAAAATTTTAAAT
1 TATTTAAAAAAATTCTAAAT
*
5656291 AATTT
1 TATTT
5656296 TTTATTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
TATTTAAAAAAATTCTAAAT
Found at i:5656488 original size:13 final size:13
Alignment explanation
Indices: 5656470--5656500 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5656460 ATCATTTTTG
5656470 ATAATAATATAAT
1 ATAATAATATAAT
*
5656483 ATAATAATATATT
1 ATAATAATATAAT
5656496 ATAAT
1 ATAAT
5656501 TGATAGTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATAATAATATAAT
Done.