Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006529.1 Hibiscus syriacus cultivar Beakdansim tig00015910_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 646883
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 3
Found at i:337655 original size:36 final size:36
Alignment explanation
Indices: 337608--337806 Score: 213
Period size: 36 Copynumber: 5.3 Consensus size: 36
337598 GACTATATGA
*
337608 AAGAAGAAGAAGAAGACGACTGTATGAAAGAAGAAG
1 AAGAAGAAGAAGAAGACGACTATATGAAAGAAGAAG
337644 AAGAAGAAGAAGAAGACGACTATATGAAAGAAGAAG
1 AAGAAGAAGAAGAAGACGACTATATGAAAGAAGAAG
* * *
337680 AAGAAGAAGAAGAATACTA-TGA-AAGAAGAAGACTATGAAAG
1 AAGAAGAAGAAGAAGACGACT-ATATG-A-AAGA--A-G-AAG
*
337721 AAGAAGAAAGAAGAAGAAGAAGACTATATGAAAGAAGAAG
1 -A--AG-AAGAAGAAGAAGACGACTATATGAAAGAAGAAG
* * *
337761 AAGAAGAAAAAGAAAAAGACTATATGAAAGAAGAAG
1 AAGAAGAAGAAGAAGACGACTATATGAAAGAAGAAG
337797 AAGAAGAAGA
1 AAGAAGAAGA
337807 CTATATGAAA
Statistics
Matches: 139, Mismatches: 11, Indels: 26
0.79 0.06 0.15
Matches are distributed among these distances:
35 3 0.02
36 94 0.68
37 6 0.04
39 2 0.01
40 4 0.03
41 4 0.03
42 2 0.01
44 6 0.04
45 15 0.11
46 3 0.02
ACGTcount: A:0.61, C:0.04, G:0.27, T:0.09
Consensus pattern (36 bp):
AAGAAGAAGAAGAAGACGACTATATGAAAGAAGAAG
Found at i:337665 original size:63 final size:63
Alignment explanation
Indices: 337495--337837 Score: 385
Period size: 63 Copynumber: 5.8 Consensus size: 63
337485 AGAGGAAGAG
337495 GAAGAAGAAGAAGAAGAC--TATGAAAGAAGAAG-A-AAGAAGAAGAAGAAGACTATATGAAA
1 GAAGAAGAAGAAGAAGACTATATGAAAGAAGAAGAAGAAGAAGAAGAAGAAGACTATATGAAA
337554 GAAGAAGAAAGAAGAAGACTATAT----G-A-AAGAAGAAG-A-AAGAAGAAGACTATATGAAA
1 GAAGAAG-AAGAAGAAGACTATATGAAAGAAGAAGAAGAAGAAGAAGAAGAAGACTATATGAAA
* * *
337610 GAAGAAGAAGAAGACGACTGTATGAAAGAAGAAGAAGAAGAAGAAGAAGACGACTATATGAAAGA
1 GAAGAAGAAGAAGAAGACTATATGAAAGAAGAAGAAGAAGAAGAAGAAGAAGACTATATG--A-A
337675 A
63 A
* ** *
337676 GAAGAAGAAGAAGAAGAATACTATGAAAGAAGAAGACTATG-A-AAGAAGAAGA--A-A-G-AA
1 GAAGAAGAAGAAGAAGACTA-TATGAAAGAAGAAGAAGAAGAAGAAGAAGAAGACTATATGAAA
* *
337733 GAAGAAGAAGA------CTATATGAAAGAAGAAGAAGAAGAAAAAGAAAAAGACTATATGAAA
1 GAAGAAGAAGAAGAAGACTATATGAAAGAAGAAGAAGAAGAAGAAGAAGAAGACTATATGAAA
337790 GAAGAAGAAGAAGAAGACTATATGAAAGAAGAAGAAGAAGAAGAAGAA
1 GAAGAAGAAGAAGAAGACTATATGAAAGAAGAAGAAGAAGAAGAAGAA
337838 ATAACTAAAG
Statistics
Matches: 238, Mismatches: 16, Indels: 56
0.77 0.05 0.18
Matches are distributed among these distances:
50 17 0.07
51 3 0.01
52 9 0.04
54 1 0.00
55 15 0.06
56 31 0.13
57 29 0.12
58 4 0.02
59 8 0.03
60 12 0.05
61 10 0.04
62 5 0.02
63 47 0.20
65 10 0.04
66 20 0.08
67 17 0.07
ACGTcount: A:0.61, C:0.04, G:0.27, T:0.09
Consensus pattern (63 bp):
GAAGAAGAAGAAGAAGACTATATGAAAGAAGAAGAAGAAGAAGAAGAAGAAGACTATATGAAA
Found at i:337759 original size:117 final size:115
Alignment explanation
Indices: 337474--337834 Score: 444
Period size: 117 Copynumber: 3.2 Consensus size: 115
337464 ATATGACGTT
* * *
337474 GAAGAAG-AAGAAGAGGAAGA-GGAAGAAGAAGAAGAAGAC-TATGAAAGAAGAAG-A-AAGAAG
1 GAAGAAGAAAGAAGAAGAATATGAAAGAAGAAGAAGAAGACTTATGAAAGAAGAAGAAGAAGAAG
*
337534 AAGAAGAAGACTATATGAAAGAAGAAG-A-AAGAAGAAGACTATATGAAA
66 AAGAAGAAGACTATATGAAAGAAGAAGAAGAAGAAGAAGAATATATGAAA
337582 GAAGAAGAAAGAAGAAGACTATATGAAAGAAGAAGAAGAAGACGACTGTATGAAAGAAGAAGAAG
1 GAAGAAGAAAGAAGAAGA--ATATGAAAGAAGAAGAAG-A-A-GACT-TATGAAAGAAGAAGAAG
*
337647 AAGAAGAAGAAGACGACTATATGAAAGAAGAAGAAGAAGAAGAAGAATACTATGAAA
60 AAGAAGAAGAAGAAGACTATATGAAAGAAGAAGAAGAAGAAGAAGAATA-TATGAAA
*
337704 GAAGAAGACTATGAAAGAAG-A-A-GAAAGAAGAAGAAGAAGACTATATGAAAGAAGAAGAAGAA
1 GAAGAAGA--AAG-AAGAAGAATATGAAAGAAGAAGAAGAAGACT-TATGAAAGAAGAAGAAGAA
* * *
337766 GAAAAAGAAAAAGACTATATG--A-AAGAAGAAGAAGAAGAAGACTATATGAAA
62 GAAGAAGAAGAAGACTATATGAAAGAAGAAGAAGAAGAAGAAGAATATATGAAA
337817 GAAGAAG-AAGAAGAAGAA
1 GAAGAAGAAAGAAGAAGAA
337835 GAAATAACTA
Statistics
Matches: 223, Mismatches: 12, Indels: 34
0.83 0.04 0.13
Matches are distributed among these distances:
108 7 0.03
109 15 0.07
110 3 0.01
111 2 0.01
112 13 0.06
113 15 0.07
114 22 0.10
115 4 0.02
117 55 0.25
118 2 0.01
119 33 0.15
120 15 0.07
121 13 0.06
122 16 0.07
124 2 0.01
125 6 0.03
ACGTcount: A:0.60, C:0.04, G:0.27, T:0.09
Consensus pattern (115 bp):
GAAGAAGAAAGAAGAAGAATATGAAAGAAGAAGAAGAAGACTTATGAAAGAAGAAGAAGAAGAAG
AAGAAGAAGACTATATGAAAGAAGAAGAAGAAGAAGAAGAATATATGAAA
Found at i:337759 original size:144 final size:139
Alignment explanation
Indices: 337560--337837 Score: 382
Period size: 144 Copynumber: 2.0 Consensus size: 139
337550 GAAAGAAGAA
*
337560 GAAAGAAGAAGACTATATGAAAGAAGAAGAAAGAAGAAGACTATATGAAAGAAGAAGAAGAAGAC
1 GAAAGAAGAAGACTATAAGAAAGAAGAAGAAAGAAGAAGACTATATGAAAGAAGAAGAAGAAGA-
* ** * *
337625 GACTGTATGAAAGA-AGAAG-AAGAAGAAGAAGAAGACGACTATATGAAAGAAGAAGAAGAAGAA
65 AAAAG-A-AAAAGACAGAAGAAAGAAGAAGAAGAAGAAGACTATATGAAAGAAGAAGAAGAAGAA
337688 GAAGAATACTAT
128 GAAGAATACTAT
337700 GAAAGAAGAAGACTATGAA-AGAAGAAGAAAGAAGAAGAAGAAGACTATATGAAAGAAGAAGAAG
1 GAAAGAAGAAGACTAT-AAGA-AAGAAG-AAG-A-AAGAAGAAGACTATATGAAAGAAGAAGAAG
* *
337764 AAGAAAAAGAAAAAGACTATATGAAAGAAGAAGAAGAAGAAGACTATATGAAAGAAGAAGAAGAA
61 AAGAAAAAGAAAAAGAC-AGAAGAAAGAAGAAGAAGAAGAAGACTATATGAAAGAAGAAGAAGAA
337829 GAAGAAGAA
125 GAAGAAGAA
337838 ATAACTAAAG
Statistics
Matches: 122, Mismatches: 8, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
140 17 0.14
141 12 0.10
142 4 0.03
143 6 0.05
144 83 0.68
ACGTcount: A:0.60, C:0.04, G:0.26, T:0.09
Consensus pattern (139 bp):
GAAAGAAGAAGACTATAAGAAAGAAGAAGAAAGAAGAAGACTATATGAAAGAAGAAGAAGAAGAA
AAAGAAAAAGACAGAAGAAAGAAGAAGAAGAAGAAGACTATATGAAAGAAGAAGAAGAAGAAGAA
GAATACTAT
Found at i:337762 original size:24 final size:24
Alignment explanation
Indices: 337526--337650 Score: 142
Period size: 28 Copynumber: 4.8 Consensus size: 24
337516 GAAAGAAGAA
337526 GAAAGAAGAAGAAGAAGACTATAT
1 GAAAGAAGAAGAAGAAGACTATAT
337550 GAAAGAAGAAGAAAGAAGAAGACTATAT
1 G--A-AAGAAG-AAGAAGAAGACTATAT
337578 GAAAGAAGAAGAAAGAAGAAGACTATAT
1 G--A-AAGAAG-AAGAAGAAGACTATAT
*
337606 GAAAGAAGAAGAAGAAGACGACTGTAT
1 GAAAGAAGAAGAAG-A-A-GACTATAT
337633 GAAAGAAGAAGAAGAAGA
1 GAAAGAAGAAGAAGAAGA
337651 AGAAGAAGAC
Statistics
Matches: 93, Mismatches: 1, Indels: 14
0.86 0.01 0.13
Matches are distributed among these distances:
24 9 0.10
25 8 0.09
26 4 0.04
27 27 0.29
28 45 0.48
ACGTcount: A:0.59, C:0.04, G:0.27, T:0.10
Consensus pattern (24 bp):
GAAAGAAGAAGAAGAAGACTATAT
Found at i:339085 original size:66 final size:67
Alignment explanation
Indices: 339000--339131 Score: 212
Period size: 66 Copynumber: 2.0 Consensus size: 67
338990 AATATTCAAG
* *
339000 CACCGGTCAAAGGGATTTCAATTATTTTCTAACGTGGTAGTCAATCCATCCACGTAAGCAGTTAA
1 CACCGGTCAAAGGGATTTCAATTATTTTCTAACATGGCAGTCAATCCATCCACGTAAGCAGTTAA
339065 CA
66 CA
* * *
339067 CACCGGTCAAA-GGATTTCAATTATTTTCTAACATTGCAGTCAATTCATCCATGTAAGCAGTTAA
1 CACCGGTCAAAGGGATTTCAATTATTTTCTAACATGGCAGTCAATCCATCCACGTAAGCAGTTAA
339131 C
66 C
339132 GTTTGACTGA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
66 49 0.82
67 11 0.18
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (67 bp):
CACCGGTCAAAGGGATTTCAATTATTTTCTAACATGGCAGTCAATCCATCCACGTAAGCAGTTAA
CA
Found at i:345663 original size:23 final size:23
Alignment explanation
Indices: 345637--345680 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
345627 TAAAAAGAGT
345637 GTTAAATGAATATATTGATGATC
1 GTTAAATGAATATATTGATGATC
*
345660 GTTAAATGAATATATTTATGA
1 GTTAAATGAATATATTGATGA
345681 AAGTTAAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.02, G:0.16, T:0.41
Consensus pattern (23 bp):
GTTAAATGAATATATTGATGATC
Found at i:345686 original size:23 final size:23
Alignment explanation
Indices: 345637--345688 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
345627 TAAAAAGAGT
**
345637 GTTAAATGAATATATTGATGATC
1 GTTAAATGAATATATTGATGAAA
*
345660 GTTAAATGAATATATTTATGAAA
1 GTTAAATGAATATATTGATGAAA
345683 GTTAAA
1 GTTAAA
345689 CGAACGTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.44, C:0.02, G:0.15, T:0.38
Consensus pattern (23 bp):
GTTAAATGAATATATTGATGAAA
Found at i:346411 original size:56 final size:56
Alignment explanation
Indices: 346350--346461 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
346340 AAACTTACGT
346350 AATAAAATTAATATTTTCAATACAAATTTATTTAATTGTATGTTAAACTACCATAC
1 AATAAAATTAATATTTTCAATACAAATTTATTTAATTGTATGTTAAACTACCATAC
346406 AATAAAATTAATATTTTCAATACAAATTTATTTAATTGTATGTTAAACTACCATAC
1 AATAAAATTAATATTTTCAATACAAATTTATTTAATTGTATGTTAAACTACCATAC
346462 GATAGAACTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.41
Consensus pattern (56 bp):
AATAAAATTAATATTTTCAATACAAATTTATTTAATTGTATGTTAAACTACCATAC
Found at i:363582 original size:15 final size:15
Alignment explanation
Indices: 363562--363633 Score: 110
Period size: 15 Copynumber: 4.9 Consensus size: 15
363552 TTCCAGAAAA
363562 TGAATTACTGGAATT
1 TGAATTACTGGAATT
*
363577 TGAATTACTGAAATT
1 TGAATTACTGGAATT
**
363592 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
363607 TGAATTACTGGAATT
1 TGAATTACTGGAATT
363622 TGAATT-CTGGAA
1 TGAATTACTGGAA
363634 AATGAATTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
14 6 0.12
15 45 0.88
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.36
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:363598 original size:30 final size:30
Alignment explanation
Indices: 363562--363642 Score: 128
Period size: 30 Copynumber: 2.7 Consensus size: 30
363552 TTCCAGAAAA
**
363562 TGAATTACTGGAATTTGAATTACTGAAATT
1 TGAATTACTGGAAAATGAATTACTGAAATT
*
363592 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGAAATT
363622 TGAATT-CTGGAAAATGAATTA
1 TGAATTACTGGAAAATGAATTA
363643 TATTTCTGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 15 0.31
30 33 0.69
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.36
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGAAATT
Found at i:363649 original size:20 final size:20
Alignment explanation
Indices: 363626--363695 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
363616 GGAATTTGAA
*
363626 TTCTGGAAAATGAATTATAT
1 TTCTGGAAAATGAATTACAT
*
363646 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
363666 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
363686 TTCTGGAAAA
1 TTCTGGAAAA
363696 CATCTGGAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:363903 original size:28 final size:28
Alignment explanation
Indices: 363861--364014 Score: 101
Period size: 29 Copynumber: 5.5 Consensus size: 28
363851 CTTTACTAAA
363861 ATATTATTGAAATATATAAATAA-TATTAT
1 ATATTATT-AAATATA-AAATAATTATTAT
*
363890 -TCATTATTAAATATAAAAAAATTATTAT
1 AT-ATTATTAAATATAAAATAATTATTAT
*
363918 ATATTATTAAA-ATAAAAATATAATATCT-T
1 ATATTATTAAATAT-AAAATA-ATTAT-TAT
* *
363947 ATATTATTATAATAT-AATTGATTATTTTAT
1 ATATTATTA-AATATAAAATAATTA--TTAT
* * *
363977 ATAATATTAAAAATATAAT-ATTA-TAT
1 ATATTATTAAATATAAAATAATTATTAT
364003 -TATTA-TAAATAT
1 ATATTATTAAATAT
364015 TAATAAATAT
Statistics
Matches: 101, Mismatches: 12, Indels: 29
0.71 0.08 0.20
Matches are distributed among these distances:
24 6 0.06
25 4 0.04
26 3 0.03
27 7 0.07
28 31 0.31
29 33 0.33
30 15 0.15
31 2 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (28 bp):
ATATTATTAAATATAAAATAATTATTAT
Found at i:363913 original size:25 final size:27
Alignment explanation
Indices: 363862--364109 Score: 85
Period size: 28 Copynumber: 9.0 Consensus size: 27
363852 TTTACTAAAA
363862 TATTATTGAAATATATAAATAATATTAT
1 TATTATT-AAATATATAAATAATATTAT
*
363890 TCATTATTAAATATA-AAAAAATTATTAT
1 T-ATTATTAAATATATAAATAA-TATTAT
*
363918 ATATTATTAAA-ATAAAAATATAATATCT-T
1 -TATTATTAAATAT-ATAA-ATAATAT-TAT
** * *
363947 ATATTATTATAATATAATTGATTATTTTAT
1 -TATTATTA-AATAT-ATAAATAATATTAT
* * *
363977 ATAATATTAAAAATAT-AATATTA-TAT
1 -TATTATTAAATATATAAATAATATTAT
364003 TATTA-TAAATAT-T-AATAA-A-TA-
1 TATTATTAAATATATAAATAATATTAT
* * *
364024 TATT-TTAAATATTTTAATAATTAATAT
1 TATTATTAAATATATAAATAA-TATTAT
* *
364051 T-TTGATGAAAATGATATTAAA-ATATTTTAT
1 TATT-AT-TAAAT-ATA-TAAATA-ATATTAT
*
364081 TATTATTAAAT-TCATAAAATAAAATTAT
1 TATTATTAAATAT-AT-AAATAATATTAT
364109 T
1 T
364110 TTGAGTATTT
Statistics
Matches: 169, Mismatches: 24, Indels: 54
0.68 0.10 0.22
Matches are distributed among these distances:
21 11 0.07
22 4 0.02
23 10 0.06
24 6 0.04
25 5 0.03
26 7 0.04
27 13 0.08
28 37 0.22
29 36 0.21
30 30 0.18
31 10 0.06
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (27 bp):
TATTATTAAATATATAAATAATATTAT
Found at i:363941 original size:57 final size:57
Alignment explanation
Indices: 363861--364007 Score: 139
Period size: 54 Copynumber: 2.6 Consensus size: 57
363851 CTTTACTAAA
* *
363861 ATATTATTGAAATATATAA-ATAATATTATTCATTATTAAATATAAAAAAATT-ATTAT
1 ATATTATTAAAATA-AAAATATAATATTATT-ATTATTAAATATAAAAAAATTGATTAT
* * * *
363918 ATATTATTAAAATAAAAATATAATA-TCTTA-TATT-ATTATAATATAATTGATTAT
1 ATATTATTAAAATAAAAATATAATATTATTATTATTAAATATAAAAAAATTGATTAT
*
363972 -T-TTATATAATATTAAAAATATAATATTA-TATTATTA
1 ATATTAT-TAA-AATAAAAATATAATATTATTATTATTA
364008 TAAATATTAA
Statistics
Matches: 75, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
52 4 0.05
53 15 0.20
54 25 0.33
55 6 0.08
56 6 0.08
57 19 0.25
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (57 bp):
ATATTATTAAAATAAAAATATAATATTATTATTATTAAATATAAAAAAATTGATTAT
Found at i:363949 original size:29 final size:27
Alignment explanation
Indices: 363861--363960 Score: 87
Period size: 28 Copynumber: 3.5 Consensus size: 27
363851 CTTTACTAAA
* *
363861 ATATTATTGAAATATATAAATAATATTAT
1 ATATTATT-AAA-ATAAAAAAAATATTAT
*
363890 -TCATTATTAAATATAAAAAAATTATTAT
1 AT-ATTATTAAA-ATAAAAAAAATATTAT
363918 ATATTATTAAAATAAAAATATAATATCT-T
1 ATATTATTAAAATAAAAA-A-AATAT-TAT
*
363947 ATATTATTATAATA
1 ATATTATTAAAATA
363961 TAATTGATTA
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
27 7 0.11
28 28 0.46
29 25 0.41
30 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (27 bp):
ATATTATTAAAATAAAAAAAATATTAT
Found at i:364001 original size:22 final size:23
Alignment explanation
Indices: 363976--364019 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
363966 GATTATTTTA
363976 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
363998 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
364020 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:364024 original size:22 final size:22
Alignment explanation
Indices: 363980--364036 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
363970 ATTTTATATA
* *
363980 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
364001 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
364023 ATATTTTAAATATT
1 ATATTATAAATATT
364037 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:364035 original size:52 final size:51
Alignment explanation
Indices: 363916--364036 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 51
363906 AAAAATTATT
**
363916 ATATATTATTAAA-A-TAAAAATATAATATCTTATATTATTATAATATAATTG
1 ATATATT-TTAAATATTAAAAATATAATA-CTTATATTATTATAATATAATAA
363967 AT-TATTTTATATAATATTAAAAATATAATA-TTATATTATTATAAATATTAATAA
1 ATATA-TTT-TA-AATATTAAAAATATAATACTTATATTATTAT-AATA-TAATAA
364021 ATATATTTTAAATATT
1 ATATATTTTAAATATT
364037 TTAATAATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 20 0.33
53 7 0.12
54 22 0.37
55 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
ATATATTTTAAATATTAAAAATATAATACTTATATTATTATAATATAATAA
Found at i:364311 original size:42 final size:42
Alignment explanation
Indices: 364208--364326 Score: 222
Period size: 41 Copynumber: 2.9 Consensus size: 42
364198 ATGAATTACA
*
364208 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
364250 TT-CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
364291 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
364327 TTCGAGGAAA
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
41 40 0.53
42 35 0.47
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:365239 original size:2 final size:2
Alignment explanation
Indices: 365232--365261 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
365222 AATAATCCAT
365232 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
365262 AACTAACCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:366300 original size:43 final size:43
Alignment explanation
Indices: 366252--366338 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
366242 ATGATCCACA
* ** *
366252 CCTTTCATTTAATTTCAATTGTTCGCCATGAATACCGCCCAAC
1 CCTTTCATTTAAATTCAATCATCCGCCATGAATACCGCCCAAC
*
366295 CCTTTCATTTAAATTCAATCATCCGCCATGAATACCGCTCAAC
1 CCTTTCATTTAAATTCAATCATCCGCCATGAATACCGCCCAAC
366338 C
1 C
366339 GTCCTTCTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (43 bp):
CCTTTCATTTAAATTCAATCATCCGCCATGAATACCGCCCAAC
Found at i:366470 original size:22 final size:22
Alignment explanation
Indices: 366440--366485 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
366430 TTTTATCAAG
*
366440 TTTTAAGAAGGTATAGTTTTTA
1 TTTTAAGAAGGTAAAGTTTTTA
* * *
366462 TTTTTAGAAGTTAAATTTTTTA
1 TTTTAAGAAGGTAAAGTTTTTA
366484 TT
1 TT
366486 ATATTATAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (22 bp):
TTTTAAGAAGGTAAAGTTTTTA
Found at i:366523 original size:18 final size:20
Alignment explanation
Indices: 366502--366542 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
366492 TAATAATTTA
366502 ATAGTTTA-T-TATTTTATT
1 ATAGTTTATTATATTTTATT
366520 ATAGTTTATTATATTTTATT
1 ATAGTTTATTATATTTTATT
366540 ATA
1 ATA
366543 CTAATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.38
19 1 0.05
20 12 0.57
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
ATAGTTTATTATATTTTATT
Found at i:366529 original size:10 final size:10
Alignment explanation
Indices: 366502--366542 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
366492 TAATAATTTA
366502 ATAGTTTATT
1 ATAGTTTATT
366512 AT--TTTATT
1 ATAGTTTATT
366520 ATAGTTTATT
1 ATAGTTTATT
*
366530 ATATTTTATT
1 ATAGTTTATT
366540 ATA
1 ATA
366543 CTAATTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 8 0.29
10 20 0.71
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (10 bp):
ATAGTTTATT
Found at i:367795 original size:31 final size:30
Alignment explanation
Indices: 367760--367817 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
367750 TCCCATTAGA
367760 TATGTTGATGGTT-GCAGTCCCTCTAATATGT
1 TATGTT-ATGGTTGGCAGTCCCT-TAATATGT
*
367791 TATGTTATTGTTGGCAGTCCCTTAATA
1 TATGTTATGGTTGGCAGTCCCTTAATA
367818 AGGCATCGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.43
Consensus pattern (30 bp):
TATGTTATGGTTGGCAGTCCCTTAATATGT
Found at i:368066 original size:102 final size:101
Alignment explanation
Indices: 367849--368077 Score: 246
Period size: 102 Copynumber: 2.3 Consensus size: 101
367839 AGCTGGTAGT
* *
367849 TGAATGTCTCCCCCTTGAACTTGAAGGCATCGTGTCATATGGGTTTGAACTAAGTGTTGTGTCGC
1 TGAATGTCTCCCCCTTGAACTTGAAGGCATCATGTCAAATGGGTTTGAACTAAGTGTTGTGTCGC
* * ** * *
367914 ATACATCTTCACATTGAGGTCAAAGAAGCTCGCAGT
66 AGACATCTCCACATCCAGGTCAAAGAAACTCGCAGA
* * *
367950 TGAATGCCTCCCCCTGGAACTTGAAGGCATCATGTCAAATGGGTATTGAA-TAGATTGTTGTGTC
1 TGAATGTCTCCCCCTTGAACTTGAAGGCATCATGTCAAATGGGT-TTGAACTA-AGTGTTGTGTC
* * * * * *
368014 G-AGGGCATCTCCATATCCATGTCAAATAAATTGGCAGA
64 GCA-GACATCTCCACATCCAGGTCAAAGAAACTCGCAGA
* *
368052 TGAATGTCTTCCCCTTGAACTAGAAG
1 TGAATGTCTCCCCCTTGAACTTGAAG
368078 CGATGTTGCC
Statistics
Matches: 104, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
101 43 0.41
102 61 0.59
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (101 bp):
TGAATGTCTCCCCCTTGAACTTGAAGGCATCATGTCAAATGGGTTTGAACTAAGTGTTGTGTCGC
AGACATCTCCACATCCAGGTCAAAGAAACTCGCAGA
Found at i:368805 original size:21 final size:22
Alignment explanation
Indices: 368779--368821 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
368769 ATTATGACTA
368779 TCGCGTTGCGATTTT-CCAATT
1 TCGCGTTGCGATTTTCCCAATT
368800 TCGCGTTGCGATTTTCCCAATT
1 TCGCGTTGCGATTTTCCCAATT
368822 CGCAATGCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.14, C:0.26, G:0.19, T:0.42
Consensus pattern (22 bp):
TCGCGTTGCGATTTTCCCAATT
Found at i:368830 original size:21 final size:21
Alignment explanation
Indices: 368785--368831 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
368775 ACTATCGCGT
**
368785 TGCGATTTTCCAATTTCGCGT
1 TGCGATTTTCCAATTTCGCAA
368806 TGCGATTTTCCCAA-TTCGCAA
1 TGCGATTTT-CCAATTTCGCAA
368827 TGCGA
1 TGCGA
368832 ATAAGTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (21 bp):
TGCGATTTTCCAATTTCGCAA
Found at i:368864 original size:21 final size:20
Alignment explanation
Indices: 368821--368869 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
368811 TTTTCCCAAT
*
368821 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
368841 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
368862 TCGCAATG
1 TCGCAATG
368870 AGATATTGCG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:368999 original size:20 final size:20
Alignment explanation
Indices: 368926--368983 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
368916 TTGCGATTAA
* *
368926 GTAAATCGCAATACGAATTA-
1 GTAAATCGCAATGC-AAATAC
*
368946 GGAAATCGCAATGCAAATAC
1 GTAAATCGCAATGCAAATAC
*
368966 GTAAATCACAATGCAAAT
1 GTAAATCGCAATGCAAAT
368984 CTTACTATCG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 4 0.12
20 28 0.88
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.21
Consensus pattern (20 bp):
GTAAATCGCAATGCAAATAC
Found at i:369592 original size:14 final size:14
Alignment explanation
Indices: 369573--369694 Score: 73
Period size: 14 Copynumber: 7.6 Consensus size: 14
369563 TTTCATTTCG
369573 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
369587 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
369606 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
369620 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
369639 CGTTACGATTCTCT
1 CGTTGCGATTCTCT
*
369653 CGTTGCGATAGTCATTTT
1 CGTTGCGAT--TC--TCT
369671 GCGTTGCGATTCTCT
1 -CGTTGCGATTCTCT
369686 CGTTGCGAT
1 CGTTGCGAT
369695 AGTCATTTCC
Statistics
Matches: 85, Mismatches: 8, Indels: 30
0.69 0.07 0.24
Matches are distributed among these distances:
14 37 0.44
15 2 0.02
16 8 0.09
17 8 0.09
18 2 0.02
19 28 0.33
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:369598 original size:33 final size:33
Alignment explanation
Indices: 369556--369718 Score: 254
Period size: 33 Copynumber: 4.9 Consensus size: 33
369546 CAAAATCGTA
369556 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
369589 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
369622 TTGCGATTTTCATTTCGCGTTACGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
** *
369655 TTGCGATAGTCATTTTGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
** *
369688 TTGCGATAGTCATTTCCGTGTTGCGATTCTC
1 TTGCGATTTTCATTT-CGCGTTGCGATTCTC
369719 ATTATCTCGT
Statistics
Matches: 122, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
33 109 0.89
34 13 0.11
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:369720 original size:20 final size:20
Alignment explanation
Indices: 369684--369743 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
369674 TTGCGATTCT
**
369684 CTCGTTGCGATAGTCATTTC
1 CTCGTTGCGATTCTCATTTC
369704 CGT-GTTGCGATTCTCATTAT-
1 C-TCGTTGCGATTCTCATT-TC
*
369724 CTCGTTGCGATTTTCATTTC
1 CTCGTTGCGATTCTCATTTC
369744 AACCAAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
19 2 0.06
20 29 0.88
21 2 0.06
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.45
Consensus pattern (20 bp):
CTCGTTGCGATTCTCATTTC
Found at i:371572 original size:17 final size:17
Alignment explanation
Indices: 371542--371574 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
371532 GTTGCTGCCA
371542 ATTCTGTTAAACTGTGT
1 ATTCTGTTAAACTGTGT
371559 ATTCT-TTAACACTGTG
1 ATTCTGTTAA-ACTGTG
371575 AAGTTAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.45
Consensus pattern (17 bp):
ATTCTGTTAAACTGTGT
Found at i:371909 original size:21 final size:21
Alignment explanation
Indices: 371885--371954 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 21
371875 TCATTCCTCG
*
371885 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTAA
* * ** * *
371906 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTAA
*
371927 AGAGGT-CCCTCCCACCATTAA
1 AGA-GTCCCCTCCCACCGTTAA
371948 AGAGTCC
1 AGAGTCC
371955 GATTCACATG
Statistics
Matches: 34, Mismatches: 13, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
20 2 0.06
21 31 0.91
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTAA
Found at i:371909 original size:42 final size:42
Alignment explanation
Indices: 371833--371921 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
371823 GACTCGCCTG
* * *
371833 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
371875 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
371917 TCATC
1 TCATC
371922 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:373323 original size:14 final size:14
Alignment explanation
Indices: 373304--373337 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
373294 ATTGTTTAAT
373304 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
373318 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
373332 TGATTT
1 TGATTT
373338 ATTTAATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.41
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:373470 original size:19 final size:19
Alignment explanation
Indices: 373446--373537 Score: 69
Period size: 19 Copynumber: 5.4 Consensus size: 19
373436 AAAAAGTACT
373446 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
373465 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
373479 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
373498 ATCACAACGCG-AAT----
1 ATCGCAATGCGAAATGAAA
* *
373512 TTTGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
373531 ATCGCAA
1 ATCGCAA
373538 CGACAAAATC
Statistics
Matches: 53, Mismatches: 10, Indels: 20
0.64 0.12 0.24
Matches are distributed among these distances:
14 17 0.32
15 4 0.08
16 2 0.04
17 2 0.04
18 4 0.08
19 24 0.45
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:373488 original size:33 final size:32
Alignment explanation
Indices: 373446--373558 Score: 154
Period size: 33 Copynumber: 3.4 Consensus size: 32
373436 AAAAAGTACT
373446 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGA-A
* *
373479 ATCGCAATGCGAAATGAAAATCACAACGCGAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAA
* * *
373511 TTTTGCAATGCGAAATGAAAATCGCAACGACAAA
1 -ATCGCAATGCGAAATGAAAATCGCAACGA-GAA
373545 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
373559 CTAAATTCGC
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
32 1 0.01
33 66 0.96
34 2 0.03
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.15
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:373586 original size:19 final size:19
Alignment explanation
Indices: 373564--373714 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
373554 CGAAACTAAA
373564 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
373583 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
373598 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * *
373616 TTCACATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
373630 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
373649 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
373664 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
373682 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
373701 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
373715 AGACATTAAG
Statistics
Matches: 96, Mismatches: 20, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 46 0.48
20 10 0.10
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:373610 original size:33 final size:32
Alignment explanation
Indices: 373568--373694 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
373558 ACTAAATTCG
373568 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* *
373601 CGTTGCGATTTTCATTTCACATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
373634 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
373667 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
373695 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:373638 original size:66 final size:66
Alignment explanation
Indices: 373561--373693 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
373551 ATGCGAAACT
373561 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCACATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCACATTGC
373626 G
66 G
* *
373627 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCACATTGC
373692 G
66 G
373693 A
1 A
373694 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCACATTGC
G
Found at i:377056 original size:21 final size:21
Alignment explanation
Indices: 377004--377059 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
376994 CGATTTTCCT
*
377004 AAATCGCAATACGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
377025 AAATCGCAATGCGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
377046 AAATCGCAATGCGA
1 AAATCGCAATGCGA
377060 TACTGACTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.21
Consensus pattern (21 bp):
AAATCGCAATGCGAATTTGGA
Found at i:377133 original size:20 final size:20
Alignment explanation
Indices: 377023--377135 Score: 77
Period size: 20 Copynumber: 5.5 Consensus size: 20
377013 TACGAATTTG
377023 GAAAATCGCAATGCGA-ATT-T
1 GAAAATCGCAA--CGAGATTCT
* * *
377043 GGAAAATCGCAATGCGATACT
1 -GAAAATCGCAACGAGATTCT
** **
377064 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATTCT
*
377084 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATTCT
***
377105 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATTCT
377125 GAAAATCGCAA
1 GAAAATCGCAA
377136 TCATCTTCAA
Statistics
Matches: 69, Mismatches: 20, Indels: 7
0.72 0.21 0.07
Matches are distributed among these distances:
19 1 0.01
20 41 0.59
21 27 0.39
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATTCT
Found at i:377424 original size:20 final size:20
Alignment explanation
Indices: 377349--377416 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
377339 CAACGGGGAA
377349 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
377369 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
377389 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
377409 ATCGCAAC
1 ATCGCAAC
377417 TAGAAAATCG
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:377428 original size:34 final size:34
Alignment explanation
Indices: 377333--377436 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 34
377323 ATTCATTTGA
** *
377333 CTATCGCAACGGGGAAATCGCAACGCGAAAATGG
1 CTATCGCAACAAGAAAATCGCAACGCGAAAATGG
377367 CTATCGCAATTCGAAATGAAAAATCGCAACGCGAAAATGG
1 CTATCGCAA--C--AA-G-AAAATCGCAACGCGAAAATGG
* *
377407 CTATCGCAACTAGAAAATCGCAATGCGAAA
1 CTATCGCAACAAGAAAATCGCAACGCGAAA
377437 TGAAAATCGC
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
34 25 0.42
35 1 0.02
36 2 0.03
38 1 0.02
39 1 0.02
40 29 0.49
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.15
Consensus pattern (34 bp):
CTATCGCAACAAGAAAATCGCAACGCGAAAATGG
Found at i:377467 original size:14 final size:14
Alignment explanation
Indices: 377448--377501 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
377438 GAAAATCGCA
377448 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
377462 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
377479 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
377495 TTGCGAT
1 TTGCGAT
377502 AGTCAGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:377467 original size:33 final size:33
Alignment explanation
Indices: 377430--377500 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
377420 AAAATCGCAA
377430 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
377463 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
377496 TGCGA
1 TGCGA
377501 TAGTCAGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:379117 original size:38 final size:40
Alignment explanation
Indices: 379075--379163 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 40
379065 CCTCTTCAAC
*
379075 GATGACAGTGGCCTCTTGAACG-GG-GGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGTGGAGGGGACTCTTGAGG
*
379113 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACG--TGGAGGGGACTCTTGAGG
*
379155 AATGACAGG
1 GATGACAGG
379164 TGAGTCGGGC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
38 20 0.47
41 2 0.05
42 21 0.49
ACGTcount: A:0.22, C:0.16, G:0.40, T:0.21
Consensus pattern (40 bp):
GATGACAGGGGCCTCTTGAACGTGGAGGGGACTCTTGAGG
Found at i:379581 original size:19 final size:20
Alignment explanation
Indices: 379527--379581 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
379517 AAACTTGCTT
**
379527 TCGCAACGCGGAAATCACTA
1 TCGCAACGCGGAAATGGCTA
379547 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGGCTA
*
379567 TCGCAATGC-GAAATG
1 TCGCAACGCGGAAATG
379582 AATTGCGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 6 0.19
20 26 0.81
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGGCTA
Found at i:379621 original size:14 final size:14
Alignment explanation
Indices: 379602--379659 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
379592 TTCATTTCGT
379602 GTTGCGATTTTGTC
1 GTTGCGATTTTGTC
*
379616 GTTGCGATTTTCATTTCAC
1 GTTGCGA-TTT--TGT--C
*
379635 ATTGCGATTTTGTC
1 GTTGCGATTTTGTC
379649 GTTGCGATTTT
1 GTTGCGATTTT
379660 CATTTCGCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
14 18 0.51
15 3 0.09
16 2 0.06
17 2 0.06
18 3 0.09
19 7 0.20
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.50
Consensus pattern (14 bp):
GTTGCGATTTTGTC
Found at i:379621 original size:33 final size:33
Alignment explanation
Indices: 379584--379675 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
379574 GCGAAATGAA
**
379584 TTGCGATTTTCATTTCGTGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
379617 TTGCGATTTTCATTTCACATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
379650 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
379676 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.13, C:0.17, G:0.21, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:379674 original size:19 final size:18
Alignment explanation
Indices: 379583--379675 Score: 67
Period size: 19 Copynumber: 5.4 Consensus size: 18
379573 TGCGAAATGA
379583 ATTGCGATTTTCATTTCG
1 ATTGCGATTTTCATTTCG
* *
379601 TGTTGCGA-TTT--TGTCG
1 -ATTGCGATTTTCATTTCG
*
379617 -TTGCGATTTTCATTTCAC
1 ATTGCGATTTTCATTTC-G
*
379635 ATTGCGA-TTT--TGTCG
1 ATTGCGATTTTCATTTCG
379650 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTCATTTCG
379667 CATTGCGAT
1 -ATTGCGAT
379676 AGCCATTTCC
Statistics
Matches: 57, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 12 0.21
15 6 0.11
16 7 0.12
17 7 0.12
18 6 0.11
19 19 0.33
ACGTcount: A:0.14, C:0.17, G:0.20, T:0.48
Consensus pattern (18 bp):
ATTGCGATTTTCATTTCG
Found at i:379694 original size:20 final size:19
Alignment explanation
Indices: 379660--379714 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
379650 TTGCGATTTT
*
379660 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
379679 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
379699 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
379715 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:380837 original size:20 final size:20
Alignment explanation
Indices: 380789--380847 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
380779 AATAGTTTCT
* *
380789 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
380809 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
380829 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
380848 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:381152 original size:22 final size:23
Alignment explanation
Indices: 381111--381155 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
381101 GATGGAGATA
*
381111 GACGGATTTTCGCCGGAGATGGG
1 GACGGATTTTCGCCGAAGATGGG
*
381134 GACGGA-TTTCGTCGAAGATGGG
1 GACGGATTTTCGCCGAAGATGGG
381156 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.20, C:0.16, G:0.42, T:0.22
Consensus pattern (23 bp):
GACGGATTTTCGCCGAAGATGGG
Found at i:381441 original size:41 final size:41
Alignment explanation
Indices: 381322--381459 Score: 161
Period size: 41 Copynumber: 3.4 Consensus size: 41
381312 CGCTTTGAAA
* * * *
381322 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTATATTATCGCGTTGCGAAAGTCAGT
* * ** * *
381363 ATTGAGTTGCGAAATTA-AGTATCGAGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTATATTATCGCGTTGCGAAAGTCAGT
*
381403 ATCGCGTTGCGATTTTATATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTATATTATCGCGTTGCGAAAGTCAGT
*
381444 ACCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
381460 CCAAATTCGC
Statistics
Matches: 78, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
40 33 0.42
41 45 0.58
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTATATTATCGCGTTGCGAAAGTCAGT
Found at i:381456 original size:20 final size:20
Alignment explanation
Indices: 381342--381455 Score: 102
Period size: 20 Copynumber: 5.7 Consensus size: 20
381332 GATTATGTAT
*
381342 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * * *
381362 TATTGAGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
381382 TATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*** * *
381402 TATCGCGTTGCGATTTTATAT
1 TATCGCGTTGCGAAAGT-CAG
*
381423 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
381443 TACCGCGTTGCGA
1 TATCGCGTTGCGA
381456 TTTTCCAAAT
Statistics
Matches: 74, Mismatches: 19, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
20 58 0.78
21 16 0.22
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:381475 original size:41 final size:41
Alignment explanation
Indices: 381389--381477 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 41
381379 AAGTATCGAG
* * * *
381389 TTGCGAAAGTCAGTATCGCGTTGCGATTTTATATTATCGCG
1 TTGCGATAGTCAGTACCGCGTTGCGATTTTATAATATCGCA
381430 TTGCGATAGTCAGTACCGCGTTGCGATTTTCCA-AAT-TCGCA
1 TTGCGATAGTCAGTACCGCGTTGCGATTTT--ATAATATCGCA
381471 TTGCGAT
1 TTGCGAT
381478 TTACTTATTC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 39 0.93
42 2 0.05
43 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (41 bp):
TTGCGATAGTCAGTACCGCGTTGCGATTTTATAATATCGCA
Found at i:381476 original size:21 final size:20
Alignment explanation
Indices: 381450--381496 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
381440 CAGTACCGCG
*
381450 TTGCGATTTTCCAAATTCGCA
1 TTGCGA-TTTACAAATTCGCA
**
381471 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACAAATTCGCA
381491 TTGCGA
1 TTGCGA
381497 ATTGGGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACAAATTCGCA
Found at i:381538 original size:21 final size:22
Alignment explanation
Indices: 381486--381538 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
381476 ATTTACTTAT
381486 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
381507 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
381528 TCGCATTGCGA
1 TCGCATTGCGA
381539 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:382903 original size:19 final size:18
Alignment explanation
Indices: 382866--382908 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
382856 TAAATTATCA
*
382866 ATAAAAATATAAAAAAAT
1 ATAAAAAAATAAAAAAAT
* *
382884 ATTAAAAAAATACAAGAAT
1 A-TAAAAAAATAAAAAAAT
382903 ATAAAA
1 ATAAAA
382909 TTTTAAAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (18 bp):
ATAAAAAAATAAAAAAAT
Found at i:384904 original size:24 final size:24
Alignment explanation
Indices: 384876--384924 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
384866 ACGTCCGTTC
384876 TTTCGGCTTCTGTATCTATTTGTA
1 TTTCGGCTTCTGTATCTATTTGTA
384900 TTTCGGCTTCTGTATCTATTTGTA
1 TTTCGGCTTCTGTATCTATTTGTA
384924 T
1 T
384925 AAATTTACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.16, G:0.16, T:0.55
Consensus pattern (24 bp):
TTTCGGCTTCTGTATCTATTTGTA
Found at i:401429 original size:37 final size:37
Alignment explanation
Indices: 401378--401482 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
401368 CCTTTTCGTC
401378 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
401415 TTACTAGGATTCAAACTCCTTAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
401452 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
401483 TCACAAGCAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:402042 original size:2 final size:2
Alignment explanation
Indices: 402022--402077 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
402012 TTTTTAATAC
* *
402022 TA TA TT TA T- TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
402063 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
402078 TTTAAAATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:403402 original size:19 final size:19
Alignment explanation
Indices: 403378--403414 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
403368 ACCTTACTAA
403378 CTCTTTTCATTTT-TTTCCT
1 CTCTTTT-ATTTTATTTCCT
403397 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
403415 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCT
Found at i:406857 original size:17 final size:17
Alignment explanation
Indices: 406810--406868 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
406800 AGATCCAATC
406810 AAGAACAAAAAAGA-AAAG
1 AAGAA-AAAAAA-ACAAAG
406828 AAGAAAAAAAAACAAAG
1 AAGAAAAAAAAACAAAG
*
406845 AA-AAAAGAGAAAC-AAG
1 AAGAAAA-AAAAACAAAG
*
406861 AATAAAAA
1 AAGAAAAA
406869 TCAAAAAGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
16 11 0.30
17 21 0.57
18 5 0.14
ACGTcount: A:0.80, C:0.05, G:0.14, T:0.02
Consensus pattern (17 bp):
AAGAAAAAAAAACAAAG
Found at i:406862 original size:30 final size:29
Alignment explanation
Indices: 406816--406882 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
406806 AATCAAGAAC
* *
406816 AAAAAAGAAAAGAAGAAAAAAAAACAAAG
1 AAAAAAGAAAACAAGAAAAAAAAACAAAA
* *
406845 AAAAAAGAGAAACAAGAATAAAAATCAAAA
1 AAAAAAGA-AAACAAGAAAAAAAAACAAAA
406875 AGAAAAAG
1 A-AAAAAG
406883 GGACAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 8 0.25
30 18 0.56
31 6 0.19
ACGTcount: A:0.79, C:0.04, G:0.13, T:0.03
Consensus pattern (29 bp):
AAAAAAGAAAACAAGAAAAAAAAACAAAA
Found at i:406881 original size:7 final size:7
Alignment explanation
Indices: 406816--406881 Score: 55
Period size: 8 Copynumber: 8.7 Consensus size: 7
406806 AATCAAGAAC
406816 AAAAAAG
1 AAAAAAG
406823 AAAAGAAG
1 AAAA-AAG
406831 AAAAAA-
1 AAAAAAG
406837 AAACAAAG
1 AAA-AAAG
406845 AAAAAAG
1 AAAAAAG
406852 AGAAACAAG
1 A-AAA-AAG
406861 AATAAAA-
1 AA-AAAAG
406868 ATCAAAAAG
1 A--AAAAAG
406877 AAAAA
1 AAAAA
406882 GGGACAAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 18
0.74 0.00 0.26
Matches are distributed among these distances:
6 3 0.06
7 19 0.38
8 20 0.40
9 8 0.16
ACGTcount: A:0.80, C:0.05, G:0.12, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:407730 original size:22 final size:22
Alignment explanation
Indices: 407656--407732 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
407646 GCTACCCCAT
*
407656 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
407678 CAAACCTATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
407700 CAAACCTTTAAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
407722 CAAACCTTTGA
1 CAAACCTTTGA
407733 CCAAACATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:408692 original size:106 final size:106
Alignment explanation
Indices: 408548--410226 Score: 2586
Period size: 106 Copynumber: 15.9 Consensus size: 106
408538 CAAGATAAGA
* * * *
408548 CAAGTTCAACTTCACAATGAAGGGACCACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
408613 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * *
408654 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
408719 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * *
408760 CAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACGACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* **
408825 CTTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * *
408866 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
408931 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
*
408972 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
409037 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* *
409078 CAAGTTCAACTTCACGACGAAGAGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
409143 ATTTCAACTTTACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * * *
409184 CAAGTTCATCTTCACGATGAAGGGACTGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * *
409249 ATTTAAACTTCACAGCGTAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * *
409290 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAATAAATAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
409355 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
*
409396 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-AAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
409460 ATTTCAACTTCACAGCGAAGGATATTGGAC-CCAAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACG
*
409501 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
409566 ATTTCAACTTCACAGCAAAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * *
409607 CAAGTTCAACTTCACGACAAAGGGACCGATGGTTGTCAACAAACAAATTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
409672 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * *
409713 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTTAGAGTCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * *
409778 ATTTTAACTTCACAACGAAGGATATTGGACTCCAGAAAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * *
409819 CAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
409884 ATTTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* *
409925 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGTCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * * *
409990 ATTTCAACTTCTCAACGAAGGATCTTGGAC-CCAAGACAACA
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACG
* * * * * *
410031 CAAGCTCAACTTCACGACGAAGGGGCGGCTGATTGTCAAC-AA-AA-TT-TC-A-TTCAGAGTCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
410090 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACA
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * * ** *
410131 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCGGTTCCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
410196 ATTTCAACTTCAC-GACGGAGGATATTGGACT
66 ATTTCAACTTCACAG-CGAAGGATATTGGACT
410227 TAGAACAATG
Statistics
Matches: 1451, Mismatches: 110, Indels: 24
0.92 0.07 0.02
Matches are distributed among these distances:
100 81 0.06
101 4 0.00
102 3 0.00
103 4 0.00
104 4 0.00
105 104 0.07
106 1250 0.86
107 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
Found at i:411009 original size:36 final size:37
Alignment explanation
Indices: 410959--411062 Score: 147
Period size: 36 Copynumber: 2.8 Consensus size: 37
410949 CTTTTTGTCC
410959 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
410996 -TGCTAGGATTCAAACTCCTTAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
411032 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
411063 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
36 33 0.57
37 25 0.43
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:411580 original size:19 final size:19
Alignment explanation
Indices: 411558--411625 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 19
411548 TTATATGTAC
411558 ATATATTTTTTATTTATTT
1 ATATATTTTTTATTTATTT
411577 ATATAATTTGTTTATTT-TTT
1 ATAT-ATTT-TTTATTTATTT
*
411597 AATACTATATTTATTATTTATAT
1 -ATA-TAT-TTT-TTATTTATTT
411620 ATATAT
1 ATATAT
411626 ATATACTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
19 4 0.10
20 7 0.17
21 16 0.39
22 12 0.29
23 2 0.05
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (19 bp):
ATATATTTTTTATTTATTT
Found at i:411995 original size:16 final size:16
Alignment explanation
Indices: 411959--411994 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
411949 TTTGTACTTA
411959 TTTTT-ATTTTTCATT
1 TTTTTCATTTTTCATT
411974 TTTTTCATTTATTCATT
1 TTTTTCATTT-TTCATT
411991 TTTT
1 TTTT
411995 CCCTCTGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 4 0.21
17 10 0.53
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTCATTTTTCATT
Found at i:415959 original size:2 final size:2
Alignment explanation
Indices: 415952--416004 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
415942 TCCATACAGC
415952 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
415993 TA TA TA TA TA TA
1 TA TA TA TA TA TA
416005 GAAAATGTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:428455 original size:24 final size:24
Alignment explanation
Indices: 428423--428472 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
428413 GATAGCCCAA
428423 AGGGGCATCAACAAGGACAATTCG
1 AGGGGCATCAACAAGGACAATTCG
428447 AGGGGCATCAACAAGGACAATTCG
1 AGGGGCATCAACAAGGACAATTCG
428471 AG
1 AG
428473 TACCTTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.20, G:0.30, T:0.12
Consensus pattern (24 bp):
AGGGGCATCAACAAGGACAATTCG
Found at i:429287 original size:21 final size:21
Alignment explanation
Indices: 429261--429302 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
429251 ATAAAGAGTT
429261 GTATGAGAAACTATTTGAAGC
1 GTATGAGAAACTATTTGAAGC
429282 GTATGAGAAACTATTTGAAGC
1 GTATGAGAAACTATTTGAAGC
429303 ACGAGAATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.29
Consensus pattern (21 bp):
GTATGAGAAACTATTTGAAGC
Found at i:434743 original size:94 final size:94
Alignment explanation
Indices: 434561--434735 Score: 291
Period size: 94 Copynumber: 1.9 Consensus size: 94
434551 ACCCAATAGT
* *
434561 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAATCAATCATT
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAAACCACAAAATCAATCATT
*
434626 GAATTTGGAAGATGAATGTGCTCAATAAC
66 GAATTTGAAAGATGAATGTGCTCAATAAC
434655 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATG-AACTC-CAAAATCAATCAT
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAAAC-CACAAAATCAATCAT
*
434718 TGGATTTGAAAGATGAAT
65 TGAATTTGAAAGATGAAT
434736 TTTGCTCATA
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
93 31 0.41
94 45 0.59
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.37
Consensus pattern (94 bp):
ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAAACCACAAAATCAATCATT
GAATTTGAAAGATGAATGTGCTCAATAAC
Found at i:434857 original size:115 final size:115
Alignment explanation
Indices: 434648--434861 Score: 333
Period size: 115 Copynumber: 1.9 Consensus size: 115
434638 TGAATGTGCT
*
434648 CAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCA
1 CAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAACCA
* *
434713 ATCATTGGATTTGAAAGATGAATTTTGCTCATAGTAGAAATAAGAAGACC
66 ATCATTGAATTTGAAAGATGAATTGTGCTCATAGTAGAAATAAGAAGACC
* * *
434763 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAAC-CACAGAAC
1 CAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATG-AACTC-CAAAAC
*
434827 CAATCATTGAATTTGGAAGATGAA-TGTGCTCATAG
64 CAATCATTGAATTTGAAAGATGAATTGTGCTCATAG
434862 CATCTTCTGA
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
115 61 0.68
116 29 0.32
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (115 bp):
CAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAACCA
ATCATTGAATTTGAAAGATGAATTGTGCTCATAGTAGAAATAAGAAGACC
Found at i:434950 original size:93 final size:93
Alignment explanation
Indices: 434765--434952 Score: 281
Period size: 93 Copynumber: 2.0 Consensus size: 93
434755 AGAAGACCCA
* * *
434765 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
1 ATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAAACCACAAAACCAA
*
434830 TCATTGAATTTGGAAGATGAATGTGCTC
66 TCATTGAATTTGAAAGATGAATGTGCTC
*
434858 ATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATG-AACTC-CAAAATCA
1 ATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAAAC-CACAAAACCA
* *
434921 ATCATTGGATTTGAAAGATGAATTTTGCTC
65 ATCATTGAATTTGAAAGATGAA-TGTGCTC
434951 AT
1 AT
434953 GGTAGAAATA
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
92 29 0.34
93 57 0.66
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (93 bp):
ATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAAACCACAAAACCAA
TCATTGAATTTGAAAGATGAATGTGCTC
Found at i:434977 original size:208 final size:209
Alignment explanation
Indices: 434529--435057 Score: 895
Period size: 208 Copynumber: 2.5 Consensus size: 209
434519 AAGTGCCATG
*
434529 TGCTCATAGTAGAAATAAGAAGACCCAATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
434594 TGGTTTGGTATGAAACCACAGAATCAATCATTGAATTTGGAAGATGAATGTGCTCAATAACATCT
66 TGGTTTGGTATGAAACCACAGAACCAATCATTGAATTTGGAAGATGAATGTGCTCAATAACATCT
*
434659 TCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATTGGATT
131 TCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATTGGATT
434724 TGAAAGATGAATTT
196 TGAAAGATGAATTT
434738 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
434803 TGGTTTGGTATGAAACCACAGAACCAATCATTGAATTTGGAAGATGAATGTGCTC-ATAGCATCT
66 TGGTTTGGTATGAAACCACAGAACCAATCATTGAATTTGGAAGATGAATGTGCTCAATAACATCT
434867 TCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATTGGATT
131 TCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATTGGATT
434932 TGAAAGATGAATTT
196 TGAAAGATGAATTT
* * * *
434946 TGCTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * *
435011 TGATTCGGTA-GGAACC-CTAGAACCGATCATTGGAA-TTGAAAGATGAA
66 TGGTTTGGTATGAAACCAC-AGAACCAATCATT-GAATTTGGAAGATGAA
435058 CTGAATGATC
Statistics
Matches: 305, Mismatches: 13, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
206 1 0.00
207 28 0.09
208 158 0.52
209 118 0.39
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33
Consensus pattern (209 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAAACCACAGAACCAATCATTGAATTTGGAAGATGAATGTGCTCAATAACATCT
TCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATTGGATT
TGAAAGATGAATTT
Found at i:436325 original size:74 final size:74
Alignment explanation
Indices: 436161--436328 Score: 178
Period size: 74 Copynumber: 2.3 Consensus size: 74
436151 AACAAGAAGC
* * * * *
436161 AAATATTGGGGCATGCTGAAGACCCTTTTCAAACAGAATCAGAAATATTGAAATATTCTGAATAT
1 AAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATATTGAAACATTCTGAACAT
436226 TTATCAGCA
66 TTATCAGCA
* * * * ** *
436235 AAATGTTGGGGTATGCTGAAAACCCATTTCAATCAGAATCAGAACTGTTGATGCATTTTGAACAC
1 AAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATATTGAAACATTCTGAACA-
*
436300 TTGTATTAGC-
65 TT-TATCAGCA
*
436310 CAATGTT-GGGCATGCTGAA
1 AAATGTTGGGGCATGCTGAA
436329 GGCCCACAAT
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
74 63 0.82
75 8 0.10
76 6 0.08
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (74 bp):
AAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATATTGAAACATTCTGAACAT
TTATCAGCA
Found at i:437265 original size:55 final size:54
Alignment explanation
Indices: 437199--437315 Score: 182
Period size: 55 Copynumber: 2.1 Consensus size: 54
437189 ACTTCAATGA
*
437199 TTACGAACATCTGAGCAGAAGCCACA-AAAAAGGATGAATGAATTGTCAAAATGTT
1 TTACGAACATCTGAGCAGAAGCCACAGAAAAA-GATGAATGAACTGTC-AAATGTT
* *
437254 TTACGAACATCTGAGCAGAAGCCACAGGAAAAGATGAATGCACTGTCAAATGTT
1 TTACGAACATCTGAGCAGAAGCCACAGAAAAAGATGAATGAACTGTCAAATGTT
437308 TTACGAAC
1 TTACGAAC
437316 CTGTTATTCT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
54 15 0.26
55 39 0.67
56 4 0.07
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (54 bp):
TTACGAACATCTGAGCAGAAGCCACAGAAAAAGATGAATGAACTGTCAAATGTT
Found at i:438412 original size:31 final size:31
Alignment explanation
Indices: 438377--438451 Score: 141
Period size: 31 Copynumber: 2.4 Consensus size: 31
438367 CTTCAGTGCA
438377 TGATGTTTCCAAAAAGCCTTAGGGAGCTTTT
1 TGATGTTTCCAAAAAGCCTTAGGGAGCTTTT
438408 TGATGTTTCCAAAAAGCCTTAGGGAGCTTTT
1 TGATGTTTCCAAAAAGCCTTAGGGAGCTTTT
*
438439 TGATGTTTTCAAA
1 TGATGTTTCCAAA
438452 GCCTTCGGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (31 bp):
TGATGTTTCCAAAAAGCCTTAGGGAGCTTTT
Found at i:438532 original size:29 final size:29
Alignment explanation
Indices: 438496--438594 Score: 198
Period size: 29 Copynumber: 3.4 Consensus size: 29
438486 ATGTTTCCAA
438496 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
438525 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
438554 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
438583 AAAGCCTTCGGG
1 AAAGCCTTCGGG
438595 TCATCTGTAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (29 bp):
AAAGCCTTCGGGAGCTTTTTGATGTTTTC
Found at i:438680 original size:76 final size:76
Alignment explanation
Indices: 438554--438746 Score: 386
Period size: 76 Copynumber: 2.5 Consensus size: 76
438544 TGATGTTTTC
438554 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
438619 GATGTTTCCAA
66 GATGTTTCCAA
438630 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
438695 GATGTTTCCAA
66 GATGTTTCCAA
438706 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGG
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGG
438747 AGCTTTTTGA
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 117 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (76 bp):
AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
GATGTTTCCAA
Found at i:438739 original size:105 final size:105
Alignment explanation
Indices: 438355--438955 Score: 869
Period size: 105 Copynumber: 5.7 Consensus size: 105
438345 CTATTTCTCA
* *
438355 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTAGGGAGCTTTTTGATGTTTCCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC--
*
438420 AAAGCCTTAGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
64 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
438462 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
438527 AGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGAG
66 AGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGG-T
* * * * ** * ** *** ***
438568 C-TTTTTGATGT-TTTCAAAGCCT--TCGGGTCATCTGTAAGTCCTTC---AG-TGCATGATGTT
1 CATCTGT-AAGTCCTTCAGTGCATGAT-GTTTC--CAAAAAG-CCTTCGGGAGCTTTTTGATGTT
*
438625 TCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
61 TTC--AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
438672 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
438737 AGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
66 AGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
438777 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
438841 AGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
66 AGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
438881 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
438946 AGCCTTCGGG
66 AGCCTTCGGG
438956 TCATCTGTAA
Statistics
Matches: 440, Mismatches: 37, Indels: 36
0.86 0.07 0.07
Matches are distributed among these distances:
103 16 0.04
104 117 0.27
105 217 0.49
106 13 0.03
107 77 0.17
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37
Consensus pattern (105 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
Found at i:438742 original size:29 final size:29
Alignment explanation
Indices: 438706--438775 Score: 140
Period size: 29 Copynumber: 2.4 Consensus size: 29
438696 ATGTTTCCAA
438706 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
438735 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
438764 AAAGCCTTCGGG
1 AAAGCCTTCGGG
438776 TCATCTGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.37
Consensus pattern (29 bp):
AAAGCCTTCGGGAGCTTTTTGATGTTTTC
Found at i:438846 original size:29 final size:29
Alignment explanation
Indices: 438799--438879 Score: 144
Period size: 29 Copynumber: 2.8 Consensus size: 29
438789 CTTCAGTGCA
*
438799 TGATGTTTCCAAAAGCCTTCGGGAGCTTTT
1 TGATGTTTTC-AAAGCCTTCGGGAGCTTTT
438829 TGATGTTTTCAAAGCCTTCGGGAGCTTTT
1 TGATGTTTTCAAAGCCTTCGGGAGCTTTT
438858 TGATGTTTTCAAAGCCTTCGGG
1 TGATGTTTTCAAAGCCTTCGGG
438880 TCATCTGTAA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 41 0.82
30 9 0.18
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (29 bp):
TGATGTTTTCAAAGCCTTCGGGAGCTTTT
Found at i:438965 original size:76 final size:76
Alignment explanation
Indices: 438839--439031 Score: 386
Period size: 76 Copynumber: 2.5 Consensus size: 76
438829 TGATGTTTTC
438839 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
438904 GATGTTTCCAA
66 GATGTTTCCAA
438915 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
438980 GATGTTTCCAA
66 GATGTTTCCAA
438991 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGG
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGG
439032 AGCTTTTTGA
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 117 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (76 bp):
AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
GATGTTTCCAA
Found at i:439024 original size:105 final size:105
Alignment explanation
Indices: 438915--439342 Score: 829
Period size: 105 Copynumber: 4.1 Consensus size: 105
438905 ATGTTTCCAA
438915 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
438980 GATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
66 GATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
439020 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
439085 GATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
66 GATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
439125 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
*
439190 GATGTTTCCAAAACGCCTTCGGGAGCTTTTTGATGTTTTC
66 GATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
* *
439230 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCAGTTCATCTGTAAGTCCTTCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
439295 GATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
66 GATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
439335 AAAGCCTT
1 AAAGCCTT
439343 AGGGTCATCT
Statistics
Matches: 319, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 319 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (105 bp):
AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
GATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
Found at i:439027 original size:29 final size:29
Alignment explanation
Indices: 438991--439060 Score: 140
Period size: 29 Copynumber: 2.4 Consensus size: 29
438981 ATGTTTCCAA
438991 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
439020 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
439049 AAAGCCTTCGGG
1 AAAGCCTTCGGG
439061 TCATCTGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.37
Consensus pattern (29 bp):
AAAGCCTTCGGGAGCTTTTTGATGTTTTC
Found at i:439132 original size:29 final size:29
Alignment explanation
Indices: 439096--439165 Score: 140
Period size: 29 Copynumber: 2.4 Consensus size: 29
439086 ATGTTTCCAA
439096 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
439125 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
439154 AAAGCCTTCGGG
1 AAAGCCTTCGGG
439166 TCATCTGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.37
Consensus pattern (29 bp):
AAAGCCTTCGGGAGCTTTTTGATGTTTTC
Found at i:439210 original size:181 final size:178
Alignment explanation
Indices: 438829--439494 Score: 658
Period size: 181 Copynumber: 3.7 Consensus size: 178
438819 GGGAGCTTTT
*
438829 TGATGTTTTCAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCC
1 TGATGTTTCCAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCC
*
438894 TTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGG-TC
66 TTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGAGC
* * * * ** * * * *** * ***
438958 -ATCTGTAAGTCCTTCAGTG-CATGATGT-TTCCAAAAAG-CCTTCGGGAGCTTTT
131 TTTTTG-ATGT-TTTCAAAGCCTTG-GGTCAT-CTGTAAGTCC-T--GCAG-TGCA
*
439010 TGATGTTTTCAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCC
1 TGATGTTTCCAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCC
439075 TTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGAGC
66 TTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGAGC
*
439140 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
131 TTTTTGATGTTTTCAAAGCCTT-GGGTCATCTGTAAGTCCTGCAGTGCA
* * * *
439189 TGATGTTTCCAAAACGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGAGC-TTTTTGAT
1 TGATGTTTCC-AAA-GCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGG-TCATCTGT-AA
* ** * * *** *** *
439253 GT-TTTCAAAGCCTTCA-G-TTCATCTGTAAGTCCTTC---AG-TGCATGATGTTTCCAAAAAGC
62 GTCCTTCAGTG-CATGATGTTTC--CAAAAAG-CCTTCGGGAGCTTTTTGATGTTTTC--AAAGC
439311 CTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCA
121 CTTCGGGAGCTTTTTGATGTTTTCAAAGCCTT-GGGTCATCTGTAAGTCCTGCAGTGCA
* * *
439370 TGATGTTTCCAAAAAGCCTTCGGAAGCTTTTTGATGTTTTCAAAGCCTTAGTGTCATCTGTAAGT
1 TGATGTTTCC--AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
* *
439435 CCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCGTTTTTGAT-ATTTCAAAGCCTT
64 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCAAAGCCTT
439495 AGGGTCATCT
Statistics
Matches: 401, Mismatches: 58, Indels: 52
0.78 0.11 0.10
Matches are distributed among these distances:
179 25 0.06
180 21 0.05
181 302 0.75
182 33 0.08
183 15 0.04
184 5 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (178 bp):
TGATGTTTCCAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCC
TTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGAGC
TTTTTGATGTTTTCAAAGCCTTGGGTCATCTGTAAGTCCTGCAGTGCA
Found at i:439240 original size:29 final size:29
Alignment explanation
Indices: 439189--439267 Score: 131
Period size: 29 Copynumber: 2.7 Consensus size: 29
439179 CTTCAGTGCA
*
439189 TGATGTTTCCAAAACGCCTTCGGGAGCTTTT
1 TGATGTTTTC-AAA-GCCTTCGGGAGCTTTT
439220 TGATGTTTTCAAAGCCTTCGGGAGCTTTT
1 TGATGTTTTCAAAGCCTTCGGGAGCTTTT
439249 TGATGTTTTCAAAGCCTTC
1 TGATGTTTTCAAAGCCTTC
439268 AGTTCATCTG
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
29 35 0.74
30 3 0.06
31 9 0.19
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (29 bp):
TGATGTTTTCAAAGCCTTCGGGAGCTTTT
Found at i:439310 original size:76 final size:75
Alignment explanation
Indices: 439230--439605 Score: 601
Period size: 76 Copynumber: 4.9 Consensus size: 75
439220 TGATGTTTTC
* *
439230 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCAGTTCATCTGTAAGTCCTTCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTT-AGGTCATCTGTAAGTCCTGCAGTGCAT
439295 GATGTTTCCAA
65 GATGTTTCCAA
439306 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTA-GGTCATCTGTAAGTCCTGCAGTGCAT
439371 GATGTTTCCAA
65 GATGTTTCCAA
*
439382 AAAGCCTTCGGAAGCTTTTTGATGTTTTCAAAGCCTTAGTGTCATCTGTAAGTCCTGCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAG-GTCATCTGTAAGTCCTGCAGTGCAT
439447 GATGTTTCCAA
65 GATGTTTCCAA
* * *
439458 AAAGCCTTCGGGAGCGTTTTTGAT-ATTTCAAAGCCTTAGGGTCATCTTTAAGTCCTGCAATGCA
1 AAAGCCTTCGGGAGC-TTTTTGATGTTTTCAAAGCCTTA-GGTCATCTGTAAGTCCTGCAGTGCA
439522 TGATGTTTCCAA
64 TGATGTTTCCAA
* * * *
439534 AAAGCTTTCGGGAGCTTTTTGATGTTTTCAAAACCTTGGGATCATCTGTAAGTCATGCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGG-TCATCTGTAAGTCCTGCAGTGCAT
439599 GATGTTT
65 GATGTTT
439606 TTAAGACCTC
Statistics
Matches: 280, Mismatches: 14, Indels: 12
0.92 0.05 0.04
Matches are distributed among these distances:
75 12 0.04
76 259 0.93
77 9 0.03
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (75 bp):
AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGTCATCTGTAAGTCCTGCAGTGCATG
ATGTTTCCAA
Found at i:439756 original size:3 final size:3
Alignment explanation
Indices: 439748--439827 Score: 90
Period size: 3 Copynumber: 26.7 Consensus size: 3
439738 CATTAATTTT
** **
439748 TTA TTA TTA TTA TTA TTA TTA AAA TTA AAA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
439796 TTAA ATA TTA TTA TTA -TA TTA TAA TTA TTA TT
1 TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
439828 TACAAACAGT
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.03
3 59 0.94
4 2 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:439784 original size:30 final size:31
Alignment explanation
Indices: 439748--439827 Score: 119
Period size: 30 Copynumber: 2.6 Consensus size: 31
439738 CATTAATTTT
439748 TTATTATTATTATTATTATTAAA-ATTAAAA
1 TTATTATTATTATTATTATTAAATATTAAAA
**
439778 TTATTATTATTATTATTATTAAATATTATTA
1 TTATTATTATTATTATTATTAAATATTAAAA
*
439809 TTA-TATTATAATTATTATT
1 TTATTATTATTATTATTATT
439828 TACAAACAGT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 38 0.83
31 8 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (31 bp):
TTATTATTATTATTATTATTAAATATTAAAA
Found at i:439785 original size:24 final size:25
Alignment explanation
Indices: 439752--439822 Score: 110
Period size: 24 Copynumber: 2.9 Consensus size: 25
439742 AATTTTTTAT
*
439752 TATTATTATTATTATTAAAATTAAA
1 TATTATTATTATTATTATAATTAAA
*
439777 -ATTATTATTATTATTATTATTAAA
1 TATTATTATTATTATTATAATTAAA
439801 TATTATTATTA-TATTATAATTA
1 TATTATTATTATTATTATAATTA
439823 TTATTTACAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
24 32 0.76
25 10 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTATTATTATTATTATAATTAAA
Found at i:439882 original size:26 final size:26
Alignment explanation
Indices: 439834--439888 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
439824 TATTTACAAA
* *
439834 CAGTTACAAACAAAACTGGACCGACC
1 CAGTTACAAACAAAACAGAACCGACC
* *
439860 CAGTTACAAACAAACCAGAACCGGCC
1 CAGTTACAAACAAAACAGAACCGACC
439886 CAG
1 CAG
439889 ACCAATCAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.33, G:0.16, T:0.09
Consensus pattern (26 bp):
CAGTTACAAACAAAACAGAACCGACC
Found at i:445454 original size:19 final size:19
Alignment explanation
Indices: 445430--445475 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
445420 ACTTGAGACA
445430 TTGCTTAAGCGATATCAAG
1 TTGCTTAAGCGATATCAAG
445449 TTGCTTAAGCGATATCAAG
1 TTGCTTAAGCGATATCAAG
*
445468 CTGCTTAA
1 TTGCTTAA
445476 CACTTGAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (19 bp):
TTGCTTAAGCGATATCAAG
Found at i:448283 original size:45 final size:42
Alignment explanation
Indices: 448184--448284 Score: 112
Period size: 45 Copynumber: 2.3 Consensus size: 42
448174 TCATTGCCGT
* **
448184 CTTCTCCAGCCAAGCCAGTGGCGGCTACTGCCTCCGTTCCCT
1 CTTCTCCAGCCAAGCCAGTGGCGACTACTGCCTCCGTTCCAA
* * *
448226 CTTCTCCTGCCAAGCCAGTGGCGACTACTACTTCCTCGGTTCCAA
1 CTTCTCCAGCCAAGCCAGTGGCG---ACTACTGCCTCCGTTCCAA
*
448271 CTTCACCAGCCAAG
1 CTTCTCCAGCCAAG
448285 ACAGCCCCTA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 22 0.46
45 26 0.54
ACGTcount: A:0.17, C:0.41, G:0.19, T:0.24
Consensus pattern (42 bp):
CTTCTCCAGCCAAGCCAGTGGCGACTACTGCCTCCGTTCCAA
Found at i:450991 original size:14 final size:14
Alignment explanation
Indices: 450972--450999 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
450962 AGTTTTGATA
450972 CTCTTGTAAGAGTT
1 CTCTTGTAAGAGTT
450986 CTCTTGTAAGAGTT
1 CTCTTGTAAGAGTT
451000 TCAAGTTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43
Consensus pattern (14 bp):
CTCTTGTAAGAGTT
Found at i:451008 original size:21 final size:21
Alignment explanation
Indices: 450982--451032 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
450972 CTCTTGTAAG
450982 AGTTCTCTTGTAAGAGTTTCA
1 AGTTCTCTTGTAAGAGTTTCA
451003 AGTTCTCTTGTAAGAGTTTCA
1 AGTTCTCTTGTAAGAGTTTCA
*
451024 A-TACTCTTG
1 AGTTCTCTTG
451033 CACAAGAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 7 0.24
21 22 0.76
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.43
Consensus pattern (21 bp):
AGTTCTCTTGTAAGAGTTTCA
Found at i:454383 original size:31 final size:31
Alignment explanation
Indices: 454323--454400 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
454313 ACGGATCGGG
* *
454323 TAACGAGCATG-GTCGAGCAACAAATTTTTT
1 TAACGAGCACGAGTCGAGCAACAAAATTTTT
* *
454353 TAACGAGCACGAGTTGAGTAACAAAATTTTT
1 TAACGAGCACGAGTCGAGCAACAAAATTTTT
*
454384 TAACAAGCACGAGTCGA
1 TAACGAGCACGAGTCGA
454401 ACACTACTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 10 0.24
31 31 0.76
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.26
Consensus pattern (31 bp):
TAACGAGCACGAGTCGAGCAACAAAATTTTT
Found at i:462463 original size:20 final size:20
Alignment explanation
Indices: 462438--462550 Score: 127
Period size: 20 Copynumber: 5.5 Consensus size: 20
462428 TTTTCCCAAT
462438 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
462458 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
*
462479 TCGTAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
462499 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
462519 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
462540 TCGCAATGCGA
1 TCGCAATGCGA
462551 TACTGACTAT
Statistics
Matches: 76, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
20 46 0.61
21 30 0.39
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:462563 original size:41 final size:41
Alignment explanation
Indices: 462536--462613 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
462526 GCGAATTGGG
* * *
462536 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
* *
462577 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
462614 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
Found at i:462564 original size:20 final size:19
Alignment explanation
Indices: 462539--462653 Score: 86
Period size: 20 Copynumber: 5.7 Consensus size: 19
462529 AATTGGGAAA
*
462539 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACT-ACT
* * *
462559 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATACTAC--T
*
462580 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATAC-TACT
*
462600 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACT-ACT
* *
462620 TTCGCAACGCGATAATACAT
1 ATCGCAACGCGATACTAC-T
*
462640 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
462654 TTTCAAAGTG
Statistics
Matches: 78, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.06
20 47 0.60
21 23 0.29
22 3 0.04
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (19 bp):
ATCGCAACGCGATACTACT
Found at i:462849 original size:22 final size:22
Alignment explanation
Indices: 462821--462864 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
462811 CACTCTCTCA
462821 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
462843 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
462865 TATCTCTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:463147 original size:20 final size:20
Alignment explanation
Indices: 463098--463150 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
463088 AAATCGCAAC
*
463098 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
** *
463117 GCGATAGTCATTTTCGTGTT
1 GCGATTTTCATTTTCGCGTT
463137 GCGATTTTCATTTT
1 GCGATTTTCATTTT
463151 TAGAAACTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.13, C:0.15, G:0.23, T:0.49
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:464496 original size:17 final size:18
Alignment explanation
Indices: 464471--464514 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
464461 TCCACTTCGG
*
464471 GAGCCATCACCTC-GCCA
1 GAGCCATCACCTCACCCA
*
464488 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
464506 GAGCCATCA
1 GAGCCATCA
464515 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.27, C:0.43, G:0.16, T:0.14
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:465021 original size:20 final size:20
Alignment explanation
Indices: 464996--465041 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
464986 TAGTTTACTT
464996 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
465016 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
465036 TCGCAA
1 TCGCAA
465042 TGCGAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:465070 original size:14 final size:14
Alignment explanation
Indices: 465051--465140 Score: 81
Period size: 14 Copynumber: 5.9 Consensus size: 14
465041 ATGCGAAATA
465051 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
465065 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
465081 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
* *
465097 AAAATCGTAATGCGAA
1 AAAATCGCAA--CGAC
465113 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
465129 AAAATCGCAACG
1 AAAATCGCAACG
465141 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
14 29 0.47
16 16 0.26
18 17 0.27
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:465093 original size:32 final size:32
Alignment explanation
Indices: 465035--465157 Score: 201
Period size: 32 Copynumber: 3.8 Consensus size: 32
465025 GGAAATGGCT
*
465035 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAATGCGAAAT-GAAATCGCAACGACAAA
465068 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
*
465100 ATCGTAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
*
465132 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATG-AAATCGCAA
465158 TGCGATTTGT
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
32 61 0.72
33 24 0.28
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGACAAA
Found at i:465193 original size:14 final size:14
Alignment explanation
Indices: 465174--465231 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
465164 TTGTGTTTCG
465174 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
465188 CGTTGCGATTTCATTTCT
1 CGTTGCGA--T--TTTGT
*
465206 CGTTGTGATTTTGT
1 CGTTGCGATTTTGT
465220 CGTTGCGATTTT
1 CGTTGCGATTTT
465232 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 23 0.64
16 2 0.06
18 11 0.31
ACGTcount: A:0.09, C:0.16, G:0.24, T:0.52
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:465216 original size:32 final size:33
Alignment explanation
Indices: 465169--465247 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
465159 GCGATTTGTG
465169 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
* *
465201 TTTCTCGTTGTGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
465234 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
465248 AGCCATTTCC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 25 0.61
33 16 0.39
ACGTcount: A:0.10, C:0.18, G:0.23, T:0.49
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:465246 original size:19 final size:19
Alignment explanation
Indices: 465220--465286 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
465210 GTGATTTTGT
**
465220 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
465239 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
465259 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
465278 CGTTGCGAT
1 CGTTGCGAT
465287 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:465266 original size:20 final size:19
Alignment explanation
Indices: 465232--465286 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
465222 TTGCGATTTT
*
465232 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
465251 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
465271 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
465287 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:466203 original size:14 final size:14
Alignment explanation
Indices: 466184--466219 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
466174 ATTGTTTAAT
466184 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
466198 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
466212 TGATTTGT
1 TGATTTGT
466220 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Done.