Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold16
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: 5287347
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 8769 characters in sequence are not A, C, G, or T
File 18 of 35
Found at i:2708581 original size:13 final size:13
Alignment explanation
Indices: 2708563--2708600 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
2708553 CATTTTTCTT
2708563 TGTATCGATACAA
1 TGTATCGATACAA
*
2708576 TGTATCGATACAC
1 TGTATCGATACAA
2708589 TGTATCGATACA
1 TGTATCGATACA
2708601 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2711093 original size:20 final size:20
Alignment explanation
Indices: 2711039--2711094 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
2711029 AAACCCTTAA
*
2711039 AAGTATCGATACATAATTCG
1 AAGTATCGATACATGATTCG
*
2711059 AAGTATCGATACATGTTTC-
1 AAGTATCGATACATGATTCG
2711078 AATGTATCGATACATGA
1 AA-GTATCGATACATGA
2711095 AAAAGATGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
AAGTATCGATACATGATTCG
Found at i:2711181 original size:13 final size:13
Alignment explanation
Indices: 2711163--2711188 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2711153 TACACAAAGT
2711163 ATGTATCGATACA
1 ATGTATCGATACA
2711176 ATGTATCGATACA
1 ATGTATCGATACA
2711189 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2711186 original size:32 final size:33
Alignment explanation
Indices: 2711145--2711208 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2711135 TAGCCAAACT
**
2711145 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2711177 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2711209 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2713161 original size:51 final size:51
Alignment explanation
Indices: 2712992--2713212 Score: 167
Period size: 51 Copynumber: 4.3 Consensus size: 51
2712982 ATTTTTCATC
** * * **
2712992 TCGGGGATACTCCAA-TCCCGATTCCATTTCCAAAACATCAATTTTTCTTAA
1 TCGGGGATACTCCAACT-CCGATTTTATTTTCAAAACACCAATTTTTCACAA
* * * * * * * * ** *
2713043 TTGGAGATACTCTAACTCTGATTTTATTTTCCGAAGCATCGATTTACCGCAA
1 TCGGGGATACTCCAACTCCGATTTTATTTT-CAAAACACCAATTTTTCACAA
* *
2713095 TCGAGGATACTCCAACTACGATTTTATTTTCAAAACACCAATTTTTCACAA
1 TCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTCACAA
* * * * * *
2713146 TTGGGGATACTCCAACCCCAATTTTATTTTCAAAATACCGA-TTTTCTATAA
1 TCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTC-ACAA
*
2713197 TCAGGGATACTCCAAC
1 TCGGGGATACTCCAAC
2713213 CTTGTTATTT
Statistics
Matches: 130, Mismatches: 37, Indels: 6
0.75 0.21 0.03
Matches are distributed among these distances:
50 5 0.04
51 86 0.66
52 39 0.30
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (51 bp):
TCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTCACAA
Found at i:2717840 original size:20 final size:20
Alignment explanation
Indices: 2717815--2717971 Score: 80
Period size: 20 Copynumber: 7.8 Consensus size: 20
2717805 TTTTCACAAT
2717815 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
*
2717835 TTGTATCGATATATTCTAGGTTTACCCA
1 TTGTATCGATACA-T-T--G-TT---CA
* *
2717863 GATGTATCGATACATT-TTGCT
1 -TTGTATCGATACATTGTT-CA
* *
2717884 TTGTATTGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
2717904 TTGTATCGAT--A-----CA
1 TTGTATCGATACATTGTTCA
*
2717917 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
2717937 TTGTATCGATACATT-TTACA
1 TTGTATCGATACATTGTT-CA
* *
2717957 ATGTATCGATCCATT
1 TTGTATCGATACATT
2717972 CAGGCATTTT
Statistics
Matches: 106, Mismatches: 13, Indels: 36
0.68 0.08 0.23
Matches are distributed among these distances:
13 12 0.11
15 1 0.01
18 1 0.01
19 1 0.01
20 67 0.63
21 3 0.03
22 1 0.01
23 2 0.02
24 1 0.01
25 2 0.02
27 1 0.01
28 3 0.03
29 11 0.10
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.43
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:2717928 original size:33 final size:33
Alignment explanation
Indices: 2717884--2717951 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
2717874 ACATTTTGCT
*
2717884 TTGTATTGATACATTGCTCATTGTATCGATACA
1 TTGTATCGATACATTGCTCATTGTATCGATACA
2717917 TTGTATCGATACATTGCTCATTGTATCGATACA
1 TTGTATCGATACATTGCTCATTGTATCGATACA
2717950 TT
1 TT
2717952 TTACAATGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (33 bp):
TTGTATCGATACATTGCTCATTGTATCGATACA
Found at i:2717951 original size:13 final size:13
Alignment explanation
Indices: 2717902--2717932 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2717892 ATACATTGCT
2717902 CATTGTATCGATA
1 CATTGTATCGATA
2717915 CATTGTATCGATA
1 CATTGTATCGATA
2717928 CATTG
1 CATTG
2717933 CTCATTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:2717962 original size:53 final size:52
Alignment explanation
Indices: 2717865--2717971 Score: 128
Period size: 53 Copynumber: 2.0 Consensus size: 52
2717855 TTTACCCAGA
* *
2717865 TGTATCGATACATTTTGCTTTGTATTGATACATTGCTCATTGTATCGATACAT
1 TGTATCGATACA-TTTGCTTTGTATCGATACATTGCTCAATGTATCGATACAT
* *
2717918 TGTATCGATACA-TTGCTCATTGTATCGATACATT-TTACAATGTATCGATCCAT
1 TGTATCGATACATTTGCT--TTGTATCGATACATTGCT-CAATGTATCGATACAT
2717971 T
1 T
2717972 CAGGCATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
51 5 0.11
52 1 0.02
53 41 0.87
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (52 bp):
TGTATCGATACATTTGCTTTGTATCGATACATTGCTCAATGTATCGATACAT
Found at i:2720357 original size:51 final size:51
Alignment explanation
Indices: 2720277--2720445 Score: 171
Period size: 51 Copynumber: 3.3 Consensus size: 51
2720267 ATTTTTCATC
* * * * * *
2720277 TTGGGGATACTCCAA-TCCCGGTTTCATTTCCCAAACATCAATTTTTCTTAA
1 TTGGGGATACTCCAACT-CCGATTTTATTTCCAAAACACCAATTTTCCATAA
* * *
2720328 TTGGGGATACTCAAACTCCGATTTTATTTCTAAAACACCCATTTTCCATAA
1 TTGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCATAA
* * * * *
2720379 TCGGGGATACTCCAACTCTGATTTTATTTTCAAAACACCGACTTTT-CACAA
1 TTGGGGATACTCCAACTCCGATTTTATTTCCAAAACACC-AATTTTCCATAA
*
2720430 TCGGGGATACTCCAAC
1 TTGGGGATACTCCAAC
2720446 CCCGTTATTT
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
51 94 0.95
52 5 0.05
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.34
Consensus pattern (51 bp):
TTGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCATAA
Found at i:2720618 original size:79 final size:78
Alignment explanation
Indices: 2720428--2720818 Score: 484
Period size: 79 Copynumber: 5.0 Consensus size: 78
2720418 GACTTTTCAC
* *
2720428 AATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGATTTTATTTCTAAAA
1 AATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAA-CCCGGTTTTATTTCTAAAA
*
2720493 CATCAATTT-T--T
65 TATCAATTTCTCAT
* * * * *
2720504 TATCGAGGATACTCCAACCCCATTATTTTCGAGGGGATACCCCAACCTCGGCTTTATTTCTAAAA
1 AATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACC-CGGTTTTATTTCTAAAA
*
2720569 TATTAATTTCTCAT
65 TATCAATTTCTCAT
* *
2720583 AATCGGGGAAACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAA
1 AATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAA-CCCGGTTTTATTTCTAAAA
* *
2720648 CATCAATTTTTCAT
65 TATCAATTTCTCAT
* * *
2720662 AGTCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAATCCCGATTTTATTTCT-AAA
1 AATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAA-CCCGGTTTTATTTCTAAAA
* * *
2720726 TCATCGATTTTTCAC
65 T-ATCAATTTCTCAT
* * *
2720741 AATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGTTATTATCTCCAAAA
1 AATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCGGTT-TTATTTCTAAAA
*
2720806 TATTAAATTTCTC
65 TA-TCAATTTCTC
2720819 GTCGAGAGAT
Statistics
Matches: 271, Mismatches: 35, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
75 2 0.01
76 62 0.23
77 1 0.00
78 8 0.03
79 185 0.68
80 13 0.05
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (78 bp):
AATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCGGTTTTATTTCTAAAAT
ATCAATTTCTCAT
Found at i:2720760 original size:158 final size:155
Alignment explanation
Indices: 2720381--2720790 Score: 576
Period size: 158 Copynumber: 2.6 Consensus size: 155
2720371 TTCCATAATC
* * *
2720381 GGGGATACTCCAACTCTGATTTTATTT-TCAAAA-CACCGACTTTTCACAATCGGGGATACTCCA
1 GGGGATACTCCAAC-CCGATTTTATTTCT-AAAATCATCGATTTTTCACAATCGGGGATACTCCA
*
2720444 ACCCCGTTATTTTCGAGGGGACACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTTATCG
64 ACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTTATCG
*
2720509 AGGATACTCCAACCCCATTATTTTCGA
129 AGGATACTCCAACCCCATTATTTCCGA
* ** ** * * *
2720536 GGGGATACCCCAACCTCGGCTTTATTTCTAAAAT-ATTAATTTCTCATAATCGGGGAAACTCCAA
1 GGGGATACTCCAACC-CGATTTTATTTCTAAAATCATCGATTTTTCACAATCGGGGATACTCCAA
* *
2720600 CCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAGT
65 CCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTT--TA-T
* *
2720665 CGGGGATACTCCAACCCCGTTATTTCCGA
127 CGAGGATACTCCAACCCCATTATTTCCGA
2720694 GGGGATACTCCAATCCCGATTTTATTTCT-AAATCATCGATTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAA-CCCGATTTTATTTCTAAAATCATCGATTTTTCACAATCGGGGATACTCCAA
2720758 CCCCGTTATTTTCGAGGGGATACTCCAACCCCG
65 CCCCGTTATTTTCGAGGGGATACTCCAACCCCG
2720791 TTATTATCTC
Statistics
Matches: 221, Mismatches: 26, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
154 1 0.00
155 104 0.47
156 1 0.00
157 6 0.03
158 107 0.48
159 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (155 bp):
GGGGATACTCCAACCCGATTTTATTTCTAAAATCATCGATTTTTCACAATCGGGGATACTCCAAC
CCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTTATCGAG
GATACTCCAACCCCATTATTTCCGA
Found at i:2728628 original size:13 final size:13
Alignment explanation
Indices: 2728602--2728628 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2728592 TACAAAACTT
2728602 ATGTATCGATACA
1 ATGTATCGATACA
2728615 ATGTATCGATACA
1 ATGTATCGATACA
2728628 A
1 A
2728629 ATTGTTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2730540 original size:55 final size:55
Alignment explanation
Indices: 2730334--2730959 Score: 613
Period size: 55 Copynumber: 10.8 Consensus size: 55
2730324 GCTTTTTTCT
*
2730334 TTTC-AAGCCCACACGAGTTGGTGGCACATTTT--AGTCCTCAAAGAGCAGGACGTTTTTTCC
1 TTTCAAAGCCCACACAAGTTGGTGG--CATTTTCCAGTCCTCAAAGAGCAGGACG------CC
* * * *
2730394 -TTCTGAAGCCCATACAAGTTGGTGGCACTTTTCTAGTCCTTAAAGAGCAGGACGCC
1 TTTC-AAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCC
*
2730450 TTTTCATTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAACAGGACGCC
1 -TTTC-----AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC
* *
2730511 TTTCAAAGCCCGCACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAACAGGACGCC
1 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC
* *
2730566 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTTAAAGAGCAGGATGCC
1 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC
*
2730621 TTTTCATTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAACAGGACGCC
1 -TTTC-----AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC
2730682 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC
1 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC
* *
2730737 TTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGATGCC
1 TTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCC
* *** * *
2730792 -TTCAAAGCCCACACGAGTTGGTGGCACACTCCAGTCCTCAAAGAGAAGGATGCATTTTTTC
1 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGC-------C
* * *
2730853 TTTTTAAAGCCCACTCAAGTTGGTGGCACCTTT--AGTCCTCAAAGAGCAGGACGCCTTTACC
1 -TTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACG------CC
* **
2730914 TTTCAAAGCCTACACAAGTTGGTGGCA-CCTCCTAGTCCTCAAAGAG
1 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCC-AGTCCTCAAAGAG
2730960 TATGACACAC
Statistics
Matches: 493, Mismatches: 35, Indels: 75
0.82 0.06 0.12
Matches are distributed among these distances:
53 2 0.00
54 46 0.09
55 200 0.41
56 9 0.02
58 4 0.01
59 5 0.01
60 36 0.07
61 106 0.22
62 59 0.12
63 23 0.05
64 2 0.00
68 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (55 bp):
TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC
Found at i:2730641 original size:171 final size:172
Alignment explanation
Indices: 2730399--2730793 Score: 713
Period size: 171 Copynumber: 2.3 Consensus size: 172
2730389 TTTCCTTCTG
* * *
2730399 AAGCCCATACAAGTTGGTGGCACTTTTCTAGTCCTTAAAGAGCAGGACGCCTTTTCATTTTAAAG
1 AAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTTAAAGAGCAGGATGCCTTTTCATTTTAAAG
*
2730464 CCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAACAGGACGCCTTTCAAAGCCCGCACAAG
66 CCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAACAGGACGCCTTTCAAAGCCCACACAAG
2730529 TTGGTGGCATTTTCCAGTCCTCAAAGAACAGGACGCCTTTCA
131 TTGGTGGCATTTTCCAGTCCTCAAAGAACAGGACGCCTTTCA
2730571 AAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTTAAAGAGCAGGATGCCTTTTCATTTTAAAG
1 AAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTTAAAGAGCAGGATGCCTTTTCATTTTAAAG
2730635 CCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAACAGGACGCCTTTCAAAGCCCACACAAG
66 CCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAACAGGACGCCTTTCAAAGCCCACACAAG
*
2730700 TTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCA
131 TTGGTGGCATTTTCCAGTCCTCAAAGAACAGGACGCCTTTCA
* *
2730742 AAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGATGCCTT
1 AAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTTAAAGAGCAGGATGCCTT
2730794 CAAAGCCCAC
Statistics
Matches: 215, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
171 191 0.89
172 24 0.11
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (172 bp):
AAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTTAAAGAGCAGGATGCCTTTTCATTTTAAAG
CCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAACAGGACGCCTTTCAAAGCCCACACAAG
TTGGTGGCATTTTCCAGTCCTCAAAGAACAGGACGCCTTTCA
Found at i:2730650 original size:116 final size:115
Alignment explanation
Indices: 2730334--2731266 Score: 695
Period size: 116 Copynumber: 8.0 Consensus size: 115
2730324 GCTTTTTTCT
* **
2730334 TTTC-AAGCCCACACGAGTTGGTGGCACATTTT--AGTCCTCAAAGAGCAGGACGTTTTTTCCTT
1 TTTCAAAGCCCACACAAGTTGGTGG--CATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT-CTT
* * * *
2730396 CTGAAGCCCATACAAGTTGGTGGCACTTTTCTAGTCCTTAAAGAGCAGGACGCC
63 -TAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCC
*
2730450 TTTTCATTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAACAGGACGCC-TTT
1 -TTTC-----AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
* *
2730514 C---AAAGCCCGCACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAACAGGACGCC
60 CTTTAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCC
* *
2730566 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTTAAAGAGCAGGATGCCTTTTCATTTT
1 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTC--TTT
*
2730631 AAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAACAGGACGCC
64 AAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCC
2730682 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC-TTTC---AA
1 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTAA
* *
2730743 AGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGATGCC
66 AGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCC
* *** * * *
2730792 -TTCAAAGCCCACACGAGTTGGTGGCACACTCCAGTCCTCAAAGAGAAGGATGCATTTTTTCTTT
1 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGC--CTTTTC--T
* *
2730856 TTAAAGCCCACTCAAGTTGGTGGCACCTTT--AGTCCTCAAAGAGCAGGACGCCTTTACC
62 TTAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACG------CC
* ** * * * *
2730914 TTTCAAAGCCTACACAAGTTGGTGGCA-CCTCCTAGTCCTCAAAGAGTATGACACACTTTATTCC
1 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCC-AGTCCTCAAAGAGCAGGACGC-C-TT-TTCT
***** * * * ** * ** ***
2730978 CCCTTGTCCTCA-AAG--AGTAGGACACACTT-CATTTCCT------TTATTTC-CC
62 TTAAAGCCCACACAAGTTGGT-GG-CACTTTTCCA-GTCCTCAAAGAGCAGGACGCC
* * * * * *
2731024 TTTTAAGGCCCACACAAGTTGGTAGCACTTTTCTAGTCCTCAAAGAGCAGGGCACCTTTTCCTTT
1 TTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT-CTTT
* ** *
2731089 CAAAGCCCACACAAGTTGGGGGCA-TTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCC
64 -AAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGA---C---GCC
* * * * * *
2731147 TTTCAAAGCCCACAAAAGTTGATGGCATTTTCTAGTCCTCAAAGAGTAGGATGCTTTTTCTTTGC
1 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTT--
* * *
2731212 AAAGCCCACACAAGTTGGTGGCAC-CTTCCAGTCCTCAAAGAGTAGGATGCC
64 AAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCC
2731263 TTTC
1 TTTC
2731267 CTTTTCAAAG
Statistics
Matches: 655, Mismatches: 101, Indels: 121
0.75 0.12 0.14
Matches are distributed among these distances:
108 2 0.00
109 50 0.08
110 129 0.20
111 31 0.05
112 8 0.01
113 1 0.00
115 8 0.01
116 154 0.24
117 53 0.08
119 3 0.00
120 2 0.00
121 19 0.03
122 83 0.13
123 109 0.17
124 3 0.00
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (115 bp):
TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTAA
AGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCC
Found at i:2730892 original size:171 final size:167
Alignment explanation
Indices: 2730334--2730959 Score: 664
Period size: 171 Copynumber: 3.6 Consensus size: 167
2730324 GCTTTTTTCT
*
2730334 TTTC-AAGCCCACACGAGTTGGTGGCACATTTT-AGTCCTCAAAGAGCAGGACGTTTTTTCC-TT
1 TTTCAAAGCCCACACAAGTTGGTGG--CATTTTCAGTCCTCAAAGAGCAGGACG-----TCCTTT
* * * * *
2730396 CTGAAGCCCATACAAGTTGGTGGCACTTTTCTAGTCCTTAAAGAGCAGGACGCCTTTTCATTTTA
59 C-AAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGATGCC-TTTC----TA
2730461 AAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAACAGGACGCC
118 AAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAACAGGACGCC
* *
2730511 TTTCAAAGCCCGCACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAACAGGACG-CCTTTCAAAGC
1 TTTCAAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAGCAGGACGTCCTTTCAAAGC
* * *
2730575 CCACACAAGTTGGTGGCA-TTTTCCAGTCCTTAAAGAGCAGGATGCCTTTTCATTTTAAAGCCCA
65 CCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGATGCC-TTTC----TAAAGCCCA
2730639 CACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAACAGGACGCC
125 CACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAACAGGACGCC
2730682 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG-CCTTTCAAAGC
1 TTTCAAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAGCAGGACGTCCTTTCAAAGC
*
2730746 CCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGATGCC-TTC-AAAGCCCACACGA
65 CCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGATGCCTTTCTAAAGCCCACACAA
*** *
2730808 GTTGGTGGCACACTCCAGTCCTCAAAGAGA-AGGATGCATTTTTTC
130 GTTGGTGGCATTTTCCAGTCCTCAAAGA-ACAGGACGC-------C
* * *
2730853 TTTTTAAAGCCCACTCAAGTTGGTGGCACCTTT-AGTCCTCAAAGAGCAGGACGCCTTTACCTTT
1 -TTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGACG----T-CCTTT
* *
2730917 CAAAGCCTACACAAGTTGGTGGCACC-TCCTAGTCCTCAAAGAG
59 CAAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAG
2730960 TATGACACAC
Statistics
Matches: 406, Mismatches: 21, Indels: 44
0.86 0.04 0.09
Matches are distributed among these distances:
164 43 0.11
165 1 0.00
169 3 0.01
171 209 0.51
172 52 0.13
173 6 0.01
176 8 0.02
177 47 0.12
178 37 0.09
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (167 bp):
TTTCAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGCAGGACGTCCTTTCAAAGCC
CACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGATGCCTTTCTAAAGCCCACACAAG
TTGGTGGCATTTTCCAGTCCTCAAAGAACAGGACGCC
Found at i:2731143 original size:61 final size:61
Alignment explanation
Indices: 2731022--2731327 Score: 375
Period size: 61 Copynumber: 5.0 Consensus size: 61
2731012 CCTTTATTTC
* * * * ***
2731022 CCTTTTAAGGCCCACACAAGTTGGTAGCACTTTTCTAGTCCTCAAAGAGCAGGGCACCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGTAGGATGCCTTTT
* * *
2731084 CCTTTCAAAGCCCACACAAGTTGGGGGCATTTTTTAGTCCTCAAAGAGCAGGATGCCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGTAGGATGCCTTTT
* *
2731145 CCTTTCAAAGCCCACAAAAGTTGATGGCATTTTCTAGTCCTCAAAGAGTAGGATG-CTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGTAGGATGCCTTTT
* ** *
2731205 TCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGTAGGATGCC-TTT
1 CCTTT-CAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGTAGGATGCCTTTT
* **
2731266 CCTTTTCAAAGCCCACACAAATTGGTGGCA-CCTCTTAGTCCTCAAAGAGTAGGATGCACTTT
1 CC-TTTCAAAGCCCACACAAGTTGGTGGCATTTTC-TAGTCCTCAAAGAGTAGGATGC-CTTT
2731328 ATTCCCCCTT
Statistics
Matches: 215, Mismatches: 23, Indels: 11
0.86 0.09 0.04
Matches are distributed among these distances:
60 12 0.06
61 171 0.80
62 30 0.14
63 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (61 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGTAGGATGCCTTTT
Found at i:2731380 original size:355 final size:355
Alignment explanation
Indices: 2730332--2731685 Score: 1377
Period size: 355 Copynumber: 3.9 Consensus size: 355
2730322 ACGCTTTTTT
* * * * ***
2730332 CTTTTCAAGCCCACACGAGTTGGTGGCACATTT-TAGTCCTCAAAGAGCAGGACGTTTTTTCC-T
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGGCACCTTTTCCTT
* * * * * * *
2730395 TCTGAAGCCCATACAAGTTGGTGGCACTTTTCTAGTCCTTAAAGAGCAGGACGCCTTTTCATTTT
66 TC-AAAGCCCACACAAGTTGGTGGCA-TTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTC
*
2730460 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGA-ACAGGACGC-----CTTT-CAAA
129 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGA-AGGATGCTTTTTCTTTGCAAA
* ** * *
2730518 GCCCGCACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAACAGGA---C--GCC-TTTCAAAGCCC
193 GCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCCTTTCCTTTTCAAAGCCC
* * * * *** *
2730577 ACACAAGTTGGTGGCA--TTTTCCAGTCCTTAAAGAGCAGGATGC-C-TT-TT-CATTTTAAAGC
258 ACACAAGTTGGTGGCACCTCTT--AGTCCTCAAAGAGTAGGACGCACTTTATTCCCCCTT---GT
* * ** ** * ** ***
2730636 CCACACAAGTTGGTGG-CA-TTTTCCA-GTCCTCAAAGAACAGGACGC
318 CCTCA-AAG-AGAAGGACACACTT-CATTTCCT------TTATTTC-C
* * *
2730681 CTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCA-GG-A-C---GCCTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGGCACCTTTTCCTT
** *
2730739 TCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATG------CC-TTCAA
66 TCAAAGCCCACACAAGTTGGTGGCATTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTCAA
* *** **
2730797 AGCCCACACGAGTTGGTGGCACACTCCAGTCCTCAAAGAGAAGGATGCATTTTTTCTTTTTAAAG
131 AGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGAAGGATGC--TTTTTCTTTGCAAAG
* * * *
2730862 CCCACTCAAGTTGGTGGCACCTT-TAGTCCTCAAAGAGCAGGACGCCTTTACC-TTTCAAAGCCT
194 CCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCCTTT-CCTTTTCAAAGCCC
* * *
2730925 ACACAAGTTGGTGGCACCTCCTAGTCCTCAAAGAGTATGACACACTTTATTCCCCCTTGTCCTCA
258 ACACAAGTTGGTGGCACCTCTTAGTCCTCAAAGAGTAGGACGCACTTTATTCCCCCTTGTCCTCA
*
2730990 AAGAGTAGGACACACTTCATTTCCTTTATTTCC
323 AAGAGAAGGACACACTTCATTTCCTTTATTTCC
* *
2731023 CTTTTAAGGCCCACACAAGTTGGTAGCACTTTTCTAGTCCTCAAAGAGCAGGGCACCTTTTCCTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGGCACCTTTTCCTT
*
2731088 TCAAAGCCCACACAAGTTGGGGGCATTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTCAA
66 TCAAAGCCCACACAAGTTGGTGGCATTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTCAA
* * * *
2731153 AGCCCACAAAAGTTGATGGCATTTTCTAGTCCTCAAAGAGTAGGATGCTTTTTCTTTGCAAAGCC
131 AGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGAAGGATGCTTTTTCTTTGCAAAGCC
*
2731218 CACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGTAGGATGCCTTTCCTTTTCAAAGCCCACA
196 CACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCCTTTCCTTTTCAAAGCCCACA
* *
2731283 CAAATTGGTGGCACCTCTTAGTCCTCAAAGAGTAGGATGCACTTTATTCCCCCTTGTCCTCAAAG
261 CAAGTTGGTGGCACCTCTTAGTCCTCAAAGAGTAGGACGCACTTTATTCCCCCTTGTCCTCAAAG
* *
2731348 AGAAGGACGCATTTCATTTCCTTCT-TTTCC
326 AGAAGGACACACTTCATTTCCTT-TATTTCC
** * * *
2731378 CTTTTAAAGCCTGCACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCGTTTTCCTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGGCACCTTTTCCTT
* * *
2731443 TCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGTAAGATGCCTTTTCCTTTCAA
66 TCAAAGCCCACACAAGTTGGTGGCATTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTCAA
* * *
2731508 AGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGATTTCTCTTTGCAAAGCC
131 AGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGAAGGATGCTTTTTCTTTGCAAAGCC
* * * * *
2731573 CTCACAAGTTGGTGGCGCCTTCCAGTCCTCAAAAAGCAGGATGCTTTTCCTTTCCAAAGCCCACA
196 CACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCCTTTCCTTTTCAAAGCCCACA
* * * * **
2731638 CGAGTTGGTGACACTTTTTAGTCCTCAAAGAGCGGGACGCACTTTATT
261 CAAGTTGGTGGCACCTCTTAGTCCTCAAAGAGTAGGACGCACTTTATT
2731686 TTCTTCTTTC
Statistics
Matches: 843, Mismatches: 119, Indels: 80
0.81 0.11 0.08
Matches are distributed among these distances:
335 45 0.05
336 2 0.00
342 67 0.08
343 68 0.08
344 5 0.01
345 2 0.00
346 1 0.00
347 3 0.00
348 55 0.07
349 103 0.12
350 4 0.00
351 2 0.00
352 3 0.00
354 37 0.04
355 400 0.47
356 46 0.05
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.28
Consensus pattern (355 bp):
CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGGCACCTTTTCCTT
TCAAAGCCCACACAAGTTGGTGGCATTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTCAA
AGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGAAGGATGCTTTTTCTTTGCAAAGCC
CACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCCTTTCCTTTTCAAAGCCCACA
CAAGTTGGTGGCACCTCTTAGTCCTCAAAGAGTAGGACGCACTTTATTCCCCCTTGTCCTCAAAG
AGAAGGACACACTTCATTTCCTTTATTTCC
Found at i:2731418 original size:294 final size:292
Alignment explanation
Indices: 2731079--2731616 Score: 812
Period size: 294 Copynumber: 1.8 Consensus size: 292
2731069 AGCAGGGCAC
* *
2731079 CTTTTCCTTTCAAAGCCCACACAAGTTGGGGGCATTTTTTAGTCCTCAAAGAGCAGGATGCCTTT
1 CTTTTCCTTTCAAAGCCCACACAAGTTGGGGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTT
* *
2731144 TCCTTTCAAAGCCCACAAAAGTTGATGGCATTTTCTAGTCCTCAAAGAGTAGGATG-CTTTTTCT
66 TCCTTTCAAAGCCCACAAAAGTTGATGGCATTTTCTAGTCCTCAAAGAGTAAGATGCCTTTTCCT
* * *
2731208 TTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGTAGGATGCCTTTC-CTTTT
131 TT-CAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATG-ATTTCTCTTTG
* * *
2731272 CAAAGCCCACACAAATTGGTGGCACC-TCTTAGTCCTCAAAGAGTAGGATGCACTTTATTCCCCC
194 CAAAGCCCACACAAATTGGTGGCACCTTC-CAGTCCTCAAAAAGCAGGATGCACTTTATTCCCCC
2731336 TTGTCCTCAAAGAGAAGGACGCATTTCATTTCCTT
258 TTGTCCTCAAAGAGAAGGACGCATTTCATTTCCTT
* ** * *
2731371 CTTTTCCCTTTTAAAGCCTGCACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCGT
1 CTTTT-CCTTTCAAAGCCCACACAAGTTGGGGGCA-TTTTCTAGTCCTCAAAGAGCAGGACGCCT
* *
2731436 TTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGTAAGATGCCTTTTC
64 TTTCCTTTCAAAGCCCACAAAAGTTGATGGCATTTTCTAGTCCTCAAAGAGTAAGATGCCTTTTC
**
2731501 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGATTTCTCTTTG
129 CTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGATTTCTCTTTG
* * *
2731566 CAAAGCCCTCACAAGTTGGTGGCGCCTTCCAGTCCTCAAAAAGCAGGATGC
194 CAAAGCCCACACAAATTGGTGGCACCTTCCAGTCCTCAAAAAGCAGGATGC
2731617 TTTTCCTTTC
Statistics
Matches: 219, Mismatches: 22, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
292 5 0.02
293 29 0.13
294 174 0.79
295 11 0.05
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (292 bp):
CTTTTCCTTTCAAAGCCCACACAAGTTGGGGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTT
TCCTTTCAAAGCCCACAAAAGTTGATGGCATTTTCTAGTCCTCAAAGAGTAAGATGCCTTTTCCT
TTCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGATTTCTCTTTGCA
AAGCCCACACAAATTGGTGGCACCTTCCAGTCCTCAAAAAGCAGGATGCACTTTATTCCCCCTTG
TCCTCAAAGAGAAGGACGCATTTCATTTCCTT
Found at i:2731502 original size:61 final size:60
Alignment explanation
Indices: 2731371--2731670 Score: 370
Period size: 61 Copynumber: 4.9 Consensus size: 60
2731361 TCATTTCCTT
* ** *
2731371 CTTTTCCCTTTTAAAGCCTGCACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACG
1 CTTTT-CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGATG
* *
2731433 CGTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGTAAGATG
1 C-TTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATG
*
2731494 CCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATG
1 -CTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATG
* * *** * *
2731555 -ATTTCTCTTTGCAAAGCCCTCACAAGTTGGTGGCGCCTTCCAGTCCTCAAAAAGCAGGATG
1 CTTTTC-CTTT-CAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATG
* *
2731616 CTTTTCCTTTCCAAAGCCCACACGAGTTGGTGACACTTTT-TAGTCCTCAAAGAGC
1 CTTTTCCTTT-CAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGC
2731671 GGGACGCACT
Statistics
Matches: 207, Mismatches: 25, Indels: 13
0.84 0.10 0.05
Matches are distributed among these distances:
59 4 0.02
60 4 0.02
61 161 0.78
62 34 0.16
63 4 0.02
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (60 bp):
CTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATG
Found at i:2732583 original size:20 final size:20
Alignment explanation
Indices: 2732558--2732681 Score: 92
Period size: 20 Copynumber: 5.8 Consensus size: 20
2732548 TTTTCACAAT
2732558 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
*
2732578 TTGTATCAATACATTATGGGTTTACCCA
1 TTGTATCGATACA-T-T--G-TT---CA
*
2732606 GATGTATCGATACATT-TTGCA
1 -TTGTATCGATACATTGTT-CA
*
2732627 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
2732647 TTGTATCGATACATT-TT-A
1 TTGTATCGATACATTGTTCA
2732665 TAATGTATCGATACATT
1 T--TGTATCGATACATT
2732682 CAGGCATTTT
Statistics
Matches: 85, Mismatches: 7, Indels: 24
0.73 0.06 0.21
Matches are distributed among these distances:
18 2 0.02
19 1 0.01
20 57 0.67
21 4 0.05
22 1 0.01
23 2 0.02
24 1 0.01
25 2 0.02
27 1 0.01
28 3 0.04
29 11 0.13
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:2735067 original size:51 final size:51
Alignment explanation
Indices: 2734972--2735076 Score: 131
Period size: 51 Copynumber: 2.1 Consensus size: 51
2734962 ATTTTTCATC
* * * *
2734972 TCGGGGATACTCCAATCCTGGTTTCATTTCCAAAACATCAATTTTTCTTAA
1 TCGGGGATACTCCAATCCTGATTTCATTTCCAAAACACCAATTTTCCATAA
* * *
2735023 TCGGGGATACTCCAACTCC-GATTTTATTTCTAAAACACCCATTTTCCATAA
1 TCGGGGATACTCCAA-TCCTGATTTCATTTCCAAAACACCAATTTTCCATAA
2735074 TCG
1 TCG
2735077 AGATCTGAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
51 43 0.93
52 3 0.07
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (51 bp):
TCGGGGATACTCCAATCCTGATTTCATTTCCAAAACACCAATTTTCCATAA
Found at i:2738030 original size:8 final size:8
Alignment explanation
Indices: 2738019--2738076 Score: 53
Period size: 8 Copynumber: 6.8 Consensus size: 8
2738009 TACCAAAAAG
2738019 AAAAAACA
1 AAAAAACA
2738027 AAAAAACCA
1 AAAAAA-CA
*
2738036 AAAAACCAAA
1 AAAAA--ACA
*
2738046 AAAAAATAA
1 AAAAAA-CA
2738055 AAAAAACA
1 AAAAAACA
*
2738063 AACAAACA
1 AAAAAACA
2738071 AAAAAA
1 AAAAAA
2738077 GGGTCCAGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 20 0.48
9 15 0.36
10 6 0.14
11 1 0.02
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.02
Consensus pattern (8 bp):
AAAAAACA
Found at i:2738057 original size:27 final size:27
Alignment explanation
Indices: 2738019--2738076 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
2738009 TACCAAAAAG
*
2738019 AAAAAACAAAAAAACCAAA-AAACCAAA
1 AAAAAACAAAAAAAACAAACAAA-CAAA
*
2738046 AAAAAATAAAAAAAACAAACAAACAAA
1 AAAAAACAAAAAAAACAAACAAACAAA
2738073 AAAA
1 AAAA
2738077 GGGTCCAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.89
28 3 0.11
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.02
Consensus pattern (27 bp):
AAAAAACAAAAAAAACAAACAAACAAA
Found at i:2739312 original size:28 final size:28
Alignment explanation
Indices: 2739269--2739608 Score: 365
Period size: 28 Copynumber: 11.9 Consensus size: 28
2739259 CATTCATCTC
* *
2739269 TTCAAAGCCCATAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
2739297 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
2739325 TTCAAAGCCCACACGAGTCGGTGGCAACTCTT
1 TTCAAAGCCCACA--AGTCAGTGGC-AC-CCT
* * * *
2739357 TTCAAAGCCCATAACTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* **
2739385 TTCAAAGCCAACAAGTCAGCAGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
2739413 TTCAAAGCCCACAAGTTAGTGGCACCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
2739441 TTCAAAGCCCACAAGTCAGTGGCATTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCCT
* * *
2739470 TTCAAAGCCCACAAGTTAGTGGTATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
2739498 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * * * *
2739526 TTCACAGCCTACAAGCCAGTGGAACCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
2739554 TTCAAAGCCCACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
2739583 TTTAAAGCCCGCACGAGTCAGTGGCA
1 TTCAAAG-CC-CACAAGTCAGTGGCA
2739609 ACTCTTTTCA
Statistics
Matches: 261, Mismatches: 43, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
28 179 0.69
29 35 0.13
30 18 0.07
31 15 0.06
32 14 0.05
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:2739523 original size:113 final size:113
Alignment explanation
Indices: 2739269--2739592 Score: 459
Period size: 113 Copynumber: 2.8 Consensus size: 113
2739259 CATTCATCTC
* * *
2739269 TTCAAAGCCCATAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCC
* *
2739334 CACACGAGTCGGTGGCAACTCTTTTCAAAGCCCATAACTTAGTGGCATCCT
66 CACA--AGTCAGTGGC-ACTCTTTTCAAAGCCCACAACTTAGTGGCATCCT
* ** *
2739385 TTCAAAGCCAACAAGTCAGCAGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCC
* * *
2739450 CACAAGTCAGTGGCATTCTTTTCAAAGCCCACAAGTTAGTGGTATCCT
66 CACAAGTCAGTGGCACTCTTTTCAAAGCCCACAACTTAGTGGCATCCT
* * * *
2739498 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCACAGCCTACAAGCCAGTGGAACCTTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCC
* *
2739563 CACAAGTTAGTGGCACTCTTTTTAAAGCCC
66 CACAAGTCAGTGGCACTCTTTTCAAAGCCC
2739593 GCACGAGTCA
Statistics
Matches: 185, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
113 114 0.62
114 9 0.05
116 62 0.34
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (113 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCC
CACAAGTCAGTGGCACTCTTTTCAAAGCCCACAACTTAGTGGCATCCT
Found at i:2739638 original size:32 final size:32
Alignment explanation
Indices: 2739281--2739652 Score: 125
Period size: 28 Copynumber: 12.8 Consensus size: 32
2739271 CAAAGCCCAT
* *
2739281 AAGTTAGTGGC-AC-CCTTTCAAAG-CC-CAC
1 AAGTTAGTGGCAACTCTTTTTAAAGCCCACAC
* * *
2739309 AAGTCAGTGGC-AC-CCTTTCAAAGCCCACAC
1 AAGTTAGTGGCAACTCTTTTTAAAGCCCACAC
* ** * *
2739339 GAGTCGGTGGCAACTCTTTTCAAAG-CC-CAT
1 AAGTTAGTGGCAACTCTTTTTAAAGCCCACAC
* * *
2739369 AACTTAGTGGC-A-TCCTTTCAAAG-CCA-AC
1 AAGTTAGTGGCAACTCTTTTTAAAGCCCACAC
* ** * *
2739397 AAGTCAGCAGC-AC-CCTTTCAAAG-CC-CAC
1 AAGTTAGTGGCAACTCTTTTTAAAGCCCACAC
*
2739425 AAGTTAGTGGC-AC-CTTTTCAAAG-CC-CAC
1 AAGTTAGTGGCAACTCTTTTTAAAGCCCACAC
* * *
2739453 AAGTCAGTGGC-ATTCTTTTCAAAG-CC-CAC
1 AAGTTAGTGGCAACTCTTTTTAAAGCCCACAC
* * *
2739482 AAGTTAGTGG-TA-TCCTTTCAAAG-CC-CAC
1 AAGTTAGTGGCAACTCTTTTTAAAGCCCACAC
* * * * *
2739510 AAGTCAGTGGC-AC-CCTTTCACAG-CC-TAC
1 AAGTTAGTGGCAACTCTTTTTAAAGCCCACAC
** *
2739538 AAGCCAGTGG-AAC-CTTTTCAAAG-CC-CAC
1 AAGTTAGTGGCAACTCTTTTTAAAGCCCACAC
*
2739566 AAGTTAGTGGC-ACTCTTTTTAAAGCCCGCAC
1 AAGTTAGTGGCAACTCTTTTTAAAGCCCACAC
* * *
2739597 GAGTCAGTGGCAACTC-TTTTCAAGTCCCACAC
1 AAGTTAGTGGCAACTCTTTTTAAAG-CCCACAC
* *
2739629 AAGTTAGTGGCACCTTTTTTTAAA
1 AAGTTAGTGGCAACTCTTTTTAAA
2739653 AAAACCCTAC
Statistics
Matches: 283, Mismatches: 42, Indels: 33
0.79 0.12 0.09
Matches are distributed among these distances:
28 163 0.58
29 37 0.13
30 23 0.08
31 23 0.08
32 31 0.11
33 6 0.02
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (32 bp):
AAGTTAGTGGCAACTCTTTTTAAAGCCCACAC
Found at i:2745417 original size:52 final size:52
Alignment explanation
Indices: 2745332--2745456 Score: 216
Period size: 52 Copynumber: 2.4 Consensus size: 52
2745322 ATATGAAAAG
* *
2745332 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
2745384 TTGCCTGCATGTATCGATACATTATAA-AATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATT-TAATAATGTATCGATACATCTGGGCAAAT
2745436 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
2745457 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
52 67 0.96
53 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:2745469 original size:52 final size:50
Alignment explanation
Indices: 2745332--2745476 Score: 193
Period size: 52 Copynumber: 2.8 Consensus size: 50
2745322 ATATGAAAAG
* *
2745332 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGCAAAT
*
2745384 TTGCCTGCATGTATCGATACATTATAA-AATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--A-AATAGTGTATCGATACATCTGGGCAAAT
2745436 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
2745477 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
49 1 0.01
50 2 0.02
52 80 0.94
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (50 bp):
TTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGCAAAT
Found at i:2745483 original size:13 final size:13
Alignment explanation
Indices: 2745465--2745489 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2745455 CAAAGATCAG
2745465 TGTATCGATACAA
1 TGTATCGATACAA
2745478 TGTATCGATACA
1 TGTATCGATACA
2745490 TTCGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2745572 original size:13 final size:13
Alignment explanation
Indices: 2745554--2745578 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2745544 AAAAAAAATA
2745554 TGTATCGATACAT
1 TGTATCGATACAT
2745567 TGTATCGATACA
1 TGTATCGATACA
2745579 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2746894 original size:13 final size:13
Alignment explanation
Indices: 2746872--2746929 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
2746862 GGCAGTAGCT
*
2746872 TTGTAGCGATACA
1 TTGTATCGATACA
2746885 TTGTATCGATACAAAA
1 TTGTATCGATAC---A
2746901 CTTATGTATCGATACA
1 --T-TGTATCGATACA
2746917 TTGTATCGATACA
1 TTGTATCGATACA
2746930 AATTGTTGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2747764 original size:20 final size:20
Alignment explanation
Indices: 2747741--2747845 Score: 84
Period size: 20 Copynumber: 4.7 Consensus size: 20
2747731 AAGTACCTAG
2747741 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
2747761 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
2747781 ATGTATCGATACATTCTATCTTTTTACCCA
1 ATGTATCGAT--A--C-A--TTTTT---CA
2747811 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
2747832 ATGTATCGATACAT
1 ATGTATCGATACAT
2747846 CTAGTTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
20 41 0.60
21 2 0.03
22 1 0.01
24 6 0.09
25 1 0.01
26 1 0.01
27 4 0.06
29 1 0.01
30 1 0.01
31 10 0.15
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:2750116 original size:24 final size:24
Alignment explanation
Indices: 2750089--2750137 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2750079 GTCATCATCG
2750089 GGGACACTCCAACCCCATTCCTCC
1 GGGACACTCCAACCCCATTCCTCC
2750113 GGGACACTCCAACCCCATTCCTCC
1 GGGACACTCCAACCCCATTCCTCC
2750137 G
1 G
2750138 AGGGGATACT
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:0.20, C:0.49, G:0.14, T:0.16
Consensus pattern (24 bp):
GGGACACTCCAACCCCATTCCTCC
Found at i:2752464 original size:156 final size:155
Alignment explanation
Indices: 2751890--2752461 Score: 470
Period size: 156 Copynumber: 3.7 Consensus size: 155
2751880 TTTTAAAAGG
* * * * *
2751890 GATGAACCTATCCTAAATGCCCACCTTCGACATAAAAGC-AGACCCGGTGACAACTTAAGACTTG
1 GATGAACCTATCCTAAATACCCACCTTCGACATAAAAGCGAAACCTGGTGACAACCTAAGACTCG
* * * * * *
2751954 GTTCA-AAAAAATTACGAAAATGCCCC-AAGGAAATACCTTCAATGTAAAAGTA-ACTG-ACACC
66 ATT-ATAAAAAATTACTAAAATGCCCCTAAGG-GATACCTTTAACGTAAAAGTATCCTGTA-ACC
* *
2752015 CTTAAAGGACATAAAAAGGATTATAGATGA
128 C-TAAAGGACTTAAAAA-GATTAGAGATGA
* * * ** *
2752045 GATGAACCAATCCTAAATACCCACCTTCGATATAAAAGCG-GACCCAGTGACAACCTAGGACTCG
1 GATGAACCTATCCTAAATACCCACCTTCGACATAAAAGCGAAACCTGGTGACAACCTAAGACTCG
* * * *
2752109 ATTCTAAAAAATTA-TAAAAATGCCCCTATAGGTATA-CTTTCAATGTGAAAA-TATCCCGATAA
66 ATTATAAAAAATTACT-AAAATGCCCCTA-AGGGATACCTTT-AACGT-AAAAGTATCCTG-TAA
*
2752171 CCCTAAATGACTTAAAAAGATTAGAGATGA
126 CCCTAAAGGACTTAAAAAGATTAGAGATGA
* * * * * * *
2752201 GATGAGCCTATCCTAAATACCCACATTC-AGCACAAAA-CGGAACCTGGTGACAACATAGGATTC
1 GATGAACCTATCCTAAATACCCACCTTCGA-CATAAAAGCGAAACCTGGTGACAACCTAAGACTC
* * * * * * * * *
2752264 AATTTTAAAAAATCACAAAAATGCCCTTAGGGGTATACTTTTGACGTCAAAGTATCCTAGTAACC
65 GATTATAAAAAATTACTAAAATGCCCCTAAGGG-ATACCTTTAACGTAAAAGTATCCT-GTAACC
2752329 CTAAAGGACTTAAAAAGATTAGA-ACT-A
128 CTAAAGGACTTAAAAAGATTAGAGA-TGA
* * * * * * *
2752356 GGGTGAACCTATCCTAAATGCCTACCTTTGGCATAAAAGC-AAACCTGTTGACAACCTAAGAGTC
1 -GATGAACCTATCCTAAATACCCACCTTCGACATAAAAGCGAAACCTGGTGACAACCTAAGACTC
*
2752420 GGTTATAGAAAAATTACTAAAATGCCCCTAAGGGATACCTTT
65 GATTATA-AAAAATTACTAAAATGCCCCTAAGGGATACCTTT
2752462 GACATATATA
Statistics
Matches: 334, Mismatches: 61, Indels: 43
0.76 0.14 0.10
Matches are distributed among these distances:
155 90 0.27
156 190 0.57
157 49 0.15
158 4 0.01
159 1 0.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (155 bp):
GATGAACCTATCCTAAATACCCACCTTCGACATAAAAGCGAAACCTGGTGACAACCTAAGACTCG
ATTATAAAAAATTACTAAAATGCCCCTAAGGGATACCTTTAACGTAAAAGTATCCTGTAACCCTA
AAGGACTTAAAAAGATTAGAGATGA
Found at i:2758619 original size:31 final size:31
Alignment explanation
Indices: 2758576--2758647 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
2758566 TTGTAAAATA
* *
2758576 TATCAATACATCTGGGTAAAAAGATAGAATG
1 TATCGATACATCTGGGTAAAAAGACAGAATG
*
2758607 TATTGATACATCTGGGTAAAAAGACAGAATG
1 TATCGATACATCTGGGTAAAAAGACAGAATG
2758638 TATCGATACA
1 TATCGATACA
2758648 CTGAAAAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.26
Consensus pattern (31 bp):
TATCGATACATCTGGGTAAAAAGACAGAATG
Found at i:2758659 original size:20 final size:20
Alignment explanation
Indices: 2758634--2758707 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
2758624 AAAAAGACAG
*
2758634 AATGTATCGATACACTGAAA
1 AATGTATCGATACATTGAAA
* * *
2758654 AATGTATCAATACATTCACA
1 AATGTATCGATACATTGAAA
*
2758674 CATGTATCGATACATTG-AA
1 AATGTATCGATACATTGAAA
*
2758693 AATGTATCTATACAT
1 AATGTATCGATACAT
2758708 CTAGGTAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 14 0.32
20 30 0.68
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:2761651 original size:166 final size:163
Alignment explanation
Indices: 2761341--2761841 Score: 605
Period size: 166 Copynumber: 3.0 Consensus size: 163
2761331 AATGACAATG
* * * * *
2761341 TTGGATGAATTTTAAAAATTTTAAATTGAGAAAAATCTCCTCGAAAACATTTATGGAATAGAAAA
1 TTGG-TGAATTTTAAAAATTATAAACTAAGAAAAATCTCCTCG-AAACATTTACGGAGTAGAAAA
* * *
2761406 CTGTGTTTTTCAAAAACATA-AGAATTTTAAAG-AAATATGAAAAACTTATGAAAATAAATGAAT
64 CT-CGTATTTCAAAAACA-AGAGAATTTTAAAGAAAAAATGAAAAACTTAT-AAAATAAATGAAT
*
2761469 TTTTCAAAAATGATTTACTATGAATCAAATGATGATAT
126 TTTTCAAAACTGATTTACTATGAATCAAATGATGATAT
* *
2761507 TTGGTGAATTTTAAAAATTATAAACTAAGAAAAATCTACTCGAAACATTTACAGAGTAGAAAACT
1 TTGGTGAATTTTAAAAATTATAAACTAAGAAAAATCTCCTCGAAACATTTACGGAGTAGAAAACT
* *
2761572 ACGTATTTCAAAAACAAGAGAATTTCAAAAGAAAAAATTAAAAACTTATCAAAATAAATGAATTT
66 -CGTATTTCAAAAACAAGAGAATTT-TAAAGAAAAAATGAAAAACTTAT-AAAATAAATGAATTT
2761637 TTCAAAACTGATTTACTATGAATCAAATGATGATAT
128 TTCAAAACTGATTTACTATGAATCAAATGATGATAT
* * * * * * *
2761673 TTGATGAATTTTAAAAATTATAAACCAAGAAAAATCGCCCCAATAACATTCACGGAGTAGAATAC
1 TTGGTGAATTTTAAAAATTATAAACTAAGAAAAATCTCCTCGA-AACATTTACGGAGTAGAAAAC
* * **
2761738 TCTGTATTTCGAAAACATGA-AATTTTTTTTTA-AAAAAATGAAAAACTTATAAAAGTAAATGAA
65 TC-GTATTTCAAAAACAAGAGAA---TTTTAAAGAAAAAATGAAAAACTTATAAAA-TAAATGAA
* * *
2761801 TTTTTCAAAACTAATTTAGTATGAATTAAATGATGATAT
125 TTTTTCAAAACTGATTTACTATGAATCAAATGATGATAT
2761840 TT
1 TT
2761842 AAAGAATTTT
Statistics
Matches: 293, Mismatches: 33, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
163 1 0.00
164 40 0.14
165 38 0.13
166 113 0.39
167 97 0.33
168 1 0.00
169 3 0.01
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (163 bp):
TTGGTGAATTTTAAAAATTATAAACTAAGAAAAATCTCCTCGAAACATTTACGGAGTAGAAAACT
CGTATTTCAAAAACAAGAGAATTTTAAAGAAAAAATGAAAAACTTATAAAATAAATGAATTTTTC
AAAACTGATTTACTATGAATCAAATGATGATAT
Found at i:2761834 original size:167 final size:165
Alignment explanation
Indices: 2761344--2761851 Score: 546
Period size: 167 Copynumber: 3.1 Consensus size: 165
2761334 GACAATGTTG
* *** * * ** *
2761344 GATGAATTTTAAAAATTTTAAATTGAGAAAAATC-TCCTCGAAAACATTTATGGAATAGAAAACT
1 GATGAATTTTAAAAATTATAAACCAAGAAAAATCGACC-C-AAAACATTCACAGAGTAGAAAACT
** * *
2761408 GTGTTTTTCAAAAACATA-AGAA---TTTTAAAGAAATATGAAAAACTTATGAAAATAAATGAAT
64 ACGTATTTCAAAAACA-AGAGAATTTTTTTAAA-AAA-ATGAAAAACTTATCAAAATAAATGAAT
*
2761469 TTTTCAAAAATGATTTACTATGAATCAAATGATGATATTT
126 TTTTCAAAACTGATTTACTATGAATCAAATGATGATATTT
* * * * * *
2761509 GGTGAATTTTAAAAATTATAAACTAAGAAAAATCTACTCGAAACATTTACAGAGTAGAAAACTAC
1 GATGAATTTTAAAAATTATAAACCAAGAAAAATCGACCCAAAACATTCACAGAGTAGAAAACTAC
**** *
2761574 GTATTTCAAAAACAAGAGAATTTCAAAAGAAAAAATTAAAAACTTATCAAAATAAATGAATTTTT
66 GTATTTCAAAAACAAGAGAATTTTTTTA-AAAAAATGAAAAACTTATCAAAATAAATGAATTTTT
2761639 CAAAACTGATTTACTATGAATCAAATGATGATATTT
130 CAAAACTGATTTACTATGAATCAAATGATGATATTT
* * *
2761675 GATGAATTTTAAAAATTATAAACCAAGAAAAATCGCCCCAATAACATTCACGGAGTAGAATACT-
1 GATGAATTTTAAAAATTATAAACCAAGAAAAATCGACCCAA-AACATTCACAGAGTAGAAAACTA
* *
2761739 CTGTATTTCGAAAACATGA-AATTTTTTTTTAAAAAAATGAAAAACTTAT-AAAAGTAAATGAAT
65 C-GTATTTCAAAAACAAGAGAA--TTTTTTTAAAAAAATGAAAAACTTATCAAAA-TAAATGAAT
* * *
2761802 TTTTCAAAACTAATTTAGTATGAATTAAATGATGATATTT
126 TTTTCAAAACTGATTTACTATGAATCAAATGATGATATTT
* *
2761842 AAAGAATTTT
1 GATGAATTTT
2761852 GATGTTCAAA
Statistics
Matches: 291, Mismatches: 41, Indels: 20
0.83 0.12 0.06
Matches are distributed among these distances:
163 1 0.00
164 37 0.13
165 31 0.11
166 107 0.37
167 109 0.37
168 6 0.02
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (165 bp):
GATGAATTTTAAAAATTATAAACCAAGAAAAATCGACCCAAAACATTCACAGAGTAGAAAACTAC
GTATTTCAAAAACAAGAGAATTTTTTTAAAAAAATGAAAAACTTATCAAAATAAATGAATTTTTC
AAAACTGATTTACTATGAATCAAATGATGATATTT
Found at i:2763151 original size:32 final size:32
Alignment explanation
Indices: 2763115--2763187 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
2763105 ATTTTTACAA
* *
2763115 TTTGTATCGATATAATGTATCGATACATAAGT
1 TTTGTATCAATAGAATGTATCGATACATAAGT
2763147 TTTGTATCAATAGAATGTATCGATACATAAGT
1 TTTGTATCAATAGAATGTATCGATACATAAGT
2763179 TTTGTATCA
1 TTTGTATCA
2763188 TACATTTATC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (32 bp):
TTTGTATCAATAGAATGTATCGATACATAAGT
Found at i:2763154 original size:19 final size:18
Alignment explanation
Indices: 2763130--2763192 Score: 55
Period size: 19 Copynumber: 3.7 Consensus size: 18
2763120 ATCGATATAA
2763130 TGTATCGATACATAAGTTT
1 TGTATC-ATACATAAGTTT
**
2763149 TGTATC--A-AT-AG-AA
1 TGTATCATACATAAGTTT
2763162 TGTATCGATACATAAGTTT
1 TGTATC-ATACATAAGTTT
2763181 TGTATCATACAT
1 TGTATCATACAT
2763193 TTATCATTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 13
0.67 0.08 0.25
Matches are distributed among these distances:
13 6 0.18
14 2 0.06
15 2 0.06
16 2 0.06
17 2 0.06
18 8 0.24
19 12 0.35
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (18 bp):
TGTATCATACATAAGTTT
Found at i:2770021 original size:52 final size:51
Alignment explanation
Indices: 2769943--2770091 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
2769933 CGCAATATGA
2769943 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
2769995 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
* **
2770047 AAATTTACCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
2770092 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.95
53 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:2770098 original size:13 final size:13
Alignment explanation
Indices: 2770080--2770104 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2770070 CAAAGATCAG
2770080 TGTATCGATACAA
1 TGTATCGATACAA
2770093 TGTATCGATACA
1 TGTATCGATACA
2770105 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2770182 original size:33 final size:33
Alignment explanation
Indices: 2770145--2770211 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2770135 AGTAGCTTGA
2770145 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
2770178 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
2770211 A
1 A
2770212 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:2770185 original size:13 final size:13
Alignment explanation
Indices: 2770167--2770191 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2770157 CAAAAAAATA
2770167 TGTATCGATACAT
1 TGTATCGATACAT
2770180 TGTATCGATACA
1 TGTATCGATACA
2770192 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2772124 original size:21 final size:22
Alignment explanation
Indices: 2772091--2772132 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
2772081 TAAAGAAATA
2772091 AAATAAAATAATAAAAAAAGAC
1 AAATAAAATAATAAAAAAAGAC
2772113 AAATAAAA-AATAAAAAAAGA
1 AAATAAAATAATAAAAAAAGA
2772133 AAAAAATCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.81, C:0.02, G:0.05, T:0.12
Consensus pattern (22 bp):
AAATAAAATAATAAAAAAAGAC
Found at i:2776510 original size:20 final size:20
Alignment explanation
Indices: 2776466--2776519 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
2776456 CTACCACTGT
2776466 TTGTATCGATACATGGCACA
1 TTGTATCGATACATGGCACA
*
2776486 CTGTATCGATACATGAAG-A-A
1 TTGTATCGATACATG--GCACA
2776506 TTGTATCGATACAT
1 TTGTATCGATACAT
2776520 TGTCCAAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 28 0.93
21 1 0.03
22 1 0.03
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (20 bp):
TTGTATCGATACATGGCACA
Found at i:2778153 original size:15 final size:15
Alignment explanation
Indices: 2778133--2778167 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2778123 AACCATCAAA
2778133 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
2778148 GATGATGATGATAAT
1 GATGATGAAGATAAT
2778163 GATGA
1 GATGA
2778168 AGTTGACTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:2785122 original size:20 final size:19
Alignment explanation
Indices: 2785097--2785150 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 19
2785087 CTACCACTGT
2785097 TTGTATCGATACATG-GCACA
1 TTGTATCGATACATGAG-A-A
2785117 TTGTATCGATACATGAAGAA
1 TTGTATCGATACATG-AGAA
2785137 TTGTATCGATACAT
1 TTGTATCGATACAT
2785151 TATCCCAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 30 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (19 bp):
TTGTATCGATACATGAGAA
Found at i:2785414 original size:25 final size:29
Alignment explanation
Indices: 2785386--2785442 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
2785376 GATCAAAGCA
2785386 TTCAA-AG-TTTTA-CTTATT-TTCTCAT
1 TTCAAGAGCTTTTATCTTATTATTCTCAT
*
2785411 TTCAAGAGCTTTTATTCTTATTATTGTCAT
1 TTCAAGAGCTTTTA-TCTTATTATTCTCAT
2785441 TT
1 TT
2785443 TTTTAAAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
25 5 0.19
26 2 0.08
27 5 0.19
29 6 0.23
30 8 0.31
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.56
Consensus pattern (29 bp):
TTCAAGAGCTTTTATCTTATTATTCTCAT
Found at i:2787824 original size:24 final size:25
Alignment explanation
Indices: 2787789--2787839 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
2787779 ATTATTTGTG
*
2787789 ATGTTTTTATT-ACTTTAA-ATTTT
1 ATGTTTTGATTAACTTTAATATTTT
*
2787812 ATGTATTTGATTAATTTTAATATTTT
1 ATGT-TTTGATTAACTTTAATATTTT
2787838 AT
1 AT
2787840 TTGAATAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 6 0.26
25 6 0.26
26 7 0.30
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (25 bp):
ATGTTTTGATTAACTTTAATATTTT
Found at i:2787828 original size:64 final size:64
Alignment explanation
Indices: 2787745--2787877 Score: 164
Period size: 64 Copynumber: 2.1 Consensus size: 64
2787735 TTTTCATGTG
*
2787745 TTTATCTATTGGATAAATTTT-ATATTTTATTTAAATTA-TTTGTGATGTTTTTATTACTTT-AA
1 TTTATCTATTGGATAAATTTTAATATTTTATTTAAA-TAGTTTGTGA--TTTTCATTACTTTGAA
2787807 AT
63 AT
* * * * *
2787809 TTTATGTATTTGATTAATTTTAATATTTTATTTGAATAGTTTGTGATTTTCATTATTTTGAAAT
1 TTTATCTATTGGATAAATTTTAATATTTTATTTAAATAGTTTGTGATTTTCATTACTTTGAAAT
2787873 TTTAT
1 TTTAT
2787878 TTGAGTATTC
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
63 11 0.18
64 29 0.48
65 20 0.33
ACGTcount: A:0.29, C:0.02, G:0.09, T:0.60
Consensus pattern (64 bp):
TTTATCTATTGGATAAATTTTAATATTTTATTTAAATAGTTTGTGATTTTCATTACTTTGAAAT
Found at i:2791528 original size:52 final size:52
Alignment explanation
Indices: 2791463--2791638 Score: 234
Period size: 52 Copynumber: 3.4 Consensus size: 52
2791453 TATGACACAT
2791463 TGAAAAATGTATCGATAC-TTTTGGTTCAAAAACCCATAATGTATCGATACAA
1 TGAAAAATGTATCGATACATTTTGG-TCAAAAACCCATAATGTATCGATACAA
* ** *
2791515 TGAATAATGTATCGATACATTCAGGTCAAAAACCCATAATGTATTGATACAA
1 TGAAAAATGTATCGATACATTTTGGTCAAAAACCCATAATGTATCGATACAA
* * * * *
2791567 TGAAAAATGTATAGATACA-TTTAGAC-CAAACCCAGAATGTATCGATACAA
1 TGAAAAATGTATCGATACATTTTGGTCAAAAACCCATAATGTATCGATACAA
2791617 T-AAAAATGTATCGATACATTTT
1 TGAAAAATGTATCGATACATTTT
2791639 CTTTCTAGAA
Statistics
Matches: 108, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
49 16 0.15
50 25 0.23
51 3 0.03
52 60 0.56
53 4 0.04
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.30
Consensus pattern (52 bp):
TGAAAAATGTATCGATACATTTTGGTCAAAAACCCATAATGTATCGATACAA
Found at i:2791716 original size:20 final size:20
Alignment explanation
Indices: 2791693--2791732 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2791683 AAATTTCAAA
*
2791693 CATGTATCCATACATTCACT
1 CATGTATCAATACATTCACT
2791713 CATGTATCAATACATTCACT
1 CATGTATCAATACATTCACT
2791733 TGTTGTATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.35
Consensus pattern (20 bp):
CATGTATCAATACATTCACT
Found at i:2792432 original size:237 final size:235
Alignment explanation
Indices: 2791957--2792417 Score: 886
Period size: 237 Copynumber: 2.0 Consensus size: 235
2791947 GAGTAAAATG
2791957 AGGTGTCTACAGGGACTATTTGCCAATTTGTTTCATGTCAAATCACTCATTTAAACCTTCACCAA
1 AGGTGTCTACAGGGACTATTTGCCAATTTGTTTCATGTCAAATCACTCATTTAAACCTTCACCAA
2792022 AAGAACTTGCAGGAGTTACTAAAATACAAATAGATCACCTTATTGTTGAAACTACATATGGATGA
66 AAGAACTTGCAGGAGTTACTAAAATACAAATAGATCACCTTATTGTTGAAACTACATATGGATGA
2792087 ACAGCTAGTTGAGCTCTAATCAAGTTCTGGGATCCCTCTTTCCGATGCTTTTCATTTAATCAGCA
131 ACAGCTAGTTGAGCTCTAATCAAGTTCTGGGATCCCTCTTTCCGATGCTTTTCATTTAATCAGCA
2792152 TGACATGACTCTAACCCTAGAAAAAATTTCAACTCACCTA
196 TGACATGACTCTAACCCTAGAAAAAATTTCAACTCACCTA
*
2792192 AGGTGTCTACAGGGACTATTTGCCAATTTGTTTCTTGTCAAATCACTCATTTAAACCTTCACCAA
1 AGGTGTCTACAGGGACTATTTGCCAATTTGTTTCATGTCAAATCACTCATTTAAACCTTCACCAA
2792257 AAGAACTTGCAGGAGTTACTAAAAAATACAAATAGATCACCTTATTGTTGAAACTACATATGGAT
66 AAGAACTTGCAGGAGTTACT--AAAATACAAATAGATCACCTTATTGTTGAAACTACATATGGAT
*
2792322 GAACAGCTAGTTGAGCTCTAATCAAGTTCTGGGATCCCTCTTTTCGATGCTTTTCATTTAATCAG
129 GAACAGCTAGTTGAGCTCTAATCAAGTTCTGGGATCCCTCTTTCCGATGCTTTTCATTTAATCAG
2792387 CATGACATGACTCTAACCCTAGAAAAAATTT
194 CATGACATGACTCTAACCCTAGAAAAAATTT
2792418 TAGCTTTCCT
Statistics
Matches: 222, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
235 84 0.38
237 138 0.62
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32
Consensus pattern (235 bp):
AGGTGTCTACAGGGACTATTTGCCAATTTGTTTCATGTCAAATCACTCATTTAAACCTTCACCAA
AAGAACTTGCAGGAGTTACTAAAATACAAATAGATCACCTTATTGTTGAAACTACATATGGATGA
ACAGCTAGTTGAGCTCTAATCAAGTTCTGGGATCCCTCTTTCCGATGCTTTTCATTTAATCAGCA
TGACATGACTCTAACCCTAGAAAAAATTTCAACTCACCTA
Found at i:2794624 original size:19 final size:19
Alignment explanation
Indices: 2794585--2794668 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
2794575 TTTCAACGAT
2794585 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
2794605 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
2794624 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
*
2794638 -TGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
2794656 TTGTATCGATACA
1 TTGTATCGATACA
2794669 ATGTAAGCTA
Statistics
Matches: 58, Mismatches: 0, Indels: 13
0.82 0.00 0.18
Matches are distributed among these distances:
13 11 0.19
15 2 0.03
17 2 0.03
19 29 0.50
20 14 0.24
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:2794643 original size:13 final size:13
Alignment explanation
Indices: 2794625--2794649 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2794615 ACATAAGTGT
2794625 TGTATCGATACAA
1 TGTATCGATACAA
2794638 TGTATCGATACA
1 TGTATCGATACA
2794650 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2794647 original size:32 final size:32
Alignment explanation
Indices: 2794606--2794673 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
2794596 CATAAAGTGT
2794606 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
2794638 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
2794670 TGTA
1 TGTA
2794674 AGCTACTGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:2794773 original size:52 final size:50
Alignment explanation
Indices: 2794705--2794858 Score: 209
Period size: 52 Copynumber: 3.0 Consensus size: 50
2794695 CGATACACTA
* *
2794705 CCCAAATGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTG
1 CCCAGATGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTG
* *
2794757 CCCAGATGTATCGATACACTATAAAATGTATCGATACATGCAGGTAAATTTG
1 CCCAGATGTATCGATACACTAT--TATGTATCGATACATGCAGGCAAATTTG
*
2794809 CCCAGATGTATCGATACACTATTAAATGTATCAATACATGCAGGCAAATT
1 CCCAGATGTATCGATACACTATT--ATGTATCGATACATGCAGGCAAATT
2794859 GTCATATTTC
Statistics
Matches: 91, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
51 2 0.02
52 89 0.98
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (50 bp):
CCCAGATGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTG
Found at i:2803927 original size:23 final size:23
Alignment explanation
Indices: 2803901--2803953 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
2803891 ACTACTATAT
*
2803901 TATATTAAATATTTTAATAATAA
1 TATATAAAATATTTTAATAATAA
*
2803924 TATATAAAATATTTTAATAATAT
1 TATATAAAATATTTTAATAATAA
2803947 TA-ATAAA
1 TATATAAA
2803954 TAATAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 5 0.18
23 23 0.82
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATATAAAATATTTTAATAATAA
Found at i:2805525 original size:17 final size:18
Alignment explanation
Indices: 2805482--2805529 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
2805472 CATTTACTAT
*
2805482 TAATTATATAATACATTAT
1 TAATTATA-AATACATTAA
* *
2805501 TAAATATAATTACA-TAA
1 TAATTATAAATACATTAA
2805518 TAATTATAAATA
1 TAATTATAAATA
2805530 TCTTTTCATA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 12 0.50
18 5 0.21
19 7 0.29
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATTATAAATACATTAA
Found at i:2805540 original size:23 final size:25
Alignment explanation
Indices: 2805482--2805530 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
2805472 CATTTACTAT
*
2805482 TAATTATATAATACATTATTAAATA
1 TAATTACATAATACATTATTAAATA
2805507 TAATTACATAATA-ATTA-TAAATA
1 TAATTACATAATACATTATTAAATA
2805530 T
1 T
2805531 CTTTTCATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.30
24 4 0.17
25 12 0.52
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (25 bp):
TAATTACATAATACATTATTAAATA
Found at i:2805641 original size:19 final size:19
Alignment explanation
Indices: 2805614--2805650 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2805604 AAATTATATA
2805614 ATTATAA-TTAAATTTTTT
1 ATTATAATTTAAATTTTTT
2805632 ATTATAAATTTAAATTTTT
1 ATTAT-AATTTAAATTTTT
2805651 ATAAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 2 0.12
20 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTATAATTTAAATTTTTT
Found at i:2806653 original size:10 final size:10
Alignment explanation
Indices: 2806629--2806712 Score: 50
Period size: 10 Copynumber: 8.4 Consensus size: 10
2806619 TAAAAGTGTA
*
2806629 TTATTAATA-
1 TTATTTATAT
2806638 TTATTTATAT
1 TTATTTATAT
*
2806648 TTATTTAAAT
1 TTATTTATAT
2806658 TTAATTTA-AT
1 TT-ATTTATAT
*
2806668 TTAAATTATA-
1 TT-ATTTATAT
** *
2806678 AAATTTAAATT
1 TTATTTATA-T
2806689 TTATATTA-AT
1 TTAT-TTATAT
2806699 TTATTTATAT
1 TTATTTATAT
2806709 TTAT
1 TTAT
2806713 AAATAAATAA
Statistics
Matches: 59, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
9 16 0.27
10 31 0.53
11 9 0.15
12 3 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTATTTATAT
Found at i:2806846 original size:10 final size:10
Alignment explanation
Indices: 2806738--2806875 Score: 55
Period size: 10 Copynumber: 14.6 Consensus size: 10
2806728 ATTTATTAAA
*
2806738 TTTAATATGT
1 TTTAATATAT
*
2806748 ATT-ATAT-T
1 TTTAATATAT
*
2806756 TTTAATTTAT
1 TTTAATATAT
*
2806766 TTTAAT-TTT
1 TTTAATATAT
* * *
2806775 TTTAAAAAAA
1 TTTAATATAT
2806785 TTT-A-ATA-
1 TTTAATATAT
2806792 TTTAATA-A-
1 TTTAATATAT
2806800 TTTAATAATAT
1 TTTAAT-ATAT
* *
2806811 TTTATTAAAT
1 TTTAATATAT
*
2806821 TTTAAATATAA
1 TTT-AATATAT
*
2806832 CTTAATATAT
1 TTTAATATAT
2806842 TTTAATATTAT
1 TTTAATA-TAT
*
2806853 ATT-ATA-AT
1 TTTAATATAT
*
2806861 ATT-ATATAT
1 TTTAATATAT
2806870 TTTAAT
1 TTTAAT
2806876 TTTTATAAAT
Statistics
Matches: 97, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
7 3 0.03
8 21 0.22
9 21 0.22
10 36 0.37
11 16 0.16
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.57
Consensus pattern (10 bp):
TTTAATATAT
Found at i:2806855 original size:13 final size:13
Alignment explanation
Indices: 2806837--2806867 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2806827 TATAACTTAA
*
2806837 TATATTTTAATAT
1 TATATTATAATAT
2806850 TATATTATAATAT
1 TATATTATAATAT
2806863 TATAT
1 TATAT
2806868 ATTTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATATTATAATAT
Found at i:2806862 original size:21 final size:20
Alignment explanation
Indices: 2806789--2806863 Score: 50
Period size: 21 Copynumber: 3.6 Consensus size: 20
2806779 AAAAAATTTA
*
2806789 ATATT-TAATAATTTAATAAT
1 ATATTATAATATTTTAAT-AT
*
2806809 ATTTTATTAA-ATTTTAA-AT
1 ATATTA-TAATATTTTAATAT
2806828 ATAACTTA-ATATATTTTAATATT
1 AT-A-TTATA-ATATTTTAATA-T
2806851 ATATTATAATATT
1 ATATTATAATATT
2806864 ATATATTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 17
0.68 0.05 0.27
Matches are distributed among these distances:
19 5 0.12
20 5 0.12
21 24 0.56
22 6 0.14
23 3 0.07
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATTATAATATTTTAATAT
Found at i:2806895 original size:29 final size:30
Alignment explanation
Indices: 2806823--2806915 Score: 88
Period size: 28 Copynumber: 3.2 Consensus size: 30
2806813 TATTAAATTT
* *
2806823 TAAATATAACTTA-ATATATTTTAA-TATTA
1 TAAATATAA-TAATATATATTTTAATTTTTA
* *
2806852 T-ATTATAATATTATATATTTTAATTTTTA
1 TAAATATAATAATATATATTTTAATTTTTA
*
2806881 TAAAT-TAATAATATATA-TTTATTTTTTA
1 TAAATATAATAATATATATTTTAATTTTTA
2806909 TATAATA
1 TA-AATA
2806916 AAAAAATTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
27 1 0.02
28 29 0.56
29 20 0.38
30 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (30 bp):
TAAATATAATAATATATATTTTAATTTTTA
Found at i:2807029 original size:21 final size:22
Alignment explanation
Indices: 2807005--2807047 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2806995 GTTGAAGTTA
2807005 AGATTTAATTTATT-TTTAAAT
1 AGATTTAATTTATTATTTAAAT
* *
2807026 AGATTTTATTTTTTATTTAAAT
1 AGATTTAATTTATTATTTAAAT
2807048 TTATATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
AGATTTAATTTATTATTTAAAT
Found at i:2807049 original size:6 final size:6
Alignment explanation
Indices: 2807040--2807114 Score: 50
Period size: 6 Copynumber: 12.3 Consensus size: 6
2807030 TTTATTTTTT
* **
2807040 ATTTAA ATTTATA TTTTAA ATTTAA TATTTTT ATTTAA ATTT-- ATTTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA -ATTTAA ATTTAA ATTTAA ATTTAA
2807088 ATATTAA A--TAA ATTTTTAA ATTTAA AT
1 AT-TTAA ATTTAA A--TTTAA ATTTAA AT
2807115 CGACAATTCA
Statistics
Matches: 54, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
4 8 0.15
6 28 0.52
7 14 0.26
8 4 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
ATTTAA
Found at i:2807054 original size:19 final size:18
Alignment explanation
Indices: 2807028--2807089 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 18
2807018 TTTTAAATAG
2807028 ATTTTATTTTTTATTTAA
1 ATTTTATTTTTTATTTAA
**
2807046 ATTTATATTTTAAATTTAA
1 ATTT-TATTTTTTATTTAA
2807065 TATTTTTATTTAAATTTATTTAA
1 -A-TTTTATTT---TTTATTTAA
2807088 AT
1 AT
2807090 ATTAAATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
18 4 0.12
19 12 0.35
20 6 0.18
21 4 0.12
22 1 0.03
23 7 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTTATTTTTTATTTAA
Found at i:2807057 original size:13 final size:14
Alignment explanation
Indices: 2807041--2807112 Score: 54
Period size: 13 Copynumber: 5.8 Consensus size: 14
2807031 TTATTTTTTA
2807041 TTTAAATTT-ATAT
1 TTTAAATTTAATAT
2807054 TTTAAATTTAATAT
1 TTTAAATTTAATAT
*
2807068 TTT-TATTTAA-A-
1 TTTAAATTTAATAT
2807079 TTT--ATTTAA-AT
1 TTTAAATTTAATAT
* *
2807090 ATTAAA-TAAAT-T
1 TTTAAATTTAATAT
2807102 TTTAAATTTAA
1 TTTAAATTTAA
2807113 ATCGACAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
10 7 0.15
11 5 0.10
12 10 0.21
13 19 0.40
14 7 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAAATTTAATAT
Found at i:2807872 original size:20 final size:20
Alignment explanation
Indices: 2807849--2807909 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 20
2807839 AAAATAAAAA
2807849 ATATTTATATTAAATATATC
1 ATATTTATATTAAATATATC
2807869 ATATTAATCATATTTAAATATATC
1 ATATT--T-ATA-TTAAATATATC
*
2807893 ATA-TAATATT-AATATAT
1 ATATTTATATTAAATATAT
2807910 TATTTTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
18 7 0.19
19 2 0.06
20 8 0.22
22 1 0.03
23 4 0.11
24 14 0.39
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATTTATATTAAATATATC
Found at i:2807882 original size:29 final size:28
Alignment explanation
Indices: 2807849--2807910 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
2807839 AAAATAAAAA
* *
2807849 ATATTTATATTAAAT-ATATCATATTAAT
1 ATATTTA-AATAAATCATATAATATTAAT
*
2807877 CATATTTAAATATATCATATAATATTAAT
1 -ATATTTAAATAAATCATATAATATTAAT
2807906 ATATT
1 ATATT
2807911 ATTTTATTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 10 0.34
29 19 0.66
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (28 bp):
ATATTTAAATAAATCATATAATATTAAT
Found at i:2810706 original size:13 final size:13
Alignment explanation
Indices: 2810688--2810713 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2810678 ATATTTTTTG
2810688 TGTATCGATACAT
1 TGTATCGATACAT
2810701 TGTATCGATACAT
1 TGTATCGATACAT
2810714 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2810724 original size:32 final size:33
Alignment explanation
Indices: 2810667--2810731 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
2810657 TACAAGCCAA
2810667 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCGATACAT
2810701 TGTATCGATACATA-TTTTGTGTATCGATACA
1 TGTATCGATACATATTTTTGTGTATCGATACA
2810732 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.55
34 14 0.45
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCGATACAT
Found at i:2810725 original size:19 final size:19
Alignment explanation
Indices: 2810667--2810731 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
2810657 TACAAGCCAA
2810667 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
2810688 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
2810701 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
2810720 TGTATCGATACA
1 TGTATCGATACA
2810732 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:2810836 original size:20 final size:20
Alignment explanation
Indices: 2810783--2810838 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
2810773 ACATCTTTTT
*
2810783 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
*
2810803 CATGTATAGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
2810822 CTGTGTATCGATACTTT
1 C-ATGTATCGATACTTT
2810839 TAAGGGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 3 0.10
20 28 0.90
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:2813279 original size:13 final size:13
Alignment explanation
Indices: 2813261--2813298 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
2813251 ATAATCCCCC
*
2813261 TGTATCGATATAG
1 TGTATCGATACAG
*
2813274 TGTATCGATACAT
1 TGTATCGATACAG
2813287 TGTATCGATACA
1 TGTATCGATACA
2813299 AAGAAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2814017 original size:24 final size:24
Alignment explanation
Indices: 2813985--2814032 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2813975 AATATTTGTG
2813985 CACAACAACTTCCTACGGAAATAT
1 CACAACAACTTCCTACGGAAATAT
2814009 CACAACAACTTCCTACGGAAATAT
1 CACAACAACTTCCTACGGAAATAT
2814033 ACTCCGCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.29, G:0.08, T:0.21
Consensus pattern (24 bp):
CACAACAACTTCCTACGGAAATAT
Found at i:2819506 original size:19 final size:20
Alignment explanation
Indices: 2819466--2819517 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
2819456 TACAAGCCAA
2819466 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA-TTTTTG
2819487 TGTATCGATACATA-TTTTG
1 TGTATCGATACATATTTTTG
2819506 TGTATCGATACA
1 TGTATCGATACA
2819518 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 17 0.55
21 14 0.45
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (20 bp):
TGTATCGATACATATTTTTG
Found at i:2819622 original size:20 final size:20
Alignment explanation
Indices: 2819569--2819624 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
2819559 ACATCTTTTT
*
2819569 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
2819589 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
2819608 CTGTGTATCGATACTTT
1 C-ATGTATCGATACTTT
2819625 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:2822065 original size:13 final size:13
Alignment explanation
Indices: 2822047--2822084 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
2822037 ATAATCCCCC
*
2822047 TGTATCGATATAG
1 TGTATCGATACAG
*
2822060 TGTATCGATACAT
1 TGTATCGATACAG
2822073 TGTATCGATACA
1 TGTATCGATACA
2822085 AAGAAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2828267 original size:19 final size:20
Alignment explanation
Indices: 2828227--2828278 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
2828217 TACAAGCCAA
2828227 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA-TTTTTG
2828248 TGTATCGATACATA-TTTTG
1 TGTATCGATACATATTTTTG
2828267 TGTATCGATACA
1 TGTATCGATACA
2828279 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 17 0.55
21 14 0.45
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (20 bp):
TGTATCGATACATATTTTTG
Found at i:2828383 original size:20 final size:20
Alignment explanation
Indices: 2828330--2828385 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
2828320 ACATCTTTTT
*
2828330 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
2828350 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
2828369 CTGTGTATCGATACTTT
1 C-ATGTATCGATACTTT
2828386 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:2830320 original size:20 final size:21
Alignment explanation
Indices: 2830275--2830321 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
2830265 TTTAACAAAT
2830275 TGTATCGATACAATAAGGCAA
1 TGTATCGATACAATAAGGCAA
*
2830296 CGTATCGATAC-ATAAGTG-AA
1 TGTATCGATACAATAAG-GCAA
2830316 TGTATC
1 TGTATC
2830322 AAACATGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (21 bp):
TGTATCGATACAATAAGGCAA
Found at i:2830499 original size:52 final size:51
Alignment explanation
Indices: 2830383--2830501 Score: 159
Period size: 51 Copynumber: 2.3 Consensus size: 51
2830373 TCTAGAATAA
* *
2830383 AAATGTATTA-ATACATTTTTCATTGTATCGATACATTCAGGTTTTTGACCC
1 AAATGTA-TAGATACATTCTTCATTATATCGATACATTCAGGTTTTTGACCC
** *
2830434 AAATGTATAGATACATTCTTCATTATATCGATATGTTCTGAGTTTTTGACCC
1 AAATGTATAGATACATTCTTCATTATATCGATACATTCAG-GTTTTTGACCC
*
2830486 AAATGTATCGATACAT
1 AAATGTATAGATACAT
2830502 GTAGGCAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
50 2 0.03
51 32 0.53
52 26 0.43
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (51 bp):
AAATGTATAGATACATTCTTCATTATATCGATACATTCAGGTTTTTGACCC
Found at i:2832890 original size:95 final size:94
Alignment explanation
Indices: 2832739--2832977 Score: 329
Period size: 95 Copynumber: 2.5 Consensus size: 94
2832729 ATTTTATTCA
*
2832739 TCGAGGATACTCCAACCCCATTCTTTCGAG-GGAATACTCCAACTCCATTTTTAAACTTGTCAAG
1 TCGAGGATACTCCAACCCCATTCTTCCGAGAGG-ATACTCCAAC-CCATTTTTAAACTTGTCAAG
* *
2832803 ATAAATCTTATTTTTGCTTAAATTATCATAT
64 ATAAATCTTATTTTTGCATAAATTATCATAG
* *
2832834 TCGAGGATACTCCAACCCCATTCTTCCGAGAGGATACCCCAACCCTGTTTTTAAACTTGTCAAGA
1 TCGAGGATACTCCAACCCCATTCTTCCGAGAGGATACTCCAACCC-ATTTTTAAACTTGTCAAGA
* *
2832899 TAAATCTTATTTTTGCATAAATTGTCATCG
65 TAAATCTTATTTTTGCATAAATTATCATAG
* * *
2832929 TCG-GGAATACTCCAACCCTATTCCTCCAAGAGGATACTCCAACCTCATT
1 TCGAGG-ATACTCCAACCCCATTCTTCCGAGAGGATACTCCAACC-CATT
2832978 CCTCCAAGGG
Statistics
Matches: 128, Mismatches: 12, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
94 4 0.03
95 121 0.95
96 3 0.02
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (94 bp):
TCGAGGATACTCCAACCCCATTCTTCCGAGAGGATACTCCAACCCATTTTTAAACTTGTCAAGAT
AAATCTTATTTTTGCATAAATTATCATAG
Found at i:2832978 original size:27 final size:28
Alignment explanation
Indices: 2832931--2833001 Score: 103
Period size: 27 Copynumber: 2.6 Consensus size: 28
2832921 TGTCATCGTC
2832931 GGGAATACTCCAACC-CTATTCCTCCAA
1 GGGAATACTCCAACCTCTATTCCTCCAA
2832958 GAGG-ATACTCCAACCTC-ATTCCTCCAA
1 G-GGAATACTCCAACCTCTATTCCTCCAA
*
2832985 GGGAATACTCCAGCCTC
1 GGGAATACTCCAACCTC
2833002 GTTTTTCAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
26 2 0.05
27 35 0.88
28 3 0.08
ACGTcount: A:0.28, C:0.37, G:0.14, T:0.21
Consensus pattern (28 bp):
GGGAATACTCCAACCTCTATTCCTCCAA
Found at i:2833765 original size:166 final size:166
Alignment explanation
Indices: 2833609--2834300 Score: 498
Period size: 166 Copynumber: 4.2 Consensus size: 166
2833599 AATTACAAGG
* * * *
2833609 TTTTTTACTTTGTAAATTTTTTTGA-AGGGATTTTTCTTGGTTGTTAGCTTTTAAAATTCATAAA
1 TTTTCTACTTCGTAAATTTTTTTGAGA-GGATTTTTCTTAGTTGTTAACTTTTAAAATTCATAAA
* * *
2833673 ATATTATTATTTAATTCATACTAAATCAATTTTTAAAAATTCATTCATTTTCATGGGTTCGT-AA
65 ATATTATTATTTAATTCATAATAAATCAATTTTCAAAAATTCATTCATTTTCATGAGTTCGTGAA
*
2833737 AGTTTTTCCTTGAAATTATCTTTTTTCAAAAAATGAAA
130 AGTTTTTCCTTGAAATT-TCTTTTTTCAAAAAATCAAA
* * * *
2833775 TTTTCTACTTCGTAAATTTTTTTGGGAGGATTTTTCTTAGTTTTTAATTTTTAAAATTCATTAAA
1 TTTTCTACTTCGTAAATTTTTTTGAGAGGATTTTTCTTAGTTGTTAACTTTTAAAATTCATAAAA
* * * * * *
2833840 TATTATTATTTAATTTATAATAAATTAGTTTTCAAAAATTCATTCATTTTTATGAGTTTGTGAAT
66 TATTATTATTTAATTCATAATAAATCAATTTTCAAAAATTCATTCATTTTCATGAGTTCGTGAAA
* * *
2833905 TTTTTTCCTTGGAATTTCTTTTTTCCAAAAAA-CAGAG
131 GTTTTTCCTTGAAATTTCTTTTTT-CAAAAAATCA-AA
* * * * *
2833942 TTTTCTACTCCGTAAA-TTTTTTCAGGAGGA-TTTT-TT--TTATT---TTTTAAAATTTATCAA
1 TTTTCTACTTCGTAAATTTTTTTGA-GAGGATTTTTCTTAGTTGTTAACTTTTAAAATTCATAAA
*** * * * * * *
2833999 ATATTATTA-TT-ATATCACGTTAAATTATTTTTCAAAAATTCCTTCATTTTCTTAAGGTT-TTG
65 ATATTATTATTTAAT-TCATAATAAATCAATTTTCAAAAATTCATTCATTTTCATGA-GTTCGTG
* * * * * *
2834061 -GATTTTTTCCTTTAAATTCTCTTATTTCCGAAAAA-CGAAG
128 AAAGTTTTTCCTTGAAATT-TCTT-TTTTCAAAAAATC-AAA
* * * * * * *
2834101 TTTTCTAC-TCTATAAATTATTTTGGGGGGATTTTTCTTCA-TTTTTAATTTTTAAAATTAATAA
1 TTTTCTACTTC-GTAAATTTTTTTGAGAGGATTTTTCTT-AGTTGTTAACTTTTAAAATTCATAA
* * * *
2834164 AATATCATTATTT-ATTCCACATTAAATCAATTTTCAAAAA-GCAATTCATTTTCATGAGTT--T
64 AATATTATTATTTAATT-CATAATAAATCAATTTTCAAAAATTC-ATTCATTTTCATGAGTTCGT
* * * * * * *
2834225 TAGATTTTTTCTTTGAAATCGTTATTTTTTTAAAAAACCGAAA
127 GAAAGTTTTTCCTTGAAAT--TTCTTTTTTCAAAAAATC-AAA
*
2834268 -TTTCTA-TTCCATAAATATTTTTTGAG-GGATTTT
1 TTTTCTACTT-CGTAAAT-TTTTTTGAGAGGATTTT
2834301 CTTTGGTATA
Statistics
Matches: 427, Mismatches: 70, Indels: 58
0.77 0.13 0.10
Matches are distributed among these distances:
158 17 0.04
159 65 0.15
160 39 0.09
161 2 0.00
163 8 0.02
165 3 0.01
166 197 0.46
167 95 0.22
168 1 0.00
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (166 bp):
TTTTCTACTTCGTAAATTTTTTTGAGAGGATTTTTCTTAGTTGTTAACTTTTAAAATTCATAAAA
TATTATTATTTAATTCATAATAAATCAATTTTCAAAAATTCATTCATTTTCATGAGTTCGTGAAA
GTTTTTCCTTGAAATTTCTTTTTTCAAAAAATCAAA
Found at i:2834557 original size:4 final size:4
Alignment explanation
Indices: 2834548--2834574 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2834538 TTTTTTAAAT
2834548 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
2834575 TACTTTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:2834717 original size:63 final size:63
Alignment explanation
Indices: 2834618--2834747 Score: 260
Period size: 63 Copynumber: 2.1 Consensus size: 63
2834608 ATGATGGCGC
2834618 TAGGTAGATCTCTTACAAGCAATATGACAAAGCATGGGTGTTTATGACATCCATTTAATGCTT
1 TAGGTAGATCTCTTACAAGCAATATGACAAAGCATGGGTGTTTATGACATCCATTTAATGCTT
2834681 TAGGTAGATCTCTTACAAGCAATATGACAAAGCATGGGTGTTTATGACATCCATTTAATGCTT
1 TAGGTAGATCTCTTACAAGCAATATGACAAAGCATGGGTGTTTATGACATCCATTTAATGCTT
2834744 TAGG
1 TAGG
2834748 AAGAACCACA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (63 bp):
TAGGTAGATCTCTTACAAGCAATATGACAAAGCATGGGTGTTTATGACATCCATTTAATGCTT
Found at i:2836687 original size:154 final size:152
Alignment explanation
Indices: 2836436--2836808 Score: 427
Period size: 154 Copynumber: 2.4 Consensus size: 152
2836426 GCATTATCCC
* * * * *
2836436 AAGTCCTTTAGGGGTA-CCGAGTACTTTTACGGCAAAGGTATCCCTTAGGGGTA-ATTTT-GTAA
1 AAGTCCTTTA-GGGTATCAG-GTACTTTTACGTCGAAGGTATCCCCTA-AGG-ACATTTTCGTAA
* * * *
2836498 TTTTTTAAAACTAACTCCTAGGTTATTGCCGAGTCCGCTTTTATGCCAAAGCTAGATAATTAGGA
62 TTTTTTAAAACCAACTCCTAGGTTATCGCCGAGTCCGCTTTTATACCAAAGCT-GACAATTAGGA
* * *
2836563 TAGGTTTA-TCTCATCT-ATTATCTTTTT
126 TAGGTTCATTCT-ATCTCA-AACCTTTTT
*
2836590 GAAGTCCTTTAGAGGTATCAGGTACTTTTACGTCGAAGGTTTCCCCTAAGG-CATTTTCGTAATT
1 -AAGTCCTTTAG-GGTATCAGGTACTTTTACGTCGAAGGTATCCCCTAAGGACATTTTCGTAATT
* * * * *
2836654 TTTTAGAACCAACTCCTAGGTTGTCGCCGAGTCCGCTTTTATACCAAAGGTGGCAGTTAGGATAG
64 TTTTAAAACCAACTCCTAGGTTATCGCCGAGTCCGCTTTTATACCAAAGCTGACAATTAGGATAG
*
2836719 GTTCATTCTATTTCAAACCTTTTT
129 GTTCATTCTATCTCAAACCTTTTT
2836743 AAGTCCTTTAGGAGTATCAGGTACTTTTACGTCGAAGGTATCCCCT-AGGAACATTTTCGTAATT
1 AAGTCCTTTAGG-GTATCAGGTACTTTTACGTCGAAGGTATCCCCTAAGG-ACATTTTCGTAATT
2836807 TT
64 TT
2836809 CCTACAAAAC
Statistics
Matches: 189, Mismatches: 20, Indels: 20
0.83 0.09 0.09
Matches are distributed among these distances:
151 4 0.02
152 43 0.23
153 45 0.24
154 58 0.31
155 37 0.20
156 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (152 bp):
AAGTCCTTTAGGGTATCAGGTACTTTTACGTCGAAGGTATCCCCTAAGGACATTTTCGTAATTTT
TTAAAACCAACTCCTAGGTTATCGCCGAGTCCGCTTTTATACCAAAGCTGACAATTAGGATAGGT
TCATTCTATCTCAAACCTTTTT
Found at i:2847901 original size:20 final size:20
Alignment explanation
Indices: 2847875--2847929 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
2847865 AAAAAGACAG
*
2847875 AATGTATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* *
2847895 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
2847915 AATGTATCGATACAT
1 AATGTATCGATACAT
2847930 CTGGGTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:2847979 original size:70 final size:71
Alignment explanation
Indices: 2847825--2847979 Score: 258
Period size: 70 Copynumber: 2.2 Consensus size: 71
2847815 TTTTAACTAG
2847825 ATGTATCGATACATTGAAAAATGTATCAATACATCTGGGTAAAAAGACAGAATGTATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATCAATACATCTGGGTAAAAAGACAGAATGTATCGATACAT
* *
2847890 TCATAC
66 TCAAAA
* *
2847896 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGT-AAAAGATAGAATGTATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATCAATACATCTGGGTAAAAAGACAGAATGTATCGATACAT
*
2847960 TGAAAA
66 TCAAAA
2847966 ATGTATCGATACAT
1 ATGTATCGATACAT
2847980 CTGGGTAAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 40 0.51
71 39 0.49
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (71 bp):
ATGTATCGATACATTGAAAAATGTATCAATACATCTGGGTAAAAAGACAGAATGTATCGATACAT
TCAAAA
Found at i:2849230 original size:86 final size:86
Alignment explanation
Indices: 2849043--2849600 Score: 476
Period size: 86 Copynumber: 6.6 Consensus size: 86
2849033 GGTGCCATTA
** * * * * * * * *
2849043 ACTTGTGGGCTTCAAAAAGG-TGCCACTAACTTGTGGGC-TTCAAAAGGGTGCCACTGACTTGTA
1 ACTTGTGGGCTT-TGAAAGGATGCCACTGACTTGTGGGCTTTGAGAAGGATACCACCGACTTATG
* * * *
2849106 GGCTTCGA-AAGGGTGCCACTA
65 GGCTTTGAGAAAGATGCCACTG
* * * * * *
2849127 ACTTGTGGGCTTTGAAAGGCTACCACTGACTTGTGGGCTTTTAGAGAGGTTGCCACCGACTTGTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAGA-AGGATACCACCGAC-T-TA
2849192 TGGGC-TT-A-AAAGATGCCACTG
63 TGGGCTTTGAGAAAGATGCCACTG
* * * *
2849213 ACTTGTGAGCTTCGAAAGGATGCTACTGACTTGTGGGCTTTGAGAAGGATACCACTGACTTATGG
1 ACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAGAAGGATACCACCGACTTATGG
* * *
2849278 GCTTTGAGTAGGATGCCTCTG
66 GCTTTGAGAAAGATGCCACTG
* * * * *
2849299 ACTTGTGGGCTTTGAGAAGGATGCCACTGACTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTG
1 ACTTGTGGGCTTTGA-AAGGATGCCACTGACTTGTGGGCTTTGAGAAGGATACCACCGACTTATG
* *
2849364 GGCTTTGAGAAGGATGCCACTA
65 GGCTTTGAGAAAGATGCCACTG
* * * * * **
2849386 ACTCGTGGGCTTTGAAAAAGATGCAACTGACTTGTGGGCTTT--G-A-G-TGCCACTGACTCGTG
1 ACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTGAGAAGGATACCACCGACTTATG
*
2849446 GGCTTTGAAAAAGATGCCACTG
65 GGCTTTGAGAAAGATGCCACTG
* * * * * * **
2849468 ACATGTGGGCTTTGAGAAGGATGCCACTGACTCGTAGGCTTTGA-AAGAATGCCACTGACTCGTG
1 ACTTGTGGGCTTTGA-AAGGATGCCACTGACTTGTGGGCTTTGAGAAGGATACCACCGACTTATG
*
2849532 GGCTTTGA-AAGGATGCCACTG
65 GGCTTTGAGAAAGATGCCACTG
* * *
2849553 ACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGTTTTGAAAAGG
1 ACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAGAAGG
2849601 GTCGTATTGA
Statistics
Matches: 399, Mismatches: 58, Indels: 33
0.81 0.12 0.07
Matches are distributed among these distances:
81 1 0.00
82 67 0.17
83 12 0.03
84 58 0.15
85 44 0.11
86 108 0.27
87 102 0.26
88 7 0.02
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.28
Consensus pattern (86 bp):
ACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAGAAGGATACCACCGACTTATGG
GCTTTGAGAAAGATGCCACTG
Found at i:2849270 original size:29 final size:29
Alignment explanation
Indices: 2848961--2849600 Score: 661
Period size: 29 Copynumber: 22.6 Consensus size: 29
2848951 CACCAACTTG
* * **
2848961 TGTGGGCTTTAGAGAAGGTTGCCACCAAC-
1 TGTGGGCTTT-GAAAAGGATGCCACTGACT
*
2848990 TGTGGGCTTT-AAAAGGATGCCACTGATT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * * * *
2849018 TGTGAGC-TTCAAAAGGGTGCCATTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
** *
2849046 TGTGGGCTTCAAAAAGG-TGCCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
2849074 TGTGGGC-TTCAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * * *
2849102 TGTAGGCTTCG-AAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
2849130 TGTGGGCTTTG-AAAGGCTACCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * * *
2849158 TGTGGGCTTTTAGAGAGGTTGCCACCGACTT
1 TGTGGGCTTTGA-AAAGGATGCCACTGAC-T
2849189 GTGTGGGC-TT-AAAA-GATGCCACTGACT
1 -TGTGGGCTTTGAAAAGGATGCCACTGACT
* * *
2849216 TGTGAGCTTCG-AAAGGATGCTACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
2849244 TGTGGGCTTTGAGAAGGATACCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* ** *
2849273 TATGGGCTTTGAGTAGGATGCCTCTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
2849302 TGTGGGCTTTGAGAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
2849331 TGTGGGCTTTGAAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
2849360 TGTGGGCTTTGAGAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * *
2849389 CGTGGGCTTTGAAAAAGATGCAACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
2849418 TGTGGGCTTTG---A-G-TGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * *
2849442 CGTGGGCTTTGAAAAAGATGCCACTGACA
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
2849471 TGTGGGCTTTGAGAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * *
2849500 CGTAGGCTTTG-AAAGAATGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
2849528 CGTGGGCTTTG-AAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
2849556 TGTGGGCTTT-AAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
2849584 TGTGGGTTTTGAAAAGG
1 TGTGGGCTTTGAAAAGG
2849601 GTCGTATTGA
Statistics
Matches: 516, Mismatches: 75, Indels: 40
0.82 0.12 0.06
Matches are distributed among these distances:
24 20 0.04
25 1 0.00
26 7 0.01
27 27 0.05
28 216 0.42
29 222 0.43
30 13 0.03
31 3 0.01
32 7 0.01
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAGGATGCCACTGACT
Found at i:2849639 original size:12 final size:13
Alignment explanation
Indices: 2849607--2849680 Score: 55
Period size: 13 Copynumber: 5.6 Consensus size: 13
2849597 AAGGGTCGTA
*
2849607 TTGACGAAAATTTC
1 TTGAC-AAAGTTTC
2849621 TTGACAAAGTTTC
1 TTGACAAAGTTTC
**
2849634 -TGACAAACATTC
1 TTGACAAAGTTTC
*
2849646 TCGACAGAAG-TTC
1 TTGACA-AAGTTTC
2849659 TTGACGATAA-TTTC
1 TTGAC-A-AAGTTTC
2849673 TTGACAAA
1 TTGACAAA
2849681 TGGCAAAAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
12 12 0.24
13 19 0.39
14 18 0.37
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (13 bp):
TTGACAAAGTTTC
Found at i:2850868 original size:14 final size:14
Alignment explanation
Indices: 2850849--2850876 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2850839 GGACCCTTCT
2850849 TTTTTGTTTTTTTA
1 TTTTTGTTTTTTTA
2850863 TTTTTGTTTTTTTA
1 TTTTTGTTTTTTTA
2850877 ACGAATGACG
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:0.07, C:0.00, G:0.07, T:0.86
Consensus pattern (14 bp):
TTTTTGTTTTTTTA
Found at i:2860643 original size:22 final size:21
Alignment explanation
Indices: 2860613--2860653 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2860603 TAGTGACTAT
*
2860613 ACAAAAATAATAGGAATGAATA
1 ACAAAAATAA-AAGAATGAATA
*
2860635 ACAAGAATAAAAGAATGAA
1 ACAAAAATAAAAGAATGAA
2860654 CATCAATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.66, C:0.05, G:0.15, T:0.15
Consensus pattern (21 bp):
ACAAAAATAAAAGAATGAATA
Found at i:2868723 original size:20 final size:20
Alignment explanation
Indices: 2868700--2868745 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
2868690 AGATGTGTCG
2868700 ATACATTTTTCAATGTATCA
1 ATACATTTTTCAATGTATCA
* *
2868720 ATACATTTTTCAGTGTATCG
1 ATACATTTTTCAATGTATCA
2868740 ATACAT
1 ATACAT
2868746 CTAGTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (20 bp):
ATACATTTTTCAATGTATCA
Found at i:2876971 original size:42 final size:42
Alignment explanation
Indices: 2876915--2877033 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
2876905 TTCTTCTCTC
* * *
2876915 CTCCTTCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
2876957 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
2876999 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
2877034 TTGAGGGCTA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.08, C:0.45, G:0.03, T:0.44
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:2876974 original size:12 final size:11
Alignment explanation
Indices: 2876948--2877023 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
2876938 TCTATTATCT
*
2876948 CTCCTGTCTCTC
1 CTCCTATCTC-C
2876960 CTCCTATCATCC
1 CTCCTATC-TCC
2876972 CTCCTATCT--
1 CTCCTATCTCC
*
2876981 CTACTATCT--
1 CTCCTATCTCC
*
2876990 CTCCTGTCTCTC
1 CTCCTATCTC-C
2877002 CTCCTATCATCC
1 CTCCTATC-TCC
*
2877014 CTCCTCTCTC
1 CTCCTATCTC
2877024 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:2876975 original size:24 final size:24
Alignment explanation
Indices: 2876939--2877024 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
2876929 CCTCCTCTCT
* *
2876939 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
2876963 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
2876984 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
2877005 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
2877025 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:2876999 original size:18 final size:18
Alignment explanation
Indices: 2876930--2877000 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
2876920 TCTGTCATCC
* *
2876930 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
2876948 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
2876970 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
2876990 CTCCTGTCTCT
1 CTCCTGTCTCT
2877001 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:2877800 original size:22 final size:22
Alignment explanation
Indices: 2877772--2877817 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
2877762 AATACTGGTT
2877772 TTTTTTTTCTCTTTTTGTATTC
1 TTTTTTTTCTCTTTTTGTATTC
* *
2877794 TTTTTTTTTTTTTTTTGTATTC
1 TTTTTTTTCTCTTTTTGTATTC
2877816 TT
1 TT
2877818 GAAAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.04, C:0.09, G:0.04, T:0.83
Consensus pattern (22 bp):
TTTTTTTTCTCTTTTTGTATTC
Found at i:2884852 original size:30 final size:30
Alignment explanation
Indices: 2884818--2884897 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
2884808 TTCTCTCCTC
* *
2884818 CTCCTGTCATC-CCTCCTCTCTCTATTATCT
1 CTCCTGTC-TCTCCTCCTATCTCTACTATCT
2884848 CTCCTGTCTCTCCTCCTATCTCTACTATCT
1 CTCCTGTCTCTCCTCCTATCTCTACTATCT
2884878 CTCCTGTCTCTCCTCCTATC
1 CTCCTGTCTCTCCTCCTATC
2884898 ATCCCTCCTC
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 2 0.04
30 45 0.96
ACGTcount: A:0.09, C:0.45, G:0.04, T:0.42
Consensus pattern (30 bp):
CTCCTGTCTCTCCTCCTATCTCTACTATCT
Found at i:2884869 original size:21 final size:21
Alignment explanation
Indices: 2884843--2884882 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2884833 CTCTCTCTAT
* *
2884843 TATCTCTCCTGTCTCTCCTCC
1 TATCTCTACTATCTCTCCTCC
2884864 TATCTCTACTATCTCTCCT
1 TATCTCTACTATCTCTCCT
2884883 GTCTCTCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.42, G:0.03, T:0.45
Consensus pattern (21 bp):
TATCTCTACTATCTCTCCTCC
Found at i:2890826 original size:30 final size:30
Alignment explanation
Indices: 2890792--2890871 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
2890782 TTCTCTCCTC
* *
2890792 CTCCTGTCATC-CCTCCTCTCTCTATTATCT
1 CTCCTGTC-TCTCCTCCTATCTCTACTATCT
2890822 CTCCTGTCTCTCCTCCTATCTCTACTATCT
1 CTCCTGTCTCTCCTCCTATCTCTACTATCT
2890852 CTCCTGTCTCTCCTCCTATC
1 CTCCTGTCTCTCCTCCTATC
2890872 ATCCCTCCTC
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 2 0.04
30 45 0.96
ACGTcount: A:0.09, C:0.45, G:0.04, T:0.42
Consensus pattern (30 bp):
CTCCTGTCTCTCCTCCTATCTCTACTATCT
Found at i:2890843 original size:21 final size:21
Alignment explanation
Indices: 2890817--2890856 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2890807 CTCTCTCTAT
* *
2890817 TATCTCTCCTGTCTCTCCTCC
1 TATCTCTACTATCTCTCCTCC
2890838 TATCTCTACTATCTCTCCT
1 TATCTCTACTATCTCTCCT
2890857 GTCTCTCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.42, G:0.03, T:0.45
Consensus pattern (21 bp):
TATCTCTACTATCTCTCCTCC
Found at i:2892922 original size:728 final size:727
Alignment explanation
Indices: 2891781--2893236 Score: 2770
Period size: 728 Copynumber: 2.0 Consensus size: 727
2891771 TAATGAATTT
*
2891781 AATCGAACTCCAAACCAAAGCTCTGATACCAATTGATGACAACCATGAACCAAGGTTGCCTAAAT
1 AATCCAACTCCAAACCAAAGCTCTGATACCAATTGATGACAACCATGAACCAAGGTTGCCTAAAT
2891846 AATGATCTTGAGATGGATTTCTAACAATAAACAGAATTATTCATGCAAGAACAGAAATTGAAAGA
66 AATGATCTTGAGATGGATTTCTAACAATAAACAGAATTATTCATGCAAGAACAGAAATTGAAAGA
* *
2891911 AGCAGAAAAAAATAACAAAATGGAATAGATTAGAGATGAAGGATGGCACCACAATCACAAGATTG
131 AGCAGAAAAAAACAAAAAAATGGAATAGATTAGAGATGAAGGATGGCACCACAATCACAAGATTG
2891976 ATAAGCCAAAAGGAATGATCGCCACAAGAGTCTTGGCCTCTTGATAAGATCCAGAAAAATTGGCT
196 ATAAGCCAAAAGGAATGATCGCCACAAGAGTCTTGGCCTCTTGATAAGATCCAGAAAAATTGGCT
2892041 CACTCAAGAACCTAAGAATCACTCTCACACAAAAATGTGTTTAATCTGCAAATATGAATGTCTGC
261 CACTCAAGAACCTAAGAATCACTCTCACACAAAAATGTGTTTAATCTGCAAATATGAATGTCTGC
2892106 CCCCTCCAAATCTGTTTACAAGAGCTTATATATGCCCTCATAAGTCATAGATAACACAAACCCTA
326 CCCCTCCAAATCTGTTTACAAGAGCTTATATATGCCCTCATAAGTCATAGATAACACAAACCCTA
2892171 AGGGGCTTATTATGCTAACAAGCCCAACTCTTACTTAAACCCAAATAACAAGTTTTTATGCTAAA
391 AGGGGCTTATTATGCTAACAAGCCCAACTCTTACTTAAACCCAAATAACAAGTTTTTATGCTAAA
2892236 TAAAGCCCAAAGCAAGTCACAACCAGCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATTCAA
456 TAAAGCCCAAAGCAAGTCACAACCAGCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATTCAA
* *
2892301 TCCATTGGAGCCCATATCTTCCAAA-ATATGCAATTAACTAGCTTGGGCTCTTCTAAGTCCAAAT
521 TCCATTGGAGCCCATATCTTCCAAACATATGCAAGTAACTAGCTTGGGCTCTTCTAACTCCAAAT
2892365 TGGATCTACTTTCAAATAGGCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTT
586 TGGATCTACTTTCAAATAGGCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTT
*
2892430 GCCTTCGTTATTGGTCCTTGAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCAATGGACCTTCC
651 GCCCTCGTTATTGGTCCTTGAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCAATGGACCTTCC
2892495 TTGGTTTTCATC
716 TTGGTTTTCATC
*
2892507 AATCCAACTCCAAACCAAAGCTCTGATACCAATTGATGACAACTATGAACCAAGGTTGCCTAAAT
1 AATCCAACTCCAAACCAAAGCTCTGATACCAATTGATGACAACCATGAACCAAGGTTGCCTAAAT
* *
2892572 AGTGATCTTGAGATGGATTTCTAAACAATAAACAGAATTATTGATGCAAGAACAGAAATTGAAAG
66 AATGATCTTGAGATGGATTTCT-AACAATAAACAGAATTATTCATGCAAGAACAGAAATTGAAAG
*
2892637 AAGCAGAAAAAAACAAAAAAATGGAATAGATTAGAGATGAAGGATGGCGCCACAATCACAAGATT
130 AAGCAGAAAAAAACAAAAAAATGGAATAGATTAGAGATGAAGGATGGCACCACAATCACAAGATT
*
2892702 GATAAGCCAAAAGGAGTGATCGCCACAAGAGTCTTGGCCTCTTGATAAGATCCAGAAAAAATTGG
195 GATAAGCCAAAAGGAATGATCGCCACAAGAGTCTTGGCCTCTTGATAAGATCCAG-AAAAATTGG
2892767 CTCACTCAAGAACCTAAGAATCACTCTCACACAAAAATGTGTTTAATCTGCAAATATGAATGTCT
259 CTCACTCAAGAACCTAAGAATCACTCTCACACAAAAATGTGTTTAATCTGCAAATATGAATGTCT
2892832 GCCCCCTCCAAATCTGTTTACAAGAGCTTATATATGCCCTCATAAGTCATAGATAACACAAACCC
324 GCCCCCTCCAAATCTGTTTACAAGAGCTTATATATGCCCTCATAAGTCATAGATAACACAAACCC
2892897 TAAGGGGCTTATTATGCTAACAAGCCCAACTCTTACTTAAACCCAAATAACAAGTTTTTATGCTA
389 TAAGGGGCTTATTATGCTAACAAGCCCAACTCTTACTTAAACCCAAATAACAAGTTTTTATGCTA
*
2892962 AATAAAGCCCTAAGCAAGTCACAACCAGCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATTC
454 AATAAAGCCCAAAGCAAGTCACAACCAGCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATTC
2893027 AATCCATTGGAGCCCATATCTTCCAAACATATGCAAGTAACTAGCTTGGGCTCTTCTAACTCCAA
519 AATCCATTGGAGCCCATATCTTCCAAACATATGCAAGTAACTAGCTTGGGCTCTTCTAACTCCAA
*
2893092 ATTGGGTCTACTTTCAAATAGGCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCT
584 ATTGGATCTACTTTCAAATAGGCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCT
2893157 TTGCCCTCGTTATTGGTCCTTGAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCAATGGACCTT
649 TTGCCCTCGTTATTGGTCCTTGAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCAATGGACCTT
2893222 CCTTGGTTTTCATC
714 CCTTGGTTTTCATC
2893236 A
1 A
2893237 CCTTGAGTCA
Statistics
Matches: 714, Mismatches: 13, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
726 84 0.12
727 157 0.22
728 295 0.41
729 178 0.25
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (727 bp):
AATCCAACTCCAAACCAAAGCTCTGATACCAATTGATGACAACCATGAACCAAGGTTGCCTAAAT
AATGATCTTGAGATGGATTTCTAACAATAAACAGAATTATTCATGCAAGAACAGAAATTGAAAGA
AGCAGAAAAAAACAAAAAAATGGAATAGATTAGAGATGAAGGATGGCACCACAATCACAAGATTG
ATAAGCCAAAAGGAATGATCGCCACAAGAGTCTTGGCCTCTTGATAAGATCCAGAAAAATTGGCT
CACTCAAGAACCTAAGAATCACTCTCACACAAAAATGTGTTTAATCTGCAAATATGAATGTCTGC
CCCCTCCAAATCTGTTTACAAGAGCTTATATATGCCCTCATAAGTCATAGATAACACAAACCCTA
AGGGGCTTATTATGCTAACAAGCCCAACTCTTACTTAAACCCAAATAACAAGTTTTTATGCTAAA
TAAAGCCCAAAGCAAGTCACAACCAGCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATTCAA
TCCATTGGAGCCCATATCTTCCAAACATATGCAAGTAACTAGCTTGGGCTCTTCTAACTCCAAAT
TGGATCTACTTTCAAATAGGCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTT
GCCCTCGTTATTGGTCCTTGAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCAATGGACCTTCC
TTGGTTTTCATC
Found at i:2905999 original size:34 final size:32
Alignment explanation
Indices: 2905936--2906000 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
2905926 TAGCCAAACT
** *
2905936 TGTATCGATACACAAAGTATGTATTGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
2905968 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACAC-AAAAAA-TGTATCGATACA
2906001 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 13 0.46
33 4 0.14
34 11 0.39
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:2910067 original size:15 final size:15
Alignment explanation
Indices: 2910047--2910077 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2910037 TAAAAATGTC
*
2910047 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2910062 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2910077 C
1 C
2910078 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2913594 original size:12 final size:11
Alignment explanation
Indices: 2913572--2913647 Score: 61
Period size: 12 Copynumber: 6.9 Consensus size: 11
2913562 AGAGAAAGAA
*
2913572 GAGAGAGGAGG
1 GAGATAGGAGG
2913583 GATGATAGGAGG
1 GA-GATAGGAGG
2913595 AGAGATAGGA--
1 -GAGATAGGAGG
*
2913605 GAGATAGTA--
1 GAGATAGGAGG
2913614 GAGATAGGAGG
1 GAGATAGGAGG
2913625 GATGATAGGAGG
1 GA-GATAGGAGG
*
2913637 AGAGACAGGAG
1 -GAGATAGGAG
2913648 AGATAATAGA
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
9 16 0.29
11 4 0.07
12 31 0.56
13 4 0.07
ACGTcount: A:0.39, C:0.01, G:0.49, T:0.11
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:2913608 original size:33 final size:30
Alignment explanation
Indices: 2913562--2913652 Score: 76
Period size: 33 Copynumber: 2.8 Consensus size: 30
2913552 TAGCCCTCAA
* *
2913562 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGG
1 AGAGATAGGAGAGAGAGGA--GA-GATAGGAGG
* *
2913595 AGAGATAGGAGAGATAGTAGAGATAGGAGG
1 AGAGATAGGAGAGAGAGGAGAGATAGGAGG
2913625 -GATGATAGGAGGAGAGACAGGAGAGATA
1 AGA-GATAGGA-GAGAG--AGGAGAGATA
2913653 ATAGAGAGAG
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
29 2 0.04
30 16 0.33
31 6 0.12
33 24 0.50
ACGTcount: A:0.44, C:0.01, G:0.45, T:0.10
Consensus pattern (30 bp):
AGAGATAGGAGAGAGAGGAGAGATAGGAGG
Found at i:2913617 original size:11 final size:9
Alignment explanation
Indices: 2913592--2913652 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
2913582 GGATGATAGG
2913592 AGGAGAGAT
1 AGGAGAGAT
2913601 AGGAGAGAT
1 AGGAGAGAT
*
2913610 AGTAGAGAT
1 AGGAGAGAT
*
2913619 AGGAGGGAT
1 AGGAGAGAT
* *
2913628 --GATAG-G
1 AGGAGAGAT
*
2913634 AGGAGAGAC
1 AGGAGAGAT
2913643 AGGAGAGAT
1 AGGAGAGAT
2913652 A
1 A
2913653 ATAGAGAGAG
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
7 3 0.08
8 4 0.10
9 33 0.82
ACGTcount: A:0.43, C:0.02, G:0.44, T:0.11
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:2913623 original size:42 final size:42
Alignment explanation
Indices: 2913562--2913680 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
2913552 TAGCCCTCAA
* * *
2913562 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGATAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
2913604 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
2913646 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
2913681 GAGAGAAGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.43, C:0.02, G:0.46, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:2918890 original size:13 final size:13
Alignment explanation
Indices: 2918872--2918909 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
2918862 CATTTTTCTT
2918872 TGTATCGATACAA
1 TGTATCGATACAA
*
2918885 TGTATCGATACAC
1 TGTATCGATACAA
2918898 TGTATCGATACA
1 TGTATCGATACA
2918910 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2921484 original size:21 final size:20
Alignment explanation
Indices: 2921438--2921490 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
2921428 GTAGCCAAAC
**
2921438 TTGTATCGATACACAAAGTA
1 TTGTATCGATACACAAAAAA
2921458 -TGTATCGATACACAAAAAAA
1 TTGTATCGATACAC-AAAAAA
2921478 TTGTATCGATACA
1 TTGTATCGATACA
2921491 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Done.