Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014933.1 Kokia drynarioides strain JFW-HI SEQ_129976, 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: 464154
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Warning! 704 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:42 original size:27 final size:27
Alignment explanation
Indices: 12--75 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
2 GGATATGGAA
12 GTGGTGGTGGTAGAGGTGGAGGAGGAG
1 GTGGTGGTGGTAGAGGTGGAGGAGGAG
* * *
39 GTGGTGGCGGTGGCGGTGGAGGAGGAG
1 GTGGTGGTGGTAGAGGTGGAGGAGGAG
66 GTGGTGGTGG
1 GTGGTGGTGG
76 AGGCAATGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.12, C:0.03, G:0.66, T:0.19
Consensus pattern (27 bp):
GTGGTGGTGGTAGAGGTGGAGGAGGAG
Found at i:105 original size:18 final size:18
Alignment explanation
Indices: 82--132 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
72 GTGGAGGCAA
*
82 TGGTTCAGGGTATGGAAG
1 TGGTTCAGGTTATGGAAG
100 TGGTTCAGGTTATGGAAG
1 TGGTTCAGGTTATGGAAG
*
118 TGGGTCAGGTTATGG
1 TGGTTCAGGTTATGG
133 CAGCAGTGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.20, C:0.06, G:0.43, T:0.31
Consensus pattern (18 bp):
TGGTTCAGGTTATGGAAG
Found at i:2665 original size:3 final size:3
Alignment explanation
Indices: 2653--2688 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
2643 TTTCATTTTA
2653 ATT A-T ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2689 AAGAGATAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:20653 original size:24 final size:24
Alignment explanation
Indices: 20626--20671 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
20616 GCATAGATAG
20626 TGCTGTCTAGATTGGGAGTAATAA
1 TGCTGTCTAGATTGGGAGTAATAA
20650 TGCTGTCTAGATTGGGAGTAAT
1 TGCTGTCTAGATTGGGAGTAAT
20672 CCTAACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.09, G:0.30, T:0.35
Consensus pattern (24 bp):
TGCTGTCTAGATTGGGAGTAATAA
Found at i:21542 original size:9 final size:9
Alignment explanation
Indices: 21528--21575 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
21518 AGGAGAATGT
21528 AGAAGAGAA
1 AGAAGAGAA
21537 AGAAGAGAA
1 AGAAGAGAA
*
21546 ATAAGAAGAA
1 AGAAG-AGAA
*
21556 AGAAAAG-A
1 AGAAGAGAA
*
21564 AGACGAGAA
1 AGAAGAGAA
21573 AGA
1 AGA
21576 GGAAGAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
8 6 0.19
9 19 0.59
10 7 0.22
ACGTcount: A:0.67, C:0.02, G:0.29, T:0.02
Consensus pattern (9 bp):
AGAAGAGAA
Found at i:33759 original size:21 final size:21
Alignment explanation
Indices: 33719--33759 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
33709 AAAAAGTCAA
*
33719 TAACATGAATCTGTCTAACCT
1 TAACATGAATCTGTCGAACCT
33740 TAACATGAAT-TGATCGAACC
1 TAACATGAATCTG-TCGAACC
33760 CAAGTTGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (21 bp):
TAACATGAATCTGTCGAACCT
Found at i:48524 original size:27 final size:26
Alignment explanation
Indices: 48477--48613 Score: 94
Period size: 27 Copynumber: 5.5 Consensus size: 26
48467 TCTGATTAGC
* *
48477 CTTTGTGGCGTACTCTAAATGGATTG
1 CTTTGTGGTGTACTCTGAATGGATTG
*
48503 TCTTTGTGGTGTACTTTGAAT-G---G
1 -CTTTGTGGTGTACTCTGAATGGATTG
*
48526 --TTATGGTGTACTCTGAATGGATTG
1 CTTTGTGGTGTACTCTGAATGGATTG
* *
48550 CCTCTGTGGTGTACTTTGAATGGATTG
1 -CTTTGTGGTGTACTCTGAATGGATTG
* * *
48577 CCTTATGGTG-A-TCCTGTAT-GATTG
1 CTTTGTGGTGTACT-CTGAATGGATTG
48601 CCTTTGTGGTGTA
1 -CTTTGTGGTGTA
48614 TTTTGTAATA
Statistics
Matches: 85, Mismatches: 15, Indels: 21
0.70 0.12 0.17
Matches are distributed among these distances:
20 16 0.19
21 1 0.01
23 1 0.01
24 7 0.08
25 13 0.15
26 9 0.11
27 38 0.45
ACGTcount: A:0.16, C:0.13, G:0.28, T:0.42
Consensus pattern (26 bp):
CTTTGTGGTGTACTCTGAATGGATTG
Found at i:49753 original size:14 final size:13
Alignment explanation
Indices: 49733--49771 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
49723 TTTGTTTTGT
49733 TTCTTCTCCTTTC
1 TTCTTCTCCTTTC
*
49746 TATCTTCTCTTCTTC
1 T-TCTTCTCCT-TTC
49761 TTCTTCTCCTT
1 TTCTTCTCCTT
49772 ATTCCTCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 2 0.09
14 16 0.73
15 4 0.18
ACGTcount: A:0.03, C:0.36, G:0.00, T:0.62
Consensus pattern (13 bp):
TTCTTCTCCTTTC
Found at i:56758 original size:13 final size:13
Alignment explanation
Indices: 56742--56769 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
56732 ATTTATTAAA
56742 AACTAAATTAACT
1 AACTAAATTAACT
56755 AACTAAATTAACT
1 AACTAAATTAACT
56768 AA
1 AA
56770 AGAACACAAT
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:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (13 bp):
AACTAAATTAACT
Found at i:58925 original size:62 final size:62
Alignment explanation
Indices: 58825--58951 Score: 152
Period size: 63 Copynumber: 2.0 Consensus size: 62
58815 ATAAAATTTT
* *
58825 TAAAAATTTAACTTTTTATATATTTTTTAGATTTTTTAAAAAATA-TATAAATTTTTTAAAAA
1 TAAAAATTTAACTTTTTATAAATTTTTTAGA-TTTTTAAAAAATATTATAAATTTTTGAAAAA
* * *
58887 TAAAAATTTTATACTTTTTATAAATATTTTTA-A-TTTTAAAAATTATTTTCAATTTTTGAAAAA
1 TAAAAA-TTTA-ACTTTTTATAAAT-TTTTTAGATTTTTAAAAAATATTATAAATTTTTGAAAAA
58950 TA
1 TA
58952 TTTTGATTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
62 17 0.30
63 20 0.36
64 13 0.23
65 6 0.11
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (62 bp):
TAAAAATTTAACTTTTTATAAATTTTTTAGATTTTTAAAAAATATTATAAATTTTTGAAAAA
Found at i:58933 original size:19 final size:19
Alignment explanation
Indices: 58901--58955 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
58891 AATTTTATAC
* *
58901 TTTTTATAAATATTTTTAA
1 TTTTTAAAAATATTTTCAA
58920 -TTTTAAAAATTATTTTCAA
1 TTTTTAAAAA-TATTTTCAA
58939 TTTTTGAAAAATATTTT
1 TTTTT-AAAAATATTTT
58956 GATTATTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 8 0.26
19 8 0.26
20 10 0.32
21 5 0.16
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTTTAAAAATATTTTCAA
Found at i:58964 original size:21 final size:22
Alignment explanation
Indices: 58919--58965 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
58909 AATATTTTTA
58919 ATTTT-AAAAATTATTTTCAAT
1 ATTTTGAAAAATTATTTTCAAT
* *
58940 -TTTTGAAAAA-TATTTTGATT
1 ATTTTGAAAAATTATTTTCAAT
58960 ATTTTG
1 ATTTTG
58966 TAATTTTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (22 bp):
ATTTTGAAAAATTATTTTCAAT
Found at i:63117 original size:14 final size:14
Alignment explanation
Indices: 63065--63117 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
63055 CAATCAAACG
*
63065 AAAAATTAAAATGT
1 AAAAATTAAAATAT
63079 AAAAATT-AAAT-T
1 AAAAATTAAAATAT
**
63091 AAAAACAAAAATAT
1 AAAAATTAAAATAT
*
63105 TAAAATTAAAATA
1 AAAAATTAAAATA
63118 AATATGACTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 6 0.19
13 8 0.25
14 18 0.56
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (14 bp):
AAAAATTAAAATAT
Found at i:66722 original size:36 final size:36
Alignment explanation
Indices: 66636--66722 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
66626 AGATGACTAT
*
66636 TGTGAAAGTGAATATGTGGGTATGCTATTCATGCCA
1 TGTGACAGTGAATATGTGGGTATGCTATTCATGCCA
* *** * *
66672 TGAGACAAAAAATATGTGGGTATGTTATTCATGTCA
1 TGTGACAGTGAATATGTGGGTATGCTATTCATGCCA
66708 TGTGACAGTGAATAT
1 TGTGACAGTGAATAT
66723 ATTGTGCTAA
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.33
Consensus pattern (36 bp):
TGTGACAGTGAATATGTGGGTATGCTATTCATGCCA
Found at i:67180 original size:24 final size:24
Alignment explanation
Indices: 67147--67226 Score: 85
Period size: 23 Copynumber: 3.3 Consensus size: 24
67137 TTAATATGTA
67147 ATGTGA-TAAATGTTGAAATATTC
1 ATGTGATTAAATGTTGAAATATTC
* *
67170 ATATGATTAAATG-TGATTAATATGTT
1 ATGTGATTAAATGTTGA--AATAT-TC
*
67196 ATGTGA-TAAATATTGAAATATTC
1 ATGTGATTAAATGTTGAAATATTC
67219 ATGTGATT
1 ATGTGATT
67227 TTTTTAGTGG
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
23 15 0.33
24 12 0.26
25 10 0.22
26 9 0.20
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.42
Consensus pattern (24 bp):
ATGTGATTAAATGTTGAAATATTC
Found at i:67181 original size:49 final size:49
Alignment explanation
Indices: 67121--67226 Score: 167
Period size: 49 Copynumber: 2.2 Consensus size: 49
67111 ATGTGATTAA
* * *
67121 ATATGACTAAATGTTATTAATATGTAATGTGATAAATGTTGAAATATTC
1 ATATGATTAAATGTGATTAATATGTAATGTGATAAATATTGAAATATTC
*
67170 ATATGATTAAATGTGATTAATATGTTATGTGATAAATATTGAAATATTC
1 ATATGATTAAATGTGATTAATATGTAATGTGATAAATATTGAAATATTC
*
67219 ATGTGATT
1 ATATGATT
67227 TTTTTAGTGG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.42
Consensus pattern (49 bp):
ATATGATTAAATGTGATTAATATGTAATGTGATAAATATTGAAATATTC
Found at i:67205 original size:25 final size:25
Alignment explanation
Indices: 67128--67206 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
67118 TAAATATGAC
*
67128 TAAATGTTATTAATATGTAATGTGA
1 TAAATGTGATTAATATGTAATGTGA
* *
67153 TAAATGTTGA--AATAT-TCATATGA
1 TAAATG-TGATTAATATGTAATGTGA
*
67176 TTAAATGTGATTAATATGTTATGTGA
1 -TAAATGTGATTAATATGTAATGTGA
67202 TAAAT
1 TAAAT
67207 ATTGAAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
23 9 0.20
24 11 0.25
25 16 0.36
26 8 0.18
ACGTcount: A:0.41, C:0.01, G:0.15, T:0.43
Consensus pattern (25 bp):
TAAATGTGATTAATATGTAATGTGA
Found at i:75288 original size:52 final size:53
Alignment explanation
Indices: 75227--75336 Score: 168
Period size: 52 Copynumber: 2.1 Consensus size: 53
75217 TTAATATGTG
*
75227 ATGTGATAAATGATGAAATATTCATGTAACTAATGTGATTAAATGTGATTAA-
1 ATGTGATAAATGATAAAATATTCATGTAACTAATGTGATTAAATGTGATTAAT
* * * *
75279 ATGTGATAAATGCTAAAATATTCATTTGACTAATGTGATTATATGTGATTAAT
1 ATGTGATAAATGATAAAATATTCATGTAACTAATGTGATTAAATGTGATTAAT
75332 ATGTG
1 ATGTG
75337 TTGTGTTAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
52 47 0.90
53 5 0.10
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.39
Consensus pattern (53 bp):
ATGTGATAAATGATAAAATATTCATGTAACTAATGTGATTAAATGTGATTAAT
Found at i:75290 original size:9 final size:10
Alignment explanation
Indices: 75258--75290 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
75248 TCATGTAACT
75258 AATGTGATTA
1 AATGTGATTA
75268 AATGTGATTA
1 AATGTGATTA
75278 AATGTGA-TA
1 AATGTGATTA
75287 AATG
1 AATG
75291 CTAAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 6 0.26
10 17 0.74
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.36
Consensus pattern (10 bp):
AATGTGATTA
Found at i:77389 original size:23 final size:23
Alignment explanation
Indices: 77363--77418 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
77353 AGTTTTAACA
77363 TTAGTTTTCTCTAGGTTTTCTCT
1 TTAGTTTTCTCTAGGTTTTCTCT
77386 TTAGTTTTCTCTAGGTTTTCTCT
1 TTAGTTTTCTCTAGGTTTTCTCT
77409 TTAGTTTTCT
1 TTAGTTTTCT
77419 TCACTTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.09, C:0.16, G:0.12, T:0.62
Consensus pattern (23 bp):
TTAGTTTTCTCTAGGTTTTCTCT
Found at i:77394 original size:12 final size:11
Alignment explanation
Indices: 77363--77418 Score: 62
Period size: 11 Copynumber: 4.9 Consensus size: 11
77353 AGTTTTAACA
77363 TTAGTTTTCTC
1 TTAGTTTTCTC
77374 -TAGGTTTTCTC
1 TTA-GTTTTCTC
77385 TTTAGTTTTCTC
1 -TTAGTTTTCTC
77397 -TAGGTTTTCTC
1 TTA-GTTTTCTC
77408 TTTAGTTTTCT
1 -TTAGTTTTCT
77419 TCACTTTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
10 4 0.10
11 16 0.41
12 15 0.38
13 4 0.10
ACGTcount: A:0.09, C:0.16, G:0.12, T:0.62
Consensus pattern (11 bp):
TTAGTTTTCTC
Found at i:84561 original size:37 final size:37
Alignment explanation
Indices: 84506--84623 Score: 166
Period size: 37 Copynumber: 3.2 Consensus size: 37
84496 TTGCATCTAA
* *
84506 GTGTATTCGGGCTATGTGCCTAGCAGGCTTCGTGCCG
1 GTGTTTTCGGGCTATGTGCCTAGCAGGCTTTGTGCCG
*
84543 GTGTTTTCGGGCTATGTGCCTAGCAGGCTTTATGCCG
1 GTGTTTTCGGGCTATGTGCCTAGCAGGCTTTGTGCCG
* *
84580 GTGTATTT-GGGCTATGTGCTTAGTAGGCCTTTGTGCCG
1 GTGT-TTTCGGGCTATGTGCCTAGCAGG-CTTTGTGCCG
84618 GTGTTT
1 GTGTTT
84624 AAAAAACTAA
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
37 57 0.78
38 16 0.22
ACGTcount: A:0.10, C:0.19, G:0.34, T:0.36
Consensus pattern (37 bp):
GTGTTTTCGGGCTATGTGCCTAGCAGGCTTTGTGCCG
Found at i:85527 original size:28 final size:28
Alignment explanation
Indices: 85441--85821 Score: 378
Period size: 28 Copynumber: 13.6 Consensus size: 28
85431 ATATAAATAA
* * *
85441 TTTTAAGATCAACTTATTTCCTAATTAT
1 TTTTAAAATCGACCTATTTCCTAATTAT
85469 TTTTAAAATCGACCT-TTT-CTAATTAT
1 TTTTAAAATCGACCTATTTCCTAATTAT
*
85495 TTTTAAAATCGATCTATTTCCTAATTAT
1 TTTTAAAATCGACCTATTTCCTAATTAT
* *
85523 TTTTAAAACCAACCTATTTCCTAATTAT
1 TTTTAAAATCGACCTATTTCCTAATTAT
* * *
85551 TTTTAAAA-CCATCCTATTCCCTTAATTAG
1 TTTTAAAATCGA-CCTATTTCC-TAATTAT
* ** *
85580 TTTTAAAATCAACCTATACCACTAACTAT
1 TTTTAAAATCGACCTATTTC-CTAATTAT
* * *
85609 TTTTAAAACCGACCTA-CT-CAAATTAT
1 TTTTAAAATCGACCTATTTCCTAATTAT
85635 TTTTAAAAT-GAGCCTATTTCCTAATTAT
1 TTTTAAAATCGA-CCTATTTCCTAATTAT
* * **
85663 TTTTAAAATAGACTTATTTTTTTAATTAT
1 TTTTAAAATCGACCTA-TTTCCTAATTAT
* *
85692 TTTTAAAATCGACCTATTCCCTAGTTAT
1 TTTTAAAATCGACCTATTTCCTAATTAT
* * * *
85720 TTTTAAAACCGGCTTATTTTCTAATTAT
1 TTTTAAAATCGACCTATTTCCTAATTAT
* *
85748 TTTTAAAATCAACCTATTTCTCTAATCAT
1 TTTTAAAATCGACCTATTTC-CTAATTAT
* *
85777 TTTTAAAATCGGCCTATTCCCCTAATTAT
1 TTTTAAAATCGACCTATT-TCCTAATTAT
*
85806 TTTTAAAATCAACCTA
1 TTTTAAAATCGACCTA
85822 ACCCCTAACC
Statistics
Matches: 290, Mismatches: 50, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
25 2 0.01
26 40 0.14
27 9 0.03
28 125 0.43
29 110 0.38
30 4 0.01
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.45
Consensus pattern (28 bp):
TTTTAAAATCGACCTATTTCCTAATTAT
Found at i:85809 original size:197 final size:194
Alignment explanation
Indices: 85455--85813 Score: 495
Period size: 197 Copynumber: 1.8 Consensus size: 194
85445 AAGATCAACT
* * *
85455 TATTTCCTAATTATTTTTAAAATCGACCTTTTCTAATTATTTTTAAAATCGATCTATTTCCTAAT
1 TATTTCCTAATTATTTTTAAAATAGACCTTTTCTAATTATTTTTAAAATCGACCTATTCCCTAAT
* *
85520 TATTTTTAAAACCAACCTATTTCCTAATTATTTTTAAAACCATCCTATTCCCTTAATTAGTTTTA
66 TATTTTTAAAACCAACCTATTTCCTAATTATTTTTAAAACCAACCTATTCCCTTAATCAGTTTTA
85585 AAATCAACCTATACCACTAACTATTTTTAAAACCGACCTACTCAAATTATTTTTAAAATGAGCC
131 AAATCAACCTATACCACTAACTATTTTTAAAACCGACCTACTCAAATTATTTTTAAAATGAGCC
* *
85649 TATTTCCTAATTATTTTTAAAATAGACTTATTTTTTTAATTATTTTTAAAATCGACCTATTCCCT
1 TATTTCCTAATTATTTTTAAAATAGAC---CTTTTCTAATTATTTTTAAAATCGACCTATTCCCT
* ** * * * * *
85714 AGTTATTTTTAAAACCGGCTTATTTTCTAATTATTTTTAAAATCAACCTATT-TCTCTAATCATT
63 AATTATTTTTAAAACCAACCTATTTCCTAATTATTTTTAAAACCAACCTATTCCCT-TAATCAGT
** * * *
85778 TTTAAAATCGGCCTATTCCCCTAATTATTTTTAAAA
127 TTTAAAATCAACCTATACCACTAACTATTTTTAAAA
85814 TCAACCTAAC
Statistics
Matches: 141, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
194 26 0.18
196 2 0.01
197 113 0.80
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.45
Consensus pattern (194 bp):
TATTTCCTAATTATTTTTAAAATAGACCTTTTCTAATTATTTTTAAAATCGACCTATTCCCTAAT
TATTTTTAAAACCAACCTATTTCCTAATTATTTTTAAAACCAACCTATTCCCTTAATCAGTTTTA
AAATCAACCTATACCACTAACTATTTTTAAAACCGACCTACTCAAATTATTTTTAAAATGAGCC
Found at i:93851 original size:29 final size:30
Alignment explanation
Indices: 93819--94047 Score: 196
Period size: 29 Copynumber: 7.9 Consensus size: 30
93809 TTTGGATGCC
* *
93819 CGAGGGGTAAAATGGAAATTTTTGGAGA-T
1 CGAGGGGTAAAATGGTAATTTTTGGACACT
*
93848 CGA-GGGTAAAATAGTAATTTTTGGACACT
1 CGAGGGGTAAAATGGTAATTTTTGGACACT
*
93877 CG-GGGGCAAAAAT-GTAATTTTTGGACA-T
1 CGAGGGG-TAAAATGGTAATTTTTGGACACT
* *
93905 CCGA-GGGTAAAATGGTAATTTTTAGAAACT
1 -CGAGGGGTAAAATGGTAATTTTTGGACACT
*
93935 C-AGGGGTAAAAAT-GTAATTTTTGGACATT
1 CGAGGGGT-AAAATGGTAATTTTTGGACACT
* *
93964 CG-GGGGTAAAATGGTAA-TTTTGGAAAGTT
1 CGAGGGGTAAAATGGTAATTTTTGGACA-CT
* * *
93993 CGA--GGTCAAAATTGTAATTTTTTTGACATT
1 CGAGGGGT-AAAATGGTAA-TTTTTGGACACT
*
94023 TGA-GGGTAAAATGGTAATTTTTGGA
1 CGAGGGGTAAAATGGTAATTTTTGGA
94048 AAGTTTGAGG
Statistics
Matches: 166, Mismatches: 17, Indels: 34
0.76 0.08 0.16
Matches are distributed among these distances:
28 44 0.27
29 88 0.53
30 24 0.14
31 10 0.06
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (30 bp):
CGAGGGGTAAAATGGTAATTTTTGGACACT
Found at i:93910 original size:58 final size:58
Alignment explanation
Indices: 93835--94049 Score: 272
Period size: 58 Copynumber: 3.7 Consensus size: 58
93825 GTAAAATGGA
* * *
93835 AATTTTTGGAGA-TCGAGGGTAAAATAGTAATTTTTGGACACTCGGGGGCAAAAATGT
1 AATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGAAACTCGGGGGCAAAAATGT
* * * *
93892 AATTTTTGGACATCCGAGGGTAAAATGGTAATTTTTAGAAACTCAGGGGTAAAAATGT
1 AATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGAAACTCGGGGGCAAAAATGT
* * * * *
93950 AATTTTTGGACATTCGGGGGTAAAATGGTAA-TTTTGGAAAGTTCGAGGTCAAAATTGT
1 AATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGAAA-CTCGGGGGCAAAAATGT
* *
94008 AATTTTTTTGACATTTGAGGGTAAAATGGTAATTTTTGGAAA
1 AA-TTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGAAA
94050 GTTTGAGGGC
Statistics
Matches: 135, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
57 19 0.14
58 81 0.60
59 26 0.19
60 9 0.07
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.34
Consensus pattern (58 bp):
AATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGAAACTCGGGGGCAAAAATGT
Found at i:93942 original size:87 final size:86
Alignment explanation
Indices: 93818--94047 Score: 229
Period size: 87 Copynumber: 2.6 Consensus size: 86
93808 ATTTGGATGC
* * *
93818 CCGAGGGGTAAAATGGAAATTTTTGGAGATCGAGGGT-AAAATAGTAATTTTTGGACACTCGGGG
1 CCGA-GGGTAAAATGGTAATTTTTAGAAATCGAGGGTAAAAAT-GTAATTTTTGGACACTCGGGG
*
93882 GCAAAAAT-GTAATTTTTGGACA-T
64 G-AAAAATGGTAA-TTTTGGAAAGT
*
93905 CCGAGGGTAAAATGGTAATTTTTAGAAACTC-AGGGGTAAAAATGTAATTTTTGGACATTCGGGG
1 CCGAGGGTAAAATGGTAATTTTTAGAAA-TCGA-GGGTAAAAATGTAATTTTTGGACACTCGGGG
*
93969 GTAAAATGGTAATTTTGGAAAGT
64 GAAAAATGGTAATTTTGGAAAGT
* * * * *
93992 TCGA-GGTCAAAATTGTAATTTTTTTGACATTTGAGGGT-AAAATGGTAATTTTTGGA
1 CCGAGGGT-AAAATGGTAA-TTTTTAGA-AATCGAGGGTAAAAAT-GTAATTTTTGGA
94048 AAGTTTGAGG
Statistics
Matches: 122, Mismatches: 11, Indels: 19
0.80 0.07 0.12
Matches are distributed among these distances:
86 38 0.31
87 53 0.43
88 29 0.24
89 2 0.02
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (86 bp):
CCGAGGGTAAAATGGTAATTTTTAGAAATCGAGGGTAAAAATGTAATTTTTGGACACTCGGGGGA
AAAATGGTAATTTTGGAAAGT
Found at i:94073 original size:30 final size:31
Alignment explanation
Indices: 94021--94102 Score: 82
Period size: 30 Copynumber: 2.7 Consensus size: 31
94011 TTTTTTGACA
* *
94021 TTTGAGGGT-AAAATGGTAATTTTTGG-AAAG
1 TTTGAGGGTCAAAAT-ATGATTTTTGGAAAAG
*
94051 TTTGAGGG-CAAAAATTTGA-TTTTGGAAAAG
1 TTTGAGGGTC-AAAATATGATTTTTGGAAAAG
*
94081 TTTGGGGGTCAAAATATGATTT
1 TTTGAGGGTCAAAATATGATTT
94103 CTAAAAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
29 6 0.14
30 29 0.67
31 8 0.19
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (31 bp):
TTTGAGGGTCAAAATATGATTTTTGGAAAAG
Found at i:95870 original size:6 final size:6
Alignment explanation
Indices: 95861--95965 Score: 83
Period size: 6 Copynumber: 17.8 Consensus size: 6
95851 TGGACTTTTA
* * * * *
95861 TTAATT TTAAAT TTAAAA TTAAAA GTAAAT TTAAAC TT-AAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* **
95908 TTAAAT TTAACT TTAAA- ACAAAT TTAAAT TTAAAAT TT-AAT CTTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT TTAAAT -TTAAAT
*
95955 ATAAAT TTAAA
1 TTAAAT TTAAA
95966 AAGGTATTGT
Statistics
Matches: 78, Mismatches: 15, Indels: 12
0.74 0.14 0.11
Matches are distributed among these distances:
5 14 0.18
6 56 0.72
7 8 0.10
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (6 bp):
TTAAAT
Found at i:95912 original size:23 final size:23
Alignment explanation
Indices: 95886--95965 Score: 74
Period size: 23 Copynumber: 3.4 Consensus size: 23
95876 AAATTAAAAG
95886 TAAATTTAAACTTAATTTAAATT
1 TAAATTTAAACTTAATTTAAATT
***
95909 TAAATTT-AACTTTAAAACAAATT
1 TAAATTTAAAC-TTAATTTAAATT
* *
95932 TAAATTTAAAATTTAATCTTAAA-A
1 TAAATTT-AAACTTAAT-TTAAATT
95956 TAAATTTAAA
1 TAAATTTAAA
95966 AAGGTATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
22 3 0.07
23 26 0.58
24 11 0.24
25 5 0.11
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (23 bp):
TAAATTTAAACTTAATTTAAATT
Found at i:95912 original size:29 final size:29
Alignment explanation
Indices: 95868--95965 Score: 108
Period size: 29 Copynumber: 3.3 Consensus size: 29
95858 TTATTAATTT
* *
95868 TAAATTTAAAATTAAAAGTAAATTTAAAC
1 TAAATTTAAATTTAAAATTAAATTTAAAC
* * *
95897 TTAATTTAAATTTAAATTTAACTTTAAAAC
1 TAAATTTAAATTTAAAATTAAATTT-AAAC
* *
95927 -AAATTTAAATTTAAAATTTAATCTTAAAA
1 TAAATTTAAATTTAAAATTAAAT-TTAAAC
95956 TAAATTTAAA
1 TAAATTTAAA
95966 AAGGTATTGT
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
29 41 0.73
30 15 0.27
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (29 bp):
TAAATTTAAATTTAAAATTAAATTTAAAC
Found at i:96732 original size:209 final size:208
Alignment explanation
Indices: 96333--96950 Score: 887
Period size: 209 Copynumber: 3.0 Consensus size: 208
96323 TCTTGATCTT
* * *
96333 CTTCTCTATATTTCATCAGGAAGATGAATGTTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
1 CTTCTCTATATCTCATCAGGAAGATGACTGTTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
* * * * * * *
96398 AAGAAGCTGGGGTTTGAAG-TTTCGCTGACATCGAGCTTTGGTTTCATTGATTTGGTCTACTTCT
66 AGGAAGCTGGGGTTCGAAGATTT-GCTCACTTTGAGC-CT-GTTTCATTGATTTGGTATACTTCT
* ** **
96462 CAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGTTTCTCTGTATCTCATCAGGA
128 CAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTATCTCATCAGGA
*
96527 AGACGAATTTGGTCCA
193 AGACGAATCTGGTCCA
* * ** *
96543 CTTCTCTGTATCTCATCAGGAATATGACCATTTTATTGCTTCGACCTACTTCTCAGTATCTCATC
1 CTTCTCTATATCTCATCAGGAAGATGACTGTTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
*
96608 AGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTGATTTCATTGATTTAGTATACTTCTCA
66 AGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTG-TTTCATTGATTTGGTATACTTCTCA
* *
96673 GTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTATGTCTCATCAGGAAG
130 GTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTATCTCATCAGGAAG
*
96738 ACGGATCTGGTCCA
195 ACGAATCTGGTCCA
96752 CTTCTCTATATCTCATCAGGAAGATGACTGTTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
1 CTTCTCTATATCTCATCAGGAAGATGACTGTTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
* * *
96817 AGGAAGCTAGGGTTCGAAGATTTACTCACTTTGAGCCTTGTTTCATTGACTTGGTATACTTCTCA
66 AGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCC-TGTTTCATTGATTTGGTATACTTCTCA
* ** * *
96882 GTATCTCATTAGGAAGATGATTGCATCACTTGTTTTGGTCCACTTCTCTGTATCTCATCAAGAAG
130 GTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTATCTCATCAGGAAG
96947 ACGA
195 ACGA
96951 CCATTTTATT
Statistics
Matches: 363, Mismatches: 42, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
208 1 0.00
209 273 0.75
210 86 0.24
211 3 0.01
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (208 bp):
CTTCTCTATATCTCATCAGGAAGATGACTGTTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
AGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTGTTTCATTGATTTGGTATACTTCTCAG
TATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTATCTCATCAGGAAGA
CGAATCTGGTCCA
Found at i:97034 original size:172 final size:172
Alignment explanation
Indices: 96745--97113 Score: 576
Period size: 172 Copynumber: 2.1 Consensus size: 172
96735 AAGACGGATC
* * **
96745 TGGTCCACTTCTCTATATCTCATCAGGAAGATGACTGTTTTATTGCTTCGACCTGCTTCTCAGTA
1 TGGTCCACTTCTCTATATCTCATCAAGAAGACGACCATTTTATTGCTTCGACCTGCTTCTCAGTA
* *
96810 TCTCATCAGGAAGCTAGGGTTCGAAGATTTACTCACTTTGAGCCTTGTTTCATTGACTTGGTATA
66 TCTCATCAGGAAGCTAGGGTTCAAAGATTTACTCACTTTGAGCCTGGTTTCATTGACTTGGTATA
* ** *
96875 CTTCTCAGTATCTCATTAGGAAGATGATTGCATCACTTGTTT
131 CTTCTCAGTATCTCATCAGGAAGATGACCGCATAACTTGTTT
* *
96917 TGGTCCACTTCTCTGTATCTCATCAAGAAGACGACCATTTTATTGCTTCGACTTGCTTCTCAGTA
1 TGGTCCACTTCTCTATATCTCATCAAGAAGACGACCATTTTATTGCTTCGACCTGCTTCTCAGTA
* * *
96982 TCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACTTTGAGCCTGGTTTCATTGACTTGGTCTA
66 TCTCATCAGGAAGCTAGGGTTCAAAGATTTACTCACTTTGAGCCTGGTTTCATTGACTTGGTATA
*
97047 CTTCTCAGTATCTCATCAGGAAGATGACCGCATAACTTTTTT
131 CTTCTCAGTATCTCATCAGGAAGATGACCGCATAACTTGTTT
**
97089 TAATCCACTTCTCTATATCTCATCA
1 TGGTCCACTTCTCTATATCTCATCA
97114 GGAAAACGGA
Statistics
Matches: 178, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
172 178 1.00
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.37
Consensus pattern (172 bp):
TGGTCCACTTCTCTATATCTCATCAAGAAGACGACCATTTTATTGCTTCGACCTGCTTCTCAGTA
TCTCATCAGGAAGCTAGGGTTCAAAGATTTACTCACTTTGAGCCTGGTTTCATTGACTTGGTATA
CTTCTCAGTATCTCATCAGGAAGATGACCGCATAACTTGTTT
Found at i:97145 original size:37 final size:37
Alignment explanation
Indices: 97092--97196 Score: 165
Period size: 37 Copynumber: 2.8 Consensus size: 37
97082 CTTTTTTTAA
* *
97092 TCCACTTCTCTATATCTCATCAGGAAAACGGATTTGG
1 TCCACTTCTCTGTATCTCATCAGGAAAACGAATTTGG
*
97129 TCCACTTCTCTGTATCTCATCAGGAAAATGAATTTGG
1 TCCACTTCTCTGTATCTCATCAGGAAAACGAATTTGG
* *
97166 TCCATTTCTCTGTATCTCATCAGGAAGACGA
1 TCCACTTCTCTGTATCTCATCAGGAAAACGA
97197 CCATTTTATT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (37 bp):
TCCACTTCTCTGTATCTCATCAGGAAAACGAATTTGG
Found at i:101074 original size:37 final size:37
Alignment explanation
Indices: 101021--101110 Score: 126
Period size: 37 Copynumber: 2.4 Consensus size: 37
101011 ACATCTAAAA
* ** *
101021 ATTCAGGTTTTGTGCCTAGTACGCTTTTTGCTGGTGT
1 ATTCAGGCTTTGTGCCTAGTACGCTTCGTGCCGGTGT
* *
101058 ATTCAGGCTTTATGCCTAGTAGGCTTCGTGCCGGTGT
1 ATTCAGGCTTTGTGCCTAGTACGCTTCGTGCCGGTGT
101095 ATTCAGGCTTTGTGCC
1 ATTCAGGCTTTGTGCC
101111 AGTGATCAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.12, C:0.20, G:0.28, T:0.40
Consensus pattern (37 bp):
ATTCAGGCTTTGTGCCTAGTACGCTTCGTGCCGGTGT
Found at i:112096 original size:21 final size:21
Alignment explanation
Indices: 112070--112121 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
112060 ATCAGGTACT
112070 GGAAATAGAAAGTTATAAATA
1 GGAAATAGAAAGTTATAAATA
112091 GGAAATAGAAAGTTATAAATA
1 GGAAATAGAAAGTTATAAATA
112112 GGAAATAGAA
1 GGAAATAGAA
112122 GTAGTGTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.58, C:0.00, G:0.21, T:0.21
Consensus pattern (21 bp):
GGAAATAGAAAGTTATAAATA
Found at i:112810 original size:21 final size:23
Alignment explanation
Indices: 112777--112821 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
112767 TGGTATTTGT
*
112777 AAATGCATAACTTGTATCGGTAG
1 AAATGCATAACTTGTATCAGTAG
112800 AAAT-CAT-ACTTGTATCAGTAG
1 AAATGCATAACTTGTATCAGTAG
112821 A
1 A
112822 GCTAGCACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.67
22 3 0.14
23 4 0.19
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (23 bp):
AAATGCATAACTTGTATCAGTAG
Found at i:125559 original size:2 final size:2
Alignment explanation
Indices: 125552--125578 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
125542 TCTATACCTG
125552 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
125579 GCACAAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:125659 original size:23 final size:21
Alignment explanation
Indices: 125633--125679 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
125623 TTTTCATCAT
125633 ATTACTAAAGTAATTTTAAAATA
1 ATTA-TAAAGTAATTTTAAAA-A
**
125656 ATTATAATTTAATTTTAAAAA
1 ATTATAAAGTAATTTTAAAAA
125677 ATT
1 ATT
125680 GTTTTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 14 0.64
23 4 0.18
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
ATTATAAAGTAATTTTAAAAA
Found at i:129715 original size:13 final size:14
Alignment explanation
Indices: 129686--129729 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
129676 AGAAATAGGG
*
129686 AATTTTGTTAGATT
1 AATTTAGTTAGATT
129700 AATTTAGTTA-ATT
1 AATTTAGTTAGATT
* *
129713 AATTTAATTAGTTT
1 AATTTAGTTAGATT
129727 AAT
1 AAT
129730 AAATATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 12 0.46
14 14 0.54
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (14 bp):
AATTTAGTTAGATT
Found at i:129957 original size:40 final size:40
Alignment explanation
Indices: 129902--129986 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 40
129892 TGGAAGTTCT
*
129902 ACTTCGATGGCGATACAGATTGTTCTAACTCTGAAAAAGG
1 ACTTCGATGGCGATACAGATTGTTCTAACTCTAAAAAAGG
129942 ACTTCGATGGCGATACAGATTGTTCTAACTCTAAAAAAGG
1 ACTTCGATGGCGATACAGATTGTTCTAACTCTAAAAAAGG
*
129982 GCTTC
1 ACTTC
129987 TCTTTTAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (40 bp):
ACTTCGATGGCGATACAGATTGTTCTAACTCTAAAAAAGG
Found at i:130034 original size:15 final size:15
Alignment explanation
Indices: 130014--130051 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
130004 AATTTTAAAT
130014 TTTATTTTTCA-TTAG
1 TTTATTTTT-ATTTAG
*
130029 TTTATTTTTATTTAT
1 TTTATTTTTATTTAG
130044 TTTATTTT
1 TTTATTTT
130052 AAGTCTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTATTTTTATTTAG
Found at i:135962 original size:8 final size:8
Alignment explanation
Indices: 135951--135975 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
135941 ATATATATAT
135951 ATTTTAAA
1 ATTTTAAA
135959 ATTTTAAA
1 ATTTTAAA
135967 ATTTTAAA
1 ATTTTAAA
135975 A
1 A
135976 GATTAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTTTAAA
Found at i:146181 original size:6 final size:6
Alignment explanation
Indices: 146172--146200 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
146162 TTATTGCTAT
146172 TGGTAA TGGTAA TGGTAA TGGTAA TGGTA
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTA
146201 GGAGAATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (6 bp):
TGGTAA
Found at i:154511 original size:20 final size:22
Alignment explanation
Indices: 154467--154511 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
154457 CCCAATTCTA
* *
154467 TTTACTCATCACTTCTCATTTC
1 TTTACTCAACACTTCTCAATTC
154489 TTTACTCAACA-TT-TCAATTC
1 TTTACTCAACACTTCTCAATTC
154509 TTT
1 TTT
154512 CATTCCCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.43
21 2 0.10
22 10 0.48
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTACTCAACACTTCTCAATTC
Found at i:159551 original size:97 final size:97
Alignment explanation
Indices: 159385--159575 Score: 346
Period size: 97 Copynumber: 2.0 Consensus size: 97
159375 ACAACCATGG
**
159385 ATACCTTAGATACTTCAAACTCTAAACTTCCCGACTTAACCAACTTGGAGTTAATATAAGAATGA
1 ATACCTTAGATACTTCAAACTCTAAACTTCCCGACTTAACCAACTCAGAGTTAATATAAGAATGA
159450 GACGAACCAAGGTCTATCAAAGCATAAACCAA
66 GACGAACCAAGGTCTATCAAAGCATAAACCAA
* *
159482 ATACCTTAGATATTTCAAACTCTAAACTTCTCGACTTAACCAACTCAGAGTTAATATAAGAATGA
1 ATACCTTAGATACTTCAAACTCTAAACTTCCCGACTTAACCAACTCAGAGTTAATATAAGAATGA
159547 GACGAACCAAGGTCTATCAAAGCATAAAC
66 GACGAACCAAGGTCTATCAAAGCATAAAC
159576 TGGAATGGAA
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
97 90 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (97 bp):
ATACCTTAGATACTTCAAACTCTAAACTTCCCGACTTAACCAACTCAGAGTTAATATAAGAATGA
GACGAACCAAGGTCTATCAAAGCATAAACCAA
Found at i:166338 original size:14 final size:12
Alignment explanation
Indices: 166309--166343 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
166299 TTAATATTGT
166309 TTTTAAAAAGTG
1 TTTTAAAAAGTG
166321 TTTTAGAAAAGTG
1 TTTTA-AAAAGTG
166334 ATTTTAAAAA
1 -TTTTAAAAA
166344 ATACTTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.24
13 11 0.52
14 5 0.24
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.40
Consensus pattern (12 bp):
TTTTAAAAAGTG
Found at i:166344 original size:14 final size:13
Alignment explanation
Indices: 166306--166344 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
166296 AGTTTAATAT
*
166306 TGTTTTTAAAAAG
1 TGTTTTAAAAAAG
*
166319 TGTTTTAGAAAAG
1 TGTTTTAAAAAAG
166332 TGATTTTAAAAAA
1 TG-TTTTAAAAAA
166345 TACTTTTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTTTTAAAAAAG
Found at i:166790 original size:36 final size:36
Alignment explanation
Indices: 166743--166814 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
166733 TTTAACATTG
166743 CTTTTAATTCAA-AA-GTACTTTTAAAAAACACTATTA
1 CTTTTAATTCAAGAATGT--TTTTAAAAAACACTATTA
*
166779 CTTTTGATTCAAGAATGTTTTTAAAAAACACTATTA
1 CTTTTAATTCAAGAATGTTTTTAAAAAACACTATTA
166815 AATAAAGGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
36 29 0.88
37 2 0.06
38 2 0.06
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40
Consensus pattern (36 bp):
CTTTTAATTCAAGAATGTTTTTAAAAAACACTATTA
Found at i:170681 original size:15 final size:15
Alignment explanation
Indices: 170632--170682 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
170622 TAAAAAAAAA
170632 TTATATTATTTTTAAT
1 TTATA-TATTTTTAAT
*
170648 TTA-ATATTTAATAATT
1 TTATATATTT-TTAA-T
*
170664 TTATATATTTTTTAT
1 TTATATATTTTTAAT
170679 TTAT
1 TTAT
170683 CAAAATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 5 0.17
15 9 0.31
16 9 0.31
17 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATATATTTTTAAT
Found at i:171729 original size:10 final size:10
Alignment explanation
Indices: 171706--171797 Score: 57
Period size: 10 Copynumber: 9.3 Consensus size: 10
171696 TATACAAATT
*
171706 TTTTTAACAT
1 TTTTTAACAA
171716 TTTTTAA-AA
1 TTTTTAACAA
* *
171725 ATTTTAATAA
1 TTTTTAACAA
171735 TTTTTAACAA
1 TTTTTAACAA
171745 TCTTTT-ACAA
1 T-TTTTAACAA
* * *
171755 TTTCTAATATT
1 TTTTTAACA-A
* *
171766 TTTTTTATAA
1 TTTTTAACAA
171776 TTTTT-ACAA
1 TTTTTAACAA
171785 TATTTT-ACAA
1 T-TTTTAACAA
171795 TTT
1 TTT
171798 CTAATTTATA
Statistics
Matches: 66, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
9 16 0.24
10 39 0.59
11 11 0.17
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTTTAACAA
Found at i:171739 original size:30 final size:31
Alignment explanation
Indices: 171705--171770 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 31
171695 ATATACAAAT
*
171705 TTTTTTAAC-ATTTTTTAAAAATTT-TAATAA
1 TTTTTTAACAATCTTTT-AAAATTTCTAATAA
* *
171735 -TTTTTAACAATCTTTTACAATTTCTAATAT
1 TTTTTTAACAATCTTTTAAAATTTCTAATAA
171765 TTTTTT
1 TTTTTT
171771 TATAATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 14 0.47
30 11 0.37
31 5 0.17
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (31 bp):
TTTTTTAACAATCTTTTAAAATTTCTAATAA
Found at i:171756 original size:29 final size:30
Alignment explanation
Indices: 171706--171769 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
171696 TATACAAATT
*
171706 TTTTTAACATTTTTTAAAAATTT-TAATAA
1 TTTTTAACATCTTTTAAAAATTTCTAATAA
* *
171735 TTTTTAACAATCTTTT-ACAATTTCTAATAT
1 TTTTTAAC-ATCTTTTAAAAATTTCTAATAA
171765 TTTTT
1 TTTTT
171770 TTATAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (30 bp):
TTTTTAACATCTTTTAAAAATTTCTAATAA
Found at i:171785 original size:40 final size:41
Alignment explanation
Indices: 171726--171802 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 41
171716 TTTTTAAAAA
*
171726 TTTTAATAATTTTTAACAATCTTTTACAATTTCTAATATTT
1 TTTTAATAATTTTTAACAATATTTTACAATTTCTAATATTT
*
171767 TTTTTATAATTTTT-ACAATATTTTACAATTTCTAAT
1 TTTTAATAATTTTTAACAATATTTTACAATTTCTAAT
171803 TTATATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 21 0.62
41 13 0.38
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (41 bp):
TTTTAATAATTTTTAACAATATTTTACAATTTCTAATATTT
Found at i:171808 original size:21 final size:21
Alignment explanation
Indices: 171747--171808 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
171737 TTTAACAATC
*
171747 TTTTACAATTTCTAATATT-TT
1 TTTTACAATTTCTAAT-TTATA
* *
171768 TTTTATAATTTTTACA---ATA
1 TTTTACAATTTCTA-ATTTATA
171787 TTTTACAATTTCTAATTTATA
1 TTTTACAATTTCTAATTTATA
171808 T
1 T
171809 ATATTCTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
18 1 0.03
19 13 0.42
21 16 0.52
22 1 0.03
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTACAATTTCTAATTTATA
Found at i:176331 original size:19 final size:20
Alignment explanation
Indices: 176295--176337 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
176285 ATAGAGGTAA
*
176295 TAAAATGTACATAATAAAAT
1 TAAAATGAACATAATAAAAT
*
176315 TAAAATGAACA-AATAAAGT
1 TAAAATGAACATAATAAAAT
176334 TAAA
1 TAAA
176338 TAAAGTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.63, C:0.05, G:0.07, T:0.26
Consensus pattern (20 bp):
TAAAATGAACATAATAAAAT
Found at i:180101 original size:24 final size:24
Alignment explanation
Indices: 180069--180121 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
180059 GAGTTGATAG
180069 CTTGAATATGATGATAGAAAGCAA
1 CTTGAATATGATGATAGAAAGCAA
180093 CTTGAATATGATGATAGAAAGCAA
1 CTTGAATATGATGATAGAAAGCAA
180117 CTTGA
1 CTTGA
180122 GGGGTAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.26
Consensus pattern (24 bp):
CTTGAATATGATGATAGAAAGCAA
Found at i:180352 original size:3 final size:3
Alignment explanation
Indices: 180344--180377 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
180334 ACTGTGGCTT
180344 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
180378 ATGTGGAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:188435 original size:25 final size:24
Alignment explanation
Indices: 188395--188442 Score: 87
Period size: 25 Copynumber: 2.0 Consensus size: 24
188385 GATTAAATTG
188395 ATAATTTTTTTATTTAATATTAAT
1 ATAATTTTTTTATTTAATATTAAT
188419 ATAATTGTTTTTATTTAATATTAA
1 ATAATT-TTTTTATTTAATATTAA
188443 ATATTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
ATAATTTTTTTATTTAATATTAAT
Found at i:194537 original size:45 final size:45
Alignment explanation
Indices: 194449--194574 Score: 166
Period size: 45 Copynumber: 2.8 Consensus size: 45
194439 GTACTTTGGC
* * **
194449 GTAGTCCATCGAGACAGTAAACAC-AAAACCATTATGGCGAATAT
1 GTAGTCCGTCGAGAAAGTAAACACGAAGGCCATTATGGCGAATAT
*
194493 GTAGTCCG-CTGGGAAAGTAAACACGAAGGCCATTATGGCGAATAT
1 GTAGTCCGTC-GAGAAAGTAAACACGAAGGCCATTATGGCGAATAT
* *
194538 GTAGTCCGTCGAGACAGTAAACATGAAGGCCATTATG
1 GTAGTCCGTCGAGAAAGTAAACACGAAGGCCATTATG
194575 ATGAATACGT
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
43 1 0.01
44 19 0.27
45 50 0.70
46 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (45 bp):
GTAGTCCGTCGAGAAAGTAAACACGAAGGCCATTATGGCGAATAT
Found at i:205308 original size:6 final size:6
Alignment explanation
Indices: 205297--205322 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
205287 TGATCAAAAT
205297 TGAAAG TGAAAG TGAAAG TGAAAG TG
1 TGAAAG TGAAAG TGAAAG TGAAAG TG
205323 TGATTGGAAT
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:0.46, C:0.00, G:0.35, T:0.19
Consensus pattern (6 bp):
TGAAAG
Found at i:206778 original size:200 final size:200
Alignment explanation
Indices: 206435--206841 Score: 571
Period size: 200 Copynumber: 2.0 Consensus size: 200
206425 CATATCTAGG
* * * * * *
206435 AAGAAAGGCAAAAGGGACATCTTAATCTATTAGACCATGCATTGAGGAAATGGTTGCAATTTTCT
1 AAGAAAGGCAAAAGGGACATCCTAATCTATTACACCATGCATTGAGGAAACGATTGAAATCTTCT
* * * *
206500 TGTCCCTTGCTACAAAGAACATGTTGATAAACTTTACGAAACGTTCGCCTCGTTCATAAAGCTCC
66 TGTCCCTTGCGACAAAGAACATGTTGATAAACTCTACGAAACGTTAGCCTCGTTAATAAAGCTCC
* * * * * *
206565 CTAAGGTGAAGCTGATCAATTGTAGTTTTTCACCAATGTTGAGTTTCTCTTCCACGTGACTGCTA
131 CTAAGGTGAAGCTGATCAATGGGAGTTTTCCAACAATGTTGAGTTTCTCATCCACGTGACTACTA
206630 GGCCA
196 GGCCA
* *
206635 AAGAAAGGCAGAAGGGACATCCTAATCTATTACAGCATGCATTGAGGAAACGATTGAAATCTTCT
1 AAGAAAGGCAAAAGGGACATCCTAATCTATTACACCATGCATTGAGGAAACGATTGAAATCTTCT
* * * *
206700 TGTCCCTTGCGACAGAGATCATGTTGATAAACTCTACGAAACGTTAGCCTTGTTAATAGAGCTCC
66 TGTCCCTTGCGACAAAGAACATGTTGATAAACTCTACGAAACGTTAGCCTCGTTAATAAAGCTCC
** * * *
206765 CTCGGGTGAAGCTGATTAATGGGGGTTTTCCAACAATGTTGAGTTTCTCATCCACGTGACTACTG
131 CTAAGGTGAAGCTGATCAATGGGAGTTTTCCAACAATGTTGAGTTTCTCATCCACGTGACTACTA
206830 GGCCA
196 GGCCA
206835 AAGAAAG
1 AAGAAAG
206842 CGCCTTTTGT
Statistics
Matches: 180, Mismatches: 27, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
200 180 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (200 bp):
AAGAAAGGCAAAAGGGACATCCTAATCTATTACACCATGCATTGAGGAAACGATTGAAATCTTCT
TGTCCCTTGCGACAAAGAACATGTTGATAAACTCTACGAAACGTTAGCCTCGTTAATAAAGCTCC
CTAAGGTGAAGCTGATCAATGGGAGTTTTCCAACAATGTTGAGTTTCTCATCCACGTGACTACTA
GGCCA
Found at i:215704 original size:26 final size:27
Alignment explanation
Indices: 215668--215724 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
215658 CCCTTGTTTG
* *
215668 TAATATAAAAAAATATACAAAT-TAAC
1 TAATACAAAAAAACATACAAATATAAC
* *
215694 TAATACAAAAAAACCTACTAATATAAC
1 TAATACAAAAAAACATACAAATATAAC
215721 TAAT
1 TAAT
215725 TATACTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.26
Consensus pattern (27 bp):
TAATACAAAAAAACATACAAATATAAC
Found at i:223955 original size:28 final size:26
Alignment explanation
Indices: 223889--223956 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 26
223879 TGTTTAAATA
*
223889 ATTTTTATTTTTTATTTCTAATATAC
1 ATTTTTATTTTTTATTTATAATATAC
* *
223915 ATTTTGATTTTTTTATTTTATAAT-TTC
1 ATTTTTA-TTTTTTA-TTTATAATATAC
*
223942 TATTTTTATATTTTA
1 -ATTTTTATTTTTTA
223957 AATTTTTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
26 6 0.18
27 15 0.44
28 13 0.38
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.69
Consensus pattern (26 bp):
ATTTTTATTTTTTATTTATAATATAC
Found at i:223967 original size:22 final size:22
Alignment explanation
Indices: 223886--223963 Score: 70
Period size: 22 Copynumber: 3.4 Consensus size: 22
223876 TTCTGTTTAA
223886 ATAATTTTTATTTTT-TATTTCTAAT
1 ATAATTTTTATTTTTATA-TT-T--T
* *
223911 ATACATTTTGATTTTTTTATTTT
1 ATA-ATTTTTATTTTTATATTTT
*
223934 ATAATTTCTATTTTTATATTTT
1 ATAATTTTTATTTTTATATTTT
223956 A-AATTTTT
1 ATAATTTTT
223964 TATTAATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
21 6 0.13
22 17 0.37
23 4 0.09
25 4 0.09
26 13 0.28
27 2 0.04
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (22 bp):
ATAATTTTTATTTTTATATTTT
Found at i:227841 original size:23 final size:27
Alignment explanation
Indices: 227786--227842 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
227776 ATATATTTAA
*
227786 AATTTATATTAAATTAAATTTTATAAAT
1 AATTTATATTAAATT-AATTTCATAAAT
227814 AATTTATATT-AATT-ATTTCA-AAAT
1 AATTTATATTAAATTAATTTCATAAAT
227838 -ATTTA
1 AATTTA
227843 AAATTTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 5 0.18
24 4 0.14
25 5 0.18
27 4 0.14
28 10 0.36
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (27 bp):
AATTTATATTAAATTAATTTCATAAAT
Found at i:229164 original size:18 final size:19
Alignment explanation
Indices: 229143--229179 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
229133 ATCCCATCCT
*
229143 TTTCTTTTTCT-TTTTCTC
1 TTTCTCTTTCTCTTTTCTC
229161 TTTCTCTTTCTCTTTTCTC
1 TTTCTCTTTCTCTTTTCTC
229180 CTCCCCTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTCTCTTTCTCTTTTCTC
Found at i:236785 original size:15 final size:15
Alignment explanation
Indices: 236751--236779 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
236741 TTAACCCAAA
236751 GATT-CAATATCTTT
1 GATTCCAATATCTTT
236765 GATTCCAATATCTTT
1 GATTCCAATATCTTT
236780 TGTTCCCGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (15 bp):
GATTCCAATATCTTT
Found at i:242640 original size:402 final size:402
Alignment explanation
Indices: 241896--242705 Score: 1467
Period size: 402 Copynumber: 2.0 Consensus size: 402
241886 AGCTGTCTAA
** *
241896 ATTTTCATAATCAGACGACAGCAGTGCAGGAGCAGTGGGCAAAGGTGAGTTGACTGATTCCCTCA
1 ATTTTCATAATCAGACGACAGCAGTGCAGGAGCAACGGGCAAAGGTGAGTTGACTGATTCCATCA
* * *
241961 TGAGAGAAGCATAACAAAACCTTGTATTTTCGCTCTCATAGTCTTCAGGTCCCTCAACCTTTCCA
66 AGAGAGAAGCAGAACAAAAACTTGTATTTTCGCTCTCATAGTCTTCAGGTCCCTCAACCTTTCCA
*
242026 TTCAGGTTCCTTTCCTCCGTTGGTTTCAAAGCAGAAAGCGGTTTGGGAATCTGGCTTTCTTCATC
131 TTCAGGTTCCTTTCCTCCGTTGGTCTCAAAGCAGAAAGCGGTTTGGGAATCTGGCTTTCTTCATC
*
242091 ACACTCCATTACATTATTCAACAATATATCCTCCTCTTCCAAAGTTGGTTCCATCAGGTGAAGTT
196 ACACTCCATTACATTATTCAACAATATATCCTCCTCTTCCAAAGTTGGTTCCATCAGATGAAGTT
242156 GGCTTTCTTGTATTGATCTTCTGTTTTCAACTTCTTTTACAACTGAAGGATCCATGTTCTCAGTG
261 GGCTTTCTTGTATTGATCTTCTGTTTTCAACTTCTTTTACAACTGAAGGATCCATGTTCTCAGTG
* * *
242221 TCTGAGCATCTCTCTGAATTCTCTCCTTCAGAGACAGAGATTACTTTTGTGACAGCCTCTGGAAG
326 TCTGAGCATCTCTCTGAATTCTCTCCTTCAGAAACAGAGATTACTTCTGTGACAGCCTCTGGAAA
242286 GATGGTCTTGCT
391 GATGGTCTTGCT
*
242298 ATTTTCATAATCAGATGACAGCAGTGCAGGAGCAACGGGCAAAGGTGAGTTGACTGATTCCATCA
1 ATTTTCATAATCAGACGACAGCAGTGCAGGAGCAACGGGCAAAGGTGAGTTGACTGATTCCATCA
*
242363 AGAGAGAAGCAGAACAAAAACTTGTATTTTCGCTCTCATAGTCTTCAGGTCCCTCAACCTTTTCA
66 AGAGAGAAGCAGAACAAAAACTTGTATTTTCGCTCTCATAGTCTTCAGGTCCCTCAACCTTTCCA
*
242428 TTCAGGTTCCTTTTCTCCGTTGGTCTCAAAGCAGAAAGCGGTTTGGGAATCTGGCTTTCTTCATC
131 TTCAGGTTCCTTTCCTCCGTTGGTCTCAAAGCAGAAAGCGGTTTGGGAATCTGGCTTTCTTCATC
*
242493 ACACTCCATTACATTATTCAACAATATATCCTCCTCTTCCAAAGTTGGTTGCATCAGATGAAGTT
196 ACACTCCATTACATTATTCAACAATATATCCTCCTCTTCCAAAGTTGGTTCCATCAGATGAAGTT
242558 GGCTTTCTTGTATTGATCTTCTGTTTTCAACTTCTTTTACAACTGAAGGATCCATGTTCTCAGTG
261 GGCTTTCTTGTATTGATCTTCTGTTTTCAACTTCTTTTACAACTGAAGGATCCATGTTCTCAGTG
* *
242623 TCTGAGTATCTCTCTGAATTCTCTCCTTCAGAAACAGAGATTGCTTCTGTGACAGCCTCTGGAAA
326 TCTGAGCATCTCTCTGAATTCTCTCCTTCAGAAACAGAGATTACTTCTGTGACAGCCTCTGGAAA
242688 GATGGTCTTGCT
391 GATGGTCTTGCT
242700 ATTTTC
1 ATTTTC
242706 TCCCATCTTC
Statistics
Matches: 391, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
402 391 1.00
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (402 bp):
ATTTTCATAATCAGACGACAGCAGTGCAGGAGCAACGGGCAAAGGTGAGTTGACTGATTCCATCA
AGAGAGAAGCAGAACAAAAACTTGTATTTTCGCTCTCATAGTCTTCAGGTCCCTCAACCTTTCCA
TTCAGGTTCCTTTCCTCCGTTGGTCTCAAAGCAGAAAGCGGTTTGGGAATCTGGCTTTCTTCATC
ACACTCCATTACATTATTCAACAATATATCCTCCTCTTCCAAAGTTGGTTCCATCAGATGAAGTT
GGCTTTCTTGTATTGATCTTCTGTTTTCAACTTCTTTTACAACTGAAGGATCCATGTTCTCAGTG
TCTGAGCATCTCTCTGAATTCTCTCCTTCAGAAACAGAGATTACTTCTGTGACAGCCTCTGGAAA
GATGGTCTTGCT
Found at i:247370 original size:21 final size:21
Alignment explanation
Indices: 247341--247384 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
247331 ATCAAAATAA
247341 TATAATTTT-ACTTTTTAACTT
1 TATAATTTTGA-TTTTTAACTT
* *
247362 TATAGTTTTGATTTTTAATTT
1 TATAATTTTGATTTTTAACTT
247383 TA
1 TA
247385 AAAAGAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.64
Consensus pattern (21 bp):
TATAATTTTGATTTTTAACTT
Found at i:255307 original size:29 final size:30
Alignment explanation
Indices: 255273--255331 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
255263 TATGGTTTCA
255273 TGTGCAATTGTATACA-AAAATTTTGATTT
1 TGTGCAATTGTATACATAAAATTTTGATTT
*
255302 TGTGCAATTGTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATAAAATTTTGATTT
255332 GATTCAATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (30 bp):
TGTGCAATTGTATACATAAAATTTTGATTT
Found at i:258928 original size:16 final size:16
Alignment explanation
Indices: 258895--258935 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
258885 GATGAGTGAG
*
258895 GGTAGTG-G-GATTTA
1 GGTAGTGAGTGATGTA
258909 GGTAGTGAGTGATGTA
1 GGTAGTGAGTGATGTA
258925 GGTAGT-AGTGA
1 GGTAGTGAGTGA
258936 AATGGGGGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 7 0.29
15 6 0.25
16 11 0.46
ACGTcount: A:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (16 bp):
GGTAGTGAGTGATGTA
Found at i:259423 original size:28 final size:28
Alignment explanation
Indices: 259384--259439 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
259374 GTTGGTCAGT
*
259384 GTAATTATTTTTAATAATAA-ATAAAAA
1 GTAATTAATTTTAATAATAAGATAAAAA
*
259411 GTAATGTAATTTTAATATTAAGATAAAAA
1 GTAAT-TAATTTTAATAATAAGATAAAAA
259440 TCAATAATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.20
28 13 0.52
29 7 0.28
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (28 bp):
GTAATTAATTTTAATAATAAGATAAAAA
Found at i:267353 original size:135 final size:135
Alignment explanation
Indices: 267201--267472 Score: 472
Period size: 135 Copynumber: 2.0 Consensus size: 135
267191 AAAGTGAAAA
267201 TAAAAAAAACTAATATAATAGATGGATTAAATTTATTATTATATTAATTTTAAAAACAGTCAAAT
1 TAAAAAAAACTAATATAATAGATGGATTAAATTTATTATTATATTAATTTTAAAAACAGTCAAAT
*
267266 GATTTTTTTTGTTAATAATTTAATACAAAAATAATCACTTTTGTTTAACTCAGGTTACATTTTAG
66 GATTTTTTTTGTTAATAATTTAATACAAAAATAATCACTTTTGTTTAACTCAGGTTACATTTTAA
267331 TCACT
131 TCACT
* * * *
267336 TAAAAAAAGCTAGTATAATAGATGGATTAAATTTATTATTATATTAATTTTAAAAACGGTTAAAT
1 TAAAAAAAACTAATATAATAGATGGATTAAATTTATTATTATATTAATTTTAAAAACAGTCAAAT
* **
267401 GATTTTTTTTGTTAATAATTTAATACAAAAATAGTCACTTTTGTTTGCCTCAGGTTACATTTTAA
66 GATTTTTTTTGTTAATAATTTAATACAAAAATAATCACTTTTGTTTAACTCAGGTTACATTTTAA
267466 TCACT
131 TCACT
267471 TA
1 TA
267473 TGTTTGAAAT
Statistics
Matches: 129, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
135 129 1.00
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (135 bp):
TAAAAAAAACTAATATAATAGATGGATTAAATTTATTATTATATTAATTTTAAAAACAGTCAAAT
GATTTTTTTTGTTAATAATTTAATACAAAAATAATCACTTTTGTTTAACTCAGGTTACATTTTAA
TCACT
Found at i:268631 original size:17 final size:16
Alignment explanation
Indices: 268593--268636 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
268583 TACTCTCTTC
268593 TATTTATT-TTTTTTT
1 TATTTATTGTTTTTTT
* *
268608 AAATTATTGCTTTTTTT
1 TATTTATTG-TTTTTTT
268625 TATTTATTGTTT
1 TATTTATTGTTT
268637 CAATTCATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 6 0.26
16 3 0.13
17 14 0.61
ACGTcount: A:0.18, C:0.02, G:0.05, T:0.75
Consensus pattern (16 bp):
TATTTATTGTTTTTTT
Found at i:270929 original size:5 final size:6
Alignment explanation
Indices: 270913--270937 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
270903 TACGAATATT
270913 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
270938 TCCGAGCCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:275566 original size:22 final size:22
Alignment explanation
Indices: 275512--275566 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
275502 TTAACTTTAG
* * *
275512 TTTAATAAAAAATGCTTATAAT
1 TTTAATAAAAAATACTAATAAA
*
275534 TTTAAAAAAAAAATACTAATAAA
1 TTT-AATAAAAAATACTAATAAA
275557 TTTAATAAAA
1 TTTAATAAAA
275567 TATCAAGTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (22 bp):
TTTAATAAAAAATACTAATAAA
Found at i:279590 original size:225 final size:225
Alignment explanation
Indices: 279196--279654 Score: 598
Period size: 225 Copynumber: 2.0 Consensus size: 225
279186 GCTCCCATTT
* * * ** * *
279196 TTAATAAAATTCCGGCTGAAAGTATAAAAGTACTGTAATGGGCCACCTTGTAGGTATTTAGTAAT
1 TTAATAAAATTCCAGCTGAAAGCATAAAAGTACTGTAACGGGCCACCTTGTAGGTATCCAATAAC
* *
279261 CACGTATGTAAAGGTATAATCGGTGATTTGACCGCAAAAGAAATAAGAAACCCAATATAGAATAT
66 CACGTAGGTAAAGGTATAATCGGTGATTTGACAGCAAAAGAAATAAGAAACCCAATATAGAATAT
** *
279326 TATTTCCAATGCGAGACGATATGATTTATTAGGTAATGTTTCAAATTTTAATGTTGGTTCATTAG
131 TATTTCCAATGCGAGACGATATGATCGATTAAGTAATGTTTCAAATTTTAATGTTGGTTCATTAG
*
279391 AATCGTATAAACCAAGACCCAAAAATCTTA
196 AATCGTATAAACCAAGACCCAAAAATCCTA
** * * *
279421 TTAATAAAATTCCAGCT-AGAAGCATACGAGTACTGTGACGGGCCTCCTTGTGGGTATCCAATAA
1 TTAATAAAATTCCAGCTGA-AAGCATAAAAGTACTGTAACGGGCCACCTTGTAGGTATCCAATAA
* * * *
279485 CCACGTAGGTAAGGGTATAA-CTGGTGATTTGACAGCGAAAGCAATAAGAAATCCAATATAGAAT
65 CCACGTAGGTAAAGGTATAATC-GGTGATTTGACAGCAAAAGAAATAAGAAACCCAATATAGAAT
*** * * * * *
279549 ATTATTTCTGGTGCGATAGGATATTATCGATTAATTAATGTTTCAAATTTTAATGTTGGTTTATT
129 ATTATTTCCAATGCGAGACGATATGATCGATTAAGTAATGTTTCAAATTTTAATGTTGGTTCATT
*
279614 AGAATCGTATAAACCAAGACCCAAAACTCCTA
194 AGAATCGTATAAACCAAGACCCAAAAATCCTA
*
279646 TTAAAAAAA
1 TTAATAAAA
279655 AATAGAACCC
Statistics
Matches: 200, Mismatches: 32, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
224 2 0.01
225 198 0.99
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (225 bp):
TTAATAAAATTCCAGCTGAAAGCATAAAAGTACTGTAACGGGCCACCTTGTAGGTATCCAATAAC
CACGTAGGTAAAGGTATAATCGGTGATTTGACAGCAAAAGAAATAAGAAACCCAATATAGAATAT
TATTTCCAATGCGAGACGATATGATCGATTAAGTAATGTTTCAAATTTTAATGTTGGTTCATTAG
AATCGTATAAACCAAGACCCAAAAATCCTA
Found at i:295211 original size:30 final size:30
Alignment explanation
Indices: 295175--295239 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
295165 ATTAATGAAG
* *
295175 ATAAAATTATATTTTAACCCCTTAAAAATA
1 ATAAAATTATAATTTAACCCATTAAAAATA
* * *
295205 ATAAAATTTTAATTTAATCCATTAAAAATT
1 ATAAAATTATAATTTAACCCATTAAAAATA
295235 ATAAA
1 ATAAA
295240 GATATAAGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.38
Consensus pattern (30 bp):
ATAAAATTATAATTTAACCCATTAAAAATA
Found at i:295588 original size:29 final size:27
Alignment explanation
Indices: 295513--295594 Score: 65
Period size: 29 Copynumber: 2.8 Consensus size: 27
295503 AATTGAAACG
*
295513 AATCAAAATTTCATGTATAAAATTACTCAA
1 AATCAAAA-TTCA--TATAAAATTACACAA
* *
295543 AATTAAAATCTATATATAAAATTACACATTA
1 AATCAAAAT-T-CATATAAAATTACACA--A
*
295574 AATCAAAATTCATATATAATT
1 AATCAAAATTCATATAAAATT
295595 TTGAAATTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
29 23 0.55
30 9 0.21
31 10 0.24
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.35
Consensus pattern (27 bp):
AATCAAAATTCATATAAAATTACACAA
Found at i:295589 original size:31 final size:29
Alignment explanation
Indices: 295513--295592 Score: 90
Period size: 31 Copynumber: 2.7 Consensus size: 29
295503 AATTGAAACG
* *
295513 AATCAAAATTTCATGTATAAAATTACTCAA
1 AATCAAAA-TTCATATATAAAATTACACAA
*
295543 AATTAAAA-TCTATATATAAAATTACACATTA
1 AATCAAAATTC-ATATATAAAATTACACA--A
295574 AATCAAAATTCATATATAA
1 AATCAAAATTCATATATAA
295593 TTTTGAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
28 2 0.05
29 15 0.36
30 7 0.17
31 16 0.38
32 2 0.05
ACGTcount: A:0.54, C:0.11, G:0.01, T:0.34
Consensus pattern (29 bp):
AATCAAAATTCATATATAAAATTACACAA
Found at i:295867 original size:15 final size:15
Alignment explanation
Indices: 295847--295884 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
295837 CTCTTAAATT
*
295847 TTTATTTTTTTTTAA
1 TTTATTTTTTTTGAA
295862 TTTATTTTTTTTGAA
1 TTTATTTTTTTTGAA
295877 TTT-TTTTT
1 TTTATTTTT
295885 AAATATACTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.82
Consensus pattern (15 bp):
TTTATTTTTTTTGAA
Found at i:302426 original size:18 final size:18
Alignment explanation
Indices: 302374--302429 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 18
302364 TAAATTATTC
*
302374 TTAATTAGTTAAATATTTT
1 TTAATTAATT-AATATTTT
302393 TTAATTACATT-A-ATTTT
1 TTAATTA-ATTAATATTTT
302410 TTAACTT-ATTAATATTTT
1 TTAA-TTAATTAATATTTT
302428 TT
1 TT
302430 TGAAGAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
16 3 0.09
17 10 0.31
18 10 0.31
19 7 0.22
20 2 0.06
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (18 bp):
TTAATTAATTAATATTTT
Found at i:302857 original size:91 final size:94
Alignment explanation
Indices: 302743--302930 Score: 301
Period size: 91 Copynumber: 2.0 Consensus size: 94
302733 CCCGACCGTC
*
302743 TAAATATCCAGCCGACATTTTGCTATAGTCCAAATGTAAAATTTCACAAATTTGTTTA-T-T-CT
1 TAAATATCCAACCGACATTTTGCTATAGTCCAAATGTAAAATTTCACAAATTTGTTTATTCTGCT
*
302805 ATTATTGCTTCCTTTATTTTCACGCTTGA
66 ATTATTGCTTCCTTTATTTACACGCTTGA
302834 TAAATATCCAACCGACATTTTGCTATAGTCCAAATGTAAAATTTCACAAATTTGTTTATTTCTGG
1 TAAATATCCAACCGACATTTTGCTATAGTCCAAATGTAAAATTTCACAAATTTGTTTA-TTCT-G
*
302899 ACTATTATTGCTTGCTTTATTTACACGCTTGA
64 -CTATTATTGCTTCCTTTATTTACACGCTTGA
302931 CTATAGCATC
Statistics
Matches: 88, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 57 0.65
93 1 0.01
94 1 0.01
97 29 0.33
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (94 bp):
TAAATATCCAACCGACATTTTGCTATAGTCCAAATGTAAAATTTCACAAATTTGTTTATTCTGCT
ATTATTGCTTCCTTTATTTACACGCTTGA
Found at i:312867 original size:12 final size:12
Alignment explanation
Indices: 312850--312878 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
312840 GCGAAACAAA
312850 AGAGAGAAAGAG
1 AGAGAGAAAGAG
312862 AGAGAGAAAGAG
1 AGAGAGAAAGAG
312874 AGAGA
1 AGAGA
312879 TAAATGTACT
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:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (12 bp):
AGAGAGAAAGAG
Found at i:313652 original size:6 final size:7
Alignment explanation
Indices: 313635--313659 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
313625 CCCTTAACAA
313635 AAAAAAC
1 AAAAAAC
313642 AAAAAAC
1 AAAAAAC
313649 AAAAAAC
1 AAAAAAC
313656 AAAA
1 AAAA
313660 GCAAAGAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:313951 original size:27 final size:27
Alignment explanation
Indices: 313921--313977 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
313911 TGGAACAACA
*
313921 AAGGTAACGAGTTCCTTAACATTGACT
1 AAGGTAACGAGTTCATTAACATTGACT
*
313948 AAGGTGACGAGTTCATTAACATTGACT
1 AAGGTAACGAGTTCATTAACATTGACT
313975 AAG
1 AAG
313978 TTTACTCGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (27 bp):
AAGGTAACGAGTTCATTAACATTGACT
Found at i:320019 original size:23 final size:22
Alignment explanation
Indices: 319978--320031 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 22
319968 TTTGAAATTT
319978 TTTAAA-TCCAAAAAGTAAAAAA
1 TTTAAATTCCAAAAAGT-AAAAA
320000 TTTAAATTCCTAAAAA-TAAAAA
1 TTTAAATTCC-AAAAAGTAAAAA
320022 TATTAAATTC
1 T-TTAAATTC
320032 AAAGTAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 12 0.41
23 12 0.41
24 5 0.17
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.31
Consensus pattern (22 bp):
TTTAAATTCCAAAAAGTAAAAA
Found at i:320359 original size:21 final size:21
Alignment explanation
Indices: 320335--320381 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
320325 TAGCATAATT
320335 CAAATATAAAGTTTAGAAATC
1 CAAATATAAAGTTTAGAAATC
* *
320356 CAAACATAAAGTTTATAAATC
1 CAAATATAAAGTTTAGAAATC
320377 CAAAT
1 CAAAT
320382 TACATAATCC
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:0.53, C:0.13, G:0.06, T:0.28
Consensus pattern (21 bp):
CAAATATAAAGTTTAGAAATC
Found at i:336237 original size:31 final size:31
Alignment explanation
Indices: 336194--336254 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
336184 TACACAATAG
*
336194 TCATTGAGCTATTTGAAAATTTTCATTTAAC
1 TCATTGAACTATTTGAAAATTTTCATTTAAC
* *
336225 TCATTGAACTATTTGATAGTTTTCATTTAA
1 TCATTGAACTATTTGAAAATTTTCATTTAA
336255 TTTACTGGAC
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:0.31, C:0.11, G:0.10, T:0.48
Consensus pattern (31 bp):
TCATTGAACTATTTGAAAATTTTCATTTAAC
Found at i:342438 original size:21 final size:19
Alignment explanation
Indices: 342393--342440 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
342383 ATCGAAACAT
*
342393 TTTGATTTTCATTGCTCTC
1 TTTGATTTGCATTGCTCTC
*
342412 TGTTGATTTGCATTGTTTCTC
1 T-TTGATTTGCATTG-CTCTC
342433 ATTTGATT
1 -TTTGATT
342441 CAATCCCCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.04
20 12 0.50
21 10 0.42
22 1 0.04
ACGTcount: A:0.12, C:0.15, G:0.15, T:0.58
Consensus pattern (19 bp):
TTTGATTTGCATTGCTCTC
Found at i:344562 original size:7 final size:7
Alignment explanation
Indices: 344550--344575 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
344540 TGGCAAAAAG
344550 AAAATAA
1 AAAATAA
344557 AAAATAA
1 AAAATAA
344564 AAAATAA
1 AAAATAA
344571 AAAAT
1 AAAAT
344576 TATTAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAATAA
Found at i:344602 original size:28 final size:28
Alignment explanation
Indices: 344559--344642 Score: 100
Period size: 28 Copynumber: 3.0 Consensus size: 28
344549 GAAAATAAAA
*
344559 AATAAAAAATA-AAAAATTATTAAAATTT
1 AATAAAAATTAGAAAAATTA-TAAAATTT
* *
344587 AATAAAAATTAGAAAAATTATAACATAT
1 AATAAAAATTAGAAAAATTATAAAATTT
*
344615 -ATAGAAATATAGAAAAATTATAAAATTT
1 AATAAAAAT-TAGAAAAATTATAAAATTT
344643 TATATAGTGA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
27 7 0.15
28 33 0.69
29 8 0.17
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (28 bp):
AATAAAAATTAGAAAAATTATAAAATTT
Found at i:344873 original size:10 final size:10
Alignment explanation
Indices: 344845--344921 Score: 52
Period size: 10 Copynumber: 7.8 Consensus size: 10
344835 AAAAGATTTT
*
344845 TTTTTATGTA
1 TTTTTATATA
344855 TTTTATATATA
1 TTTT-TATATA
344866 TTTTTATA-A
1 TTTTTATATA
*
344875 TTTTTATAAA
1 TTTTTATATA
** *
344885 AGTTTACA-A
1 TTTTTATATA
344894 TTTATTATATA
1 TTT-TTATATA
* *
344905 TTATTAT-GA
1 TTTTTATATA
344914 TTTTTATA
1 TTTTTATA
344922 AAAAAAATCT
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
9 18 0.35
10 22 0.42
11 12 0.23
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (10 bp):
TTTTTATATA
Found at i:345012 original size:9 final size:9
Alignment explanation
Indices: 344968--345012 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
344958 TAAAATTTAA
*
344968 TAATTTTTA
1 TAATTTTTT
344977 TAATTTTTGT
1 TAATTTTT-T
*
344987 TTATTTTTT
1 TAATTTTTT
344996 T-ATTTTTT
1 TAATTTTTT
345004 TAATTTTTT
1 TAATTTTTT
345013 GTCACATGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 8 0.25
9 17 0.53
10 7 0.22
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (9 bp):
TAATTTTTT
Found at i:350155 original size:9 final size:10
Alignment explanation
Indices: 350132--350157 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
350122 ATCTTCAATT
350132 TTTTTTATTA
1 TTTTTTATTA
350142 TTTTTTATTA
1 TTTTTTATTA
350152 TTTTTT
1 TTTTTT
350158 TCAGCTTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTATTA
Found at i:354545 original size:16 final size:17
Alignment explanation
Indices: 354514--354551 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
354504 GATTGAGATT
*
354514 TTAAAATTCTAAAAAAA
1 TTAAAATTCGAAAAAAA
354531 TTAAAATT-GAAAAAAA
1 TTAAAATTCGAAAAAAA
354547 TTAAA
1 TTAAA
354552 TCCACAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (17 bp):
TTAAAATTCGAAAAAAA
Found at i:356195 original size:26 final size:28
Alignment explanation
Indices: 356155--356217 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 28
356145 TTAAGATGAC
356155 TATATAAAAACTTTTAATAAATA-AAAAA
1 TATAT-AAAACTTTTAATAAATATAAAAA
* *
356183 TATATAAAA-TTTTACTAAATATTAAAA
1 TATATAAAACTTTTAATAAATATAAAAA
356210 TAATATAA
1 T-ATATAA
356218 TATAAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 11 0.35
27 9 0.29
28 11 0.35
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (28 bp):
TATATAAAACTTTTAATAAATATAAAAA
Found at i:357317 original size:26 final size:25
Alignment explanation
Indices: 357283--357332 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
357273 ATAATTTCCT
* *
357283 AAACCCTAAATTACAAAAATCCTTAC
1 AAACCCTAAA-CAAAAAAATCCTTAC
*
357309 AAACTCTAAACAAAAAAATCCTTA
1 AAACCCTAAACAAAAAAATCCTTA
357333 AAAAACATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.22
Consensus pattern (25 bp):
AAACCCTAAACAAAAAAATCCTTAC
Found at i:357331 original size:25 final size:27
Alignment explanation
Indices: 357297--357346 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
357287 CCTAAATTAC
*
357297 AAAAATCCTT-ACAAAC-TCTAAACAA
1 AAAAATCCTTAAAAAACATCTAAACAA
357322 AAAAATCCTTAAAAAACATCTAAAC
1 AAAAATCCTTAAAAAACATCTAAAC
357347 CCTAACACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 5 0.23
27 7 0.32
ACGTcount: A:0.58, C:0.22, G:0.00, T:0.20
Consensus pattern (27 bp):
AAAAATCCTTAAAAAACATCTAAACAA
Found at i:357686 original size:45 final size:46
Alignment explanation
Indices: 357625--357711 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 46
357615 TATTAAGGAG
357625 TTTAATACTCTTTAAGTAAATTCTCAAGTTC-AATTTATAAAAAGT
1 TTTAATACTCTTTAAGTAAATTCTCAAGTTCAAATTTATAAAAAGT
* * * *
357670 TTTATTACTCTTTAAGTAAATTGTCGAGTTCAAATTTTTAAA
1 TTTAATACTCTTTAAGTAAATTCTCAAGTTCAAATTTATAAA
357712 GAATCTGACC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 28 0.76
46 9 0.24
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (46 bp):
TTTAATACTCTTTAAGTAAATTCTCAAGTTCAAATTTATAAAAAGT
Found at i:359712 original size:59 final size:58
Alignment explanation
Indices: 359639--359932 Score: 326
Period size: 59 Copynumber: 5.1 Consensus size: 58
359629 CGGACATCCA
* * *
359639 GGTAAAATGGTAATTTTTGGAAGTGTCAGGGTAAAAAATGAGATTTTTGGAAGTTTGGG
1 GGTAAAATGGTAATTTTTGGAAGTTTCGGGGT-AAAAATGGGATTTTTGGAAGTTTGGG
* *
359698 GGTAAAACGGTAATTTTTAGG-AGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTTGGG
1 GGTAAAATGGTAATTTTT-GGAAGTTTCG-GGGTAAAAATGGGATTTTTGGAAGTTTGGG
* * * *
359757 GATAAAATGGCAATTTTAGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGGG
1 GGTAAAATGGTAATTTTTGGAAGTTTCGGGGT-AAAAATGGGATTTTTGGAAGTTTGGG
* * * * * *
359816 GGTAAAATGGTAATTCTTGGAAGTTTTGGGGTCAAAATGGGACTTTTAGAAGTTTAGG
1 GGTAAAATGGTAATTTTTGGAAGTTTCGGGGTAAAAATGGGATTTTTGGAAGTTTGGG
* * * * * *
359874 GGTAAAATTGG--ACTTTTGAAAGTTTAGGGGT-AAAATGGTAATTTTGGAAGTTTTGG
1 GGTAAAA-TGGTAATTTTTGGAAGTTTCGGGGTAAAAATGGGATTTTTGGAAGTTTGGG
359930 GGT
1 GGT
359933 CAATTTTTCA
Statistics
Matches: 203, Mismatches: 27, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
56 24 0.12
57 16 0.08
58 34 0.17
59 124 0.61
60 5 0.02
ACGTcount: A:0.30, C:0.03, G:0.32, T:0.35
Consensus pattern (58 bp):
GGTAAAATGGTAATTTTTGGAAGTTTCGGGGTAAAAATGGGATTTTTGGAAGTTTGGG
Found at i:359713 original size:29 final size:29
Alignment explanation
Indices: 359639--359932 Score: 237
Period size: 29 Copynumber: 10.1 Consensus size: 29
359629 CGGACATCCA
* **
359639 GGTAAAATGGTAATTTTTGGAAGTGTCAG
1 GGTAAAATGGTAATTTTTGGAAGTTTGGG
359668 GGTAAAAAAT-G-AGATTTTTGGAAGTTTGGG
1 GGT--AAAATGGTA-ATTTTTGGAAGTTTGGG
* *
359698 GGTAAAACGGTAATTTTTAGG-AGTTTCGAG
1 GGTAAAATGGTAATTTTT-GGAAGTTT-GGG
* *
359728 GTTAAAAATGG-GATTTTTGGAAGTTTGGG
1 GGT-AAAATGGTAATTTTTGGAAGTTTGGG
* * * *
359757 GATAAAATGGCAATTTTAGGAAGTTTTGG
1 GGTAAAATGGTAATTTTTGGAAGTTTGGG
*
359786 GGTCAAAAATGG-GATTTTTGGAAGTTTGGG
1 GGT--AAAATGGTAATTTTTGGAAGTTTGGG
* *
359816 GGTAAAATGGTAATTCTTGGAAGTTTTGG
1 GGTAAAATGGTAATTTTTGGAAGTTTGGG
* * * *
359845 GGTCAAAATGG-GACTTTTAGAAGTTTAGG
1 GGT-AAAATGGTAATTTTTGGAAGTTTGGG
* * *
359874 GGTAAAATTGG--ACTTTTGAAAGTTTAGG
1 GGTAAAA-TGGTAATTTTTGGAAGTTTGGG
*
359902 GGTAAAATGGTAA-TTTTGGAAGTTTTGG
1 GGTAAAATGGTAATTTTTGGAAGTTTGGG
359930 GGT
1 GGT
359933 CAATTTTTCA
Statistics
Matches: 219, Mismatches: 29, Indels: 35
0.77 0.10 0.12
Matches are distributed among these distances:
27 3 0.01
28 60 0.27
29 77 0.35
30 61 0.28
31 18 0.08
ACGTcount: A:0.30, C:0.03, G:0.32, T:0.35
Consensus pattern (29 bp):
GGTAAAATGGTAATTTTTGGAAGTTTGGG
Found at i:359773 original size:28 final size:27
Alignment explanation
Indices: 359639--359932 Score: 221
Period size: 28 Copynumber: 10.1 Consensus size: 27
359629 CGGACATCCA
* **
359639 GGTAAAATGGTAATTTTTGGAAGTGTCAG
1 GGTAAAATGGGAA-TTTTGGAAGT-TTGG
* *
359668 GGTAAAAAATGAGATTTTTGGAAGTTTGGG
1 GGT--AAAATGGGAATTTTGGAAGTTT-GG
* *
359698 GGTAAAACGGTAATTTTTAGG-AGTTTCGAG
1 GGTAAAATGGGAA-TTTT-GGAAGTTT-G-G
* *
359728 GTTAAAAATGGGATTTTTGGAAGTTTGG
1 GGT-AAAATGGGAATTTTGGAAGTTTGG
*
359756 GGATAAAATGGCAATTTTAGGAAGTTTTGG
1 GG-TAAAATGGGAATTTT-GGAAG-TTTGG
*
359786 GGTCAAAAATGGGATTTTTGGAAGTTTGGG
1 GGT--AAAATGGGAATTTTGGAAGTTT-GG
*
359816 GGTAAAATGGTAATTCTTGGAAGTTTTGG
1 GGTAAAATGGGAATT-TTGGAAG-TTTGG
* *
359845 GGTCAAAATGGGACTTTTAGAAGTTTAGG
1 GGT-AAAATGGGAATTTTGGAAGTTT-GG
* * *
359874 GGTAAAATTGGACTTTTGAAAGTTTAGG
1 GGTAAAATGGGAATTTTGGAAGTTT-GG
*
359902 GGTAAAATGGTAATTTTGGAAGTTTTGG
1 GGTAAAATGGGAATTTTGGAAG-TTTGG
359930 GGT
1 GGT
359933 CAATTTTTCA
Statistics
Matches: 215, Mismatches: 31, Indels: 39
0.75 0.11 0.14
Matches are distributed among these distances:
28 78 0.36
29 53 0.25
30 58 0.27
31 26 0.12
ACGTcount: A:0.30, C:0.03, G:0.32, T:0.35
Consensus pattern (27 bp):
GGTAAAATGGGAATTTTGGAAGTTTGG
Found at i:361585 original size:6 final size:6
Alignment explanation
Indices: 361569--361657 Score: 55
Period size: 6 Copynumber: 15.3 Consensus size: 6
361559 ACATTCAAAA
**
361569 TAAATTT TAAATT TAAATT TATAA-- TAAATT TAAATT T-AAGC TAAATT
1 TAAA-TT TAAATT TAAATT TA-AATT TAAATT TAAATT TAAATT TAAATT
* * * *
361616 TAAATT TATAA-- TAAACT TAATTT TAAA-A TAAATT TAAGTT TA
1 TAAATT TA-AATT TAAATT TAAATT TAAATT TAAATT TAAATT TA
361658 TTAGGCCCAG
Statistics
Matches: 64, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
4 4 0.06
5 11 0.17
6 41 0.64
7 8 0.12
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (6 bp):
TAAATT
Found at i:361596 original size:17 final size:17
Alignment explanation
Indices: 361576--361658 Score: 105
Period size: 17 Copynumber: 4.9 Consensus size: 17
361566 AAATAAATTT
361576 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
*
361593 TAAATTTAAATTTA-AGC
1 TAAATTTAAATTTATA-A
361610 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
* * *
361627 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAA
*
361644 TAAATTTAAGTTTAT
1 TAAATTTAAATTTAT
361659 TAGGCCCAGA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
16 1 0.02
17 54 0.96
18 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:361616 original size:34 final size:34
Alignment explanation
Indices: 361576--361658 Score: 121
Period size: 34 Copynumber: 2.4 Consensus size: 34
361566 AAATAAATTT
* **
361576 TAAATTTAAATTTATAATAAATTTAAATTTAAGC
1 TAAATTTAAATTTATAATAAACTTAAATTTAAAA
*
361610 TAAATTTAAATTTATAATAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAATAAACTTAAATTTAAAA
*
361644 TAAATTTAAGTTTAT
1 TAAATTTAAATTTAT
361659 TAGGCCCAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (34 bp):
TAAATTTAAATTTATAATAAACTTAAATTTAAAA
Found at i:362506 original size:204 final size:205
Alignment explanation
Indices: 362139--362754 Score: 1027
Period size: 205 Copynumber: 3.0 Consensus size: 205
362129 ATTTGCTCAC
* * * *
362139 ATCGGGCGTAAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCGGGAAGATGACTGCGTCGTTTG
1 ATCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTG
* * * * * *
362204 TTTCAATTCGTTTCTCTGTATCTCATCAGGAAAACGAATTTGGTTCACTTCTCCGTATCTTATCA
66 TTTTAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTTCGTATCTTATCA
* * *
362269 GGAAGCTAACCTTTTACGGCTTCGACTTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAGG
131 GGAAGCTAACCTTTTATGACTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAGG
362334 ATTTGTTCGT
196 ATTTGTTCGT
* *
362344 ATCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATTGTTT-
1 ATCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTG
362408 TTTTAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTTCGTATCTTATCA
66 TTTTAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTTCGTATCTTATCA
* *
362473 GGAAGCTAACCTTTTATTACTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCAAGG
131 GGAAGCTAACCTTTTATGACTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAGG
362538 ATTTGTTCGT
196 ATTTGTTCGT
* *
362548 ATCGAGCATGAGTTTGATTTGATCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTG
1 ATCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTG
* * *
362613 TTTTAATCTGCTTCTCTGTATCTTATCAGGAAGACGAATTTGGTCTACTTCTTCGTATCTTATCA
66 TTTTAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTTCGTATCTTATCA
362678 GGAAGCTAACCTTTTATGACTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAGG
131 GGAAGCTAACCTTTTATGACTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAGG
362743 ATTTGTTCGT
196 ATTTGTTCGT
362753 AT
1 AT
362755 NNNNNNNNNN
Statistics
Matches: 384, Mismatches: 26, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
204 189 0.49
205 195 0.51
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (205 bp):
ATCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTG
TTTTAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTTCGTATCTTATCA
GGAAGCTAACCTTTTATGACTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAGG
ATTTGTTCGT
Found at i:362718 original size:205 final size:205
Alignment explanation
Indices: 362149--362754 Score: 1011
Period size: 204 Copynumber: 3.0 Consensus size: 205
362139 ATCGGGCGTA
* * *
362149 AGTTTGATTTGGTCTTCTTCTCAGTATCTCATCGGGAAGATGACTGCGTCGTTTGTTTCAAT-TC
1 AGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTTAATCT-
* * *
362213 GTTTCTCTGTATCTCATCAGGAAAACGAATTTGGT-TCACTTCTCCGTATCTTATCAGGAAGCTA
65 GCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCT-ACTTCTTCGTATCTTATCAGGAAGCTA
* * *
362277 ACCTTTTACGGCTTCGACTTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAGGATTTGTTC
129 ACCTTTTATGACTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAGGATTTGTTC
*
362342 GTATCGAGCGTG
194 GTATCGAGCATG
* * *
362354 AGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATTGTTT-TTTTAATCCG
1 AGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTTAATCTG
*
362418 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTTCGTATCTTATCAGGAAGCTAAC
66 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCTACTTCTTCGTATCTTATCAGGAAGCTAAC
* *
362483 CTTTTATTACTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCAAGGATTTGTTCGT
131 CTTTTATGACTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAGGATTTGTTCGT
362548 ATCGAGCATG
196 ATCGAGCATG
*
362558 AGTTTGATTTGATCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTTAATCTG
1 AGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTTAATCTG
*
362623 CTTCTCTGTATCTTATCAGGAAGACGAATTTGGTCTACTTCTTCGTATCTTATCAGGAAGCTAAC
66 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCTACTTCTTCGTATCTTATCAGGAAGCTAAC
362688 CTTTTATGACTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAGGATTTGTTCGT
131 CTTTTATGACTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAGGATTTGTTCGT
362753 AT
196 AT
362755 NNNNNNNNNN
Statistics
Matches: 374, Mismatches: 24, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
204 187 0.50
205 187 0.50
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (205 bp):
AGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTTAATCTG
CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCTACTTCTTCGTATCTTATCAGGAAGCTAAC
CTTTTATGACTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAGGATTTGTTCGT
ATCGAGCATG
Found at i:367486 original size:29 final size:29
Alignment explanation
Indices: 367440--367507 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
367430 TAAGATTGGT
* **
367440 TTTAAATTGATCCAAATTTATTTTTA-CA
1 TTTAAATTTATCCAAATTTAAATTTATCA
* *
367468 TTTAAATTTATCTTAAATTTAAATTTATCT
1 TTTAAATTTATC-CAAATTTAAATTTATCA
367498 TTTAAATTTA
1 TTTAAATTTA
367508 AATTGATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 11 0.33
29 11 0.33
30 11 0.33
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.54
Consensus pattern (29 bp):
TTTAAATTTATCCAAATTTAAATTTATCA
Found at i:367489 original size:17 final size:17
Alignment explanation
Indices: 367453--367511 Score: 73
Period size: 17 Copynumber: 3.3 Consensus size: 17
367443 AAATTGATCC
* *
367453 AAATTTATTTTTACATTT
1 AAATTTA-TCTTAAATTT
367471 AAATTTATCTTAAATTT
1 AAATTTATCTTAAATTT
367488 AAATTTATCTTTTAAATTT
1 AAATTTATC--TTAAATTT
367507 AAATT
1 AAATT
367512 GATTTAGAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
17 17 0.46
18 7 0.19
19 13 0.35
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTTATCTTAAATTT
Found at i:368247 original size:21 final size:21
Alignment explanation
Indices: 368220--368281 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
368210 ATTATTATGG
368220 TAATAATAATAATAATAATAT
1 TAATAATAATAATAATAATAT
* *
368241 TACTAAT-ATCATTAATAATAT
1 TAATAATAAT-AATAATAATAT
* **
368262 TAATAACAGCAATAATAATA
1 TAATAATAATAATAATAATA
368282 ATAAACATTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
20 2 0.06
21 30 0.94
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.35
Consensus pattern (21 bp):
TAATAATAATAATAATAATAT
Found at i:368265 original size:18 final size:18
Alignment explanation
Indices: 368220--368301 Score: 74
Period size: 18 Copynumber: 4.4 Consensus size: 18
368210 ATTATTATGG
* *
368220 TAATAATAATAATAATAA
1 TAATAATAATAACATTAA
* * *
368238 TATTACTAATATCATTAA
1 TAATAATAATAACATTAA
* **
368256 TAATATTAATAACAGCAA
1 TAATAATAATAACATTAA
368274 TAATAATAATAAACATTAA
1 TAATAATAAT-AACATTAA
368293 TAATTAATA
1 TAA-TAATA
368302 TTTTTCAAAA
Statistics
Matches: 49, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
18 35 0.71
19 9 0.18
20 5 0.10
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.35
Consensus pattern (18 bp):
TAATAATAATAACATTAA
Found at i:368296 original size:3 final size:3
Alignment explanation
Indices: 368220--368285 Score: 53
Period size: 3 Copynumber: 22.0 Consensus size: 3
368210 ATTATTATGG
* * * *
368220 TAA TAA TAA TAA TAA TAA TAT TAC TAA T-A TCAT TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* * *
368265 TAA CAG CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
368286 ACATTAATAA
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
2 2 0.04
3 47 0.94
4 1 0.02
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:369266 original size:30 final size:29
Alignment explanation
Indices: 369224--369512 Score: 244
Period size: 30 Copynumber: 9.8 Consensus size: 29
369214 TAAAGGCCCT
*
369224 AAACTATCCAAAAATTATATTTTTGACCCCA
1 AAACT-TCCAAAAATTACATTTTT-ACCCCA
* ** *
369255 AAACTTTCAAAAATTTTA-TTTTACCCCT
1 AAACTTCCAAAAATTACATTTTTACCCCA
* * *
369283 AAAC-TCTCAAAAATTCCATTTTTAACCTCG
1 AAACTTC-CAAAAATTACATTTTT-ACCCCA
*
369313 AAACTTCCAAAAAATACATTTTTACCCTC-
1 AAACTTCCAAAAATTACATTTTTACCC-CA
* * ***
369342 GAACTTCCAAAAATTCCATTTTTGACCTTG
1 AAACTTCCAAAAATTACATTTTT-ACCCCA
* *
369372 AAACTTCCAAAAATTACATTTCTACCCCC
1 AAACTTCCAAAAATTACATTTTTACCCCA
* * *
369401 AAACTTCCCAAAATTCCATTTTTAACCTCA
1 AAACTTCCAAAAATTACATTTTT-ACCCCA
* *
369431 AAACTTCCAAAAATTACGTTTTTACTCTC-
1 AAACTTCCAAAAATTACATTTTTAC-CCCA
* * *
369460 AAACTCCCAAAAATTCCATTTTTGACCCTA
1 AAACTTCCAAAAATTACATTTTT-ACCCCA
369490 AAACTTCCAAAAATTACCATTTT
1 AAACTTCCAAAAATTA-CATTTT
369513 GCCCTCGGAT
Statistics
Matches: 209, Mismatches: 37, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
27 1 0.00
28 18 0.09
29 77 0.37
30 100 0.48
31 13 0.06
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTACCCCA
Found at i:369292 original size:28 final size:30
Alignment explanation
Indices: 369220--369297 Score: 97
Period size: 28 Copynumber: 2.6 Consensus size: 30
369210 ACCCTAAAGG
369220 CCCTAAACTATCCAAAAATTATATTTTTGAC
1 CCCTAAACTAT-CAAAAATTATATTTTTGAC
* * *
369251 CCCAAAACTTTCAAAAATTTTA-TTTT-AC
1 CCCTAAACTATCAAAAATTATATTTTTGAC
*
369279 CCCTAAACTCTCAAAAATT
1 CCCTAAACTATCAAAAATT
369298 CCATTTTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 19 0.45
29 4 0.10
30 10 0.24
31 9 0.21
ACGTcount: A:0.40, C:0.24, G:0.01, T:0.35
Consensus pattern (30 bp):
CCCTAAACTATCAAAAATTATATTTTTGAC
Found at i:369437 original size:118 final size:118
Alignment explanation
Indices: 369225--369603 Score: 403
Period size: 118 Copynumber: 3.2 Consensus size: 118
369215 AAAGGCCCTA
** * * ** *
369225 AACTATCCAAAAATTATATTTTTGACCCCAAAACTTTCAAAAATTTTATTTTACCCCTAAAC-TC
1 AACTATCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACATTTTACCCCCAAACTTC
* * *
369289 TCAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAAATACATTTTTACCCTCG
66 -CCAAAATTCCATTTTTAACCTCAAAACTTCCAAAAATTACATTTTTACCCTCG
* *
369343 AACT-TCCAAAAATTCCATTTTTGACCTTGAAACTTCCAAAAATTACATTTCTACCCCCAAACTT
1 AACTATCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACATTT-TACCCCCAAACTT
* * *
369407 CCCAAAATTCCATTTTTAACCTCAAAACTTCCAAAAATTACGTTTTTACTCTCA
65 CCCAAAATTCCATTTTTAACCTCAAAACTTCCAAAAATTACATTTTTACCCTCG
* * * **
369461 AACT-CCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACCATTTTGCCCTCGGA-TG
1 AACTATCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTA-CATTTTACCCCCAAACT-
** ** *
369524 T-CCAAAATTTCCATTTTTTAACC-CTAAAACTTTTAAAAATTACCCTTTTACCCCCG
64 TCCCAAAA-TTCCA-TTTTTAACCTC-AAAACTTCCAAAAATTACATTTTTACCCTCG
* *
369580 AA-TGTCCAAAAATTTCATTTTTGA
1 AACTATCCAAAAATTCCATTTTTGA
369604 TCCCGGTTTT
Statistics
Matches: 222, Mismatches: 31, Indels: 15
0.83 0.12 0.06
Matches are distributed among these distances:
117 45 0.20
118 117 0.53
119 60 0.27
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.35
Consensus pattern (118 bp):
AACTATCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACATTTTACCCCCAAACTTC
CCAAAATTCCATTTTTAACCTCAAAACTTCCAAAAATTACATTTTTACCCTCG
Found at i:369529 original size:59 final size:59
Alignment explanation
Indices: 369225--369660 Score: 349
Period size: 59 Copynumber: 7.4 Consensus size: 59
369215 AAAGGCCCTA
** * * ** *
369225 AACTATCCAAAAATTATATTTTTGACCCCAAAACTTTCAAAAATT-TTATTTTACCC-CTA
1 AACT-TCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACCATTTTACCCTC-G
* * *
369284 AAC-TCTCAAAAATTCCATTTTT-AACCTCGAAACTTCCAAAAAATA-CATTTTTACCCTCG
1 AACTTC-CAAAAATTCCATTTTTGACCCT-AAAACTTCCAAAAATTACCA-TTTTACCCTCG
* * * *
369343 AACTTCCAAAAATTCCATTTTTGACCTTGAAACTTCCAAAAATTA-CATTTCTACCCCCA
1 AACTTCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACCATTT-TACCCTCG
* * ** * *
369402 AACTTCCCAAAATTCCATTTTT-AACCTCAAAACTTCCAAAAATTACGTTTTTACTCTCA
1 AACTTCCAAAAATTCCATTTTTGACCCT-AAAACTTCCAAAAATTACCATTTTACCCTCG
* *
369461 AACTCCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACCATTTTGCCCTCG
1 AACTTCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACCATTTTACCCTCG
* * * ** * *
369520 GA-TGTCCAAAATTTCCATTTTTTAACCCTAAAACTTTTAAAAATTACCCTTTTACCCCCG
1 AACT-TCCAAAAATTCCA-TTTTTGACCCTAAAACTTCCAAAAATTACCATTTTACCCTCG
* ****
369580 AA-TGTCCAAAAATTTCATTTTTGATCCC--GGTTTTCCTAAAAATTACCATTTTACCC-CTG
1 AACT-TCCAAAAATTCCATTTTTGA-CCCTAAAACTTCC-AAAAATTACCATTTTACCCTC-G
369639 AA-TGTCCAAAAATTCCATTTTT
1 AACT-TCCAAAAATTCCATTTTT
369661 TATCCTGATT
Statistics
Matches: 310, Mismatches: 51, Indels: 32
0.79 0.13 0.08
Matches are distributed among these distances:
57 5 0.02
58 38 0.12
59 201 0.65
60 66 0.21
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (59 bp):
AACTTCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACCATTTTACCCTCG
Found at i:369565 original size:60 final size:60
Alignment explanation
Indices: 369290--369721 Score: 288
Period size: 59 Copynumber: 7.3 Consensus size: 60
369280 CCTAAACTCT
* * * *
369290 CAAAAATTCCA-TTTTTAA-CCTCGAAACTTCCAAAAAATA-CATTTTTACCCTCGAACT-TC
1 CAAAATTTCCATTTTTTAACCCT-AAAACTTCCAAAAATTACCA-TTTTACCCCCGAA-TGTC
* * * * *
369349 CAAAAATTCCA-TTTTTGACCTTGAAACTTCCAAAAATTA-CATTTCTACCCCCAAACT-TCC
1 CAAAATTTCCATTTTTTAACCCTAAAACTTCCAAAAATTACCATTT-TACCCCCGAA-TGT-C
** * * * *
369409 CAAAA-TTCCA-TTTTTAA-CCTCAAAACTTCCAAAAATTACGTTTTTACTCTCAAACT-CC
1 CAAAATTTCCATTTTTTAACCCT-AAAACTTCCAAAAATTACCATTTTACCCCCGAA-TGTC
* * * * *
369467 CAAAAATTCCA-TTTTTGACCCTAAAACTTCCAAAAATTACCATTTTGCCCTCGGATGTC
1 CAAAATTTCCATTTTTTAACCCTAAAACTTCCAAAAATTACCATTTTACCCCCGAATGTC
** *
369526 CAAAATTTCCATTTTTTAACCCTAAAACTTTTAAAAATTACCCTTTTACCCCCGAATGTC
1 CAAAATTTCCATTTTTTAACCCTAAAACTTCCAAAAATTACCATTTTACCCCCGAATGTC
* * **** *
369586 CAAAAATTT-CATTTTTGATCCC--GGTTTTCCTAAAAATTACCATTTTACCCCTGAATGTC
1 C-AAAATTTCCATTTTTTAACCCTAAAACTTCC-AAAAATTACCATTTTACCCCCGAATGTC
* * * ** * *
369645 CAAAAATTCCATTTTTT-ATCCT-GATTTTCCGAAAAATTACCATCTTACCCCCCAATGTC
1 CAAAATTTCCATTTTTTAACCCTAAAACTTCC-AAAAATTACCATTTTACCCCCGAATGTC
*
369704 CAATAA-TTCTATTTTTTA
1 CAA-AATTTCCATTTTTTA
369722 TCCCGATTTT
Statistics
Matches: 309, Mismatches: 49, Indels: 29
0.80 0.13 0.07
Matches are distributed among these distances:
58 22 0.07
59 211 0.68
60 69 0.22
61 7 0.02
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (60 bp):
CAAAATTTCCATTTTTTAACCCTAAAACTTCCAAAAATTACCATTTTACCCCCGAATGTC
Found at i:369590 original size:29 final size:29
Alignment explanation
Indices: 369558--369711 Score: 100
Period size: 29 Copynumber: 5.2 Consensus size: 29
369548 TAAAACTTTT
*
369558 AAAAATTACCCTTTTACCCCCGAATGTCC
1 AAAAATTACCATTTTACCCCCGAATGTCC
* * ** *
369587 AAAAATT-TCATTTTTGA-TCCCGGTTTTCC
1 AAAAATTACCA-TTTT-ACCCCCGAATGTCC
*
369616 TAAAAATTACCATTTTACCCCTGAATGTCC
1 -AAAAATTACCATTTTACCCCCGAATGTCC
* * * *
369646 AAAAATT-CCATTTTTTA-TCCTGATTTTCC
1 AAAAATTACCA--TTTTACCCCCGAATGTCC
* *
369675 GAAAAATTACCATCTTACCCCCCAATGTCC
1 -AAAAATTACCATTTTACCCCCGAATGTCC
*
369705 AATAATT
1 AAAAATT
369712 CTATTTTTTA
Statistics
Matches: 93, Mismatches: 22, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
28 4 0.04
29 46 0.49
30 38 0.41
31 5 0.05
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCCCGAATGTCC
Done.