Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 119 of 235
Found at i:40603120 original size:33 final size:33
Alignment explanation
Indices: 40603083--40603151 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
40603073 CTTCAGCCGC
40603083 CGCATACCCCTCAGCCTTGGCCACCACGCCCCA
1 CGCATACCCCTCAGCCTTGGCCACCACGCCCCA
* * *
40603116 CGCATGCCCCTCAGCCTTGGTCACCACGCTCCA
1 CGCATACCCCTCAGCCTTGGCCACCACGCCCCA
40603149 CGC
1 CGC
40603152 GTCTGACACT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.16, C:0.52, G:0.17, T:0.14
Consensus pattern (33 bp):
CGCATACCCCTCAGCCTTGGCCACCACGCCCCA
Found at i:40604249 original size:12 final size:12
Alignment explanation
Indices: 40604232--40604317 Score: 54
Period size: 12 Copynumber: 7.2 Consensus size: 12
40604222 TTTTTTGTTG
*
40604232 TTTATATTTTTA
1 TTTATATTATTA
40604244 TTTATATTATTA
1 TTTATATTATTA
*
40604256 -TTAGTATCATTA
1 TTTA-TATTATTA
40604268 -TTATTATTATTA
1 TTTA-TATTATTA
* ** *
40604280 TCTCCATTACTA
1 TTTATATTATTA
40604292 -TTATTATTATTA
1 TTTA-TATTATTA
40604304 -TTATTATTATTA
1 TTTA-TATTATTA
40604316 TT
1 TT
40604318 CTCTTGTTAT
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
11 4 0.07
12 52 0.90
13 2 0.03
ACGTcount: A:0.30, C:0.06, G:0.01, T:0.63
Consensus pattern (12 bp):
TTTATATTATTA
Found at i:40604356 original size:20 final size:21
Alignment explanation
Indices: 40604331--40604370 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
40604321 TTGTTATATT
*
40604331 ACTATTATTGTTA-TATTATC
1 ACTATTATTCTTACTATTATC
*
40604351 ACTATTTTTCTTACTATTAT
1 ACTATTATTCTTACTATTAT
40604371 TATTACTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.28, C:0.12, G:0.03, T:0.57
Consensus pattern (21 bp):
ACTATTATTCTTACTATTATC
Found at i:40604390 original size:3 final size:3
Alignment explanation
Indices: 40604248--40604375 Score: 91
Period size: 3 Copynumber: 42.7 Consensus size: 3
40604238 TTTTTATTTA
* * *
40604248 TAT TAT TAT TAG TAT CAT TAT TAT TAT TAT TAT CTCCAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -T--AT TAT TAT TAT
* * * * *
40604296 TAT TAT TAT TAT TAT TAT TAT T-C TCT TGT TA- TAT TAC TAT TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
40604342 TA- TAT TAT CAC TAT TTT TCT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
40604376 CTACAACTAT
Statistics
Matches: 96, Mismatches: 23, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
2 5 0.05
3 87 0.91
4 1 0.01
5 1 0.01
6 2 0.02
ACGTcount: A:0.29, C:0.09, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:40604687 original size:15 final size:15
Alignment explanation
Indices: 40604667--40604697 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
40604657 TATTATTTTC
40604667 TATTTATTACTATTA
1 TATTTATTACTATTA
40604682 TATTTATTACTATTA
1 TATTTATTACTATTA
40604697 T
1 T
40604698 TAATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTATTACTATTA
Found at i:40604804 original size:15 final size:15
Alignment explanation
Indices: 40604786--40604823 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
40604776 CCCACTTAGC
40604786 TATTATTACTATTAT
1 TATTATTACTATTAT
*
40604801 TATTTTTACTATTAT
1 TATTATTACTATTAT
*
40604816 AATTATTA
1 TATTATTA
40604824 TTAATCTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTATTACTATTAT
Found at i:40609226 original size:6 final size:6
Alignment explanation
Indices: 40609213--40609265 Score: 85
Period size: 6 Copynumber: 9.3 Consensus size: 6
40609203 AGGCAAATGC
40609213 AAAA-A AAAAG- AAAA-A AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
40609258 AAAAGA AA
1 AAAAGA AA
40609266 CCTAACAACA
Statistics
Matches: 45, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
5 12 0.27
6 33 0.73
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:40609831 original size:4 final size:4
Alignment explanation
Indices: 40609829--40609880 Score: 86
Period size: 4 Copynumber: 12.8 Consensus size: 4
40609819 TTCAAAAAAA
*
40609829 AAAG AAAG AAAG AAAG AAAA AAAG AAAG AAAG AAAG AAAG AAAG AGAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A-AAG
40609878 AAA
1 AAA
40609881 AAGGAGAGGC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
4 41 0.91
5 4 0.09
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:40611055 original size:64 final size:64
Alignment explanation
Indices: 40610949--40611076 Score: 220
Period size: 64 Copynumber: 2.0 Consensus size: 64
40610939 TCATTCATAA
*
40610949 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
* * *
40611013 CACATTTAGTTAGGAGCATTTGATTCATTTCAATCATTGCATCCTAATTATTTGGCATAAGCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
40611077 AGATACATGA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (64 bp):
CACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
Found at i:40611411 original size:87 final size:87
Alignment explanation
Indices: 40611320--40611651 Score: 474
Period size: 87 Copynumber: 3.8 Consensus size: 87
40611310 AATTTACAGA
* * * * *
40611320 CCTTAAACCCCTAAGCAGTAGGAG-AACAGGTTGAATTCATAGATCTT-ATCACCCTAAGCAGTA
1 CCTTAACCCCCTAAGCAGTAGG-GTAACAGGCTAAATTTACAGATCTTGA-CACCCTAAGCAGTA
** *
40611383 GGGAAACAGATCAAAGACGAAGGG
64 GGGAAACAGATCAAAGGTGATGGG
40611407 CCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAGATCTTGACACCCTAAGCAGTAGG
1 CCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAGATCTTGACACCCTAAGCAGTAGG
40611472 GAAACAGATCAAAGGTGATGGG
66 GAAACAGATCAAAGGTGATGGG
*
40611494 CTTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAGATCTTGACACCCTAAGCAGTAGG
1 CCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAGATCTTGACACCCTAAGCAGTAGG
40611559 GAAACAGATCAAAGGTGATGGG
66 GAAACAGATCAAAGGTGATGGG
* * ** *
40611581 CTTTAACCCCCTAAGCAGTAGGGTAACAAGCCGAATTTACAGA-CTT-AAACCCCTAAGCAGTAG
1 CCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAGATCTTGACA-CCCTAAGCAGTAG
*
40611644 GGTAACAG
65 GGAAACAG
40611652 GATAAATTCA
Statistics
Matches: 228, Mismatches: 14, Indels: 7
0.92 0.06 0.03
Matches are distributed among these distances:
85 2 0.01
86 24 0.11
87 201 0.88
88 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (87 bp):
CCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAGATCTTGACACCCTAAGCAGTAGG
GAAACAGATCAAAGGTGATGGG
Found at i:40611433 original size:130 final size:130
Alignment explanation
Indices: 40611147--40611954 Score: 589
Period size: 130 Copynumber: 6.2 Consensus size: 130
40611137 GAATCCACAA
* * *
40611147 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAGATCTTAAACCCCTAAGCAGTAG
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTTACAGACCTTAAACCCCTAAGCAGTAG
* * * ** *
40611212 GGTAACAGATCGAATT-GCAGATCTTATCTCCCTAAGCAGTAGTGG-AGTAGATCGAAGACGAAG
66 GGTAACAGGTCGAATTCACAGATCTTATCACCCTAAGCAGTAG-GGAAACAGATCAAAGACGAAG
40611275 G
130 G
* * *
40611276 GTCTTGACCCCCTAAGCAGTAGGGTAACAAGCCGAATTTACAGACCTTAAACCCCTAAGCAGTAG
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTTACAGACCTTAAACCCCTAAGCAGTAG
* *
40611341 GAG-AACAGGTTGAATTCATAGATCTTATCACCCTAAGCAGTAGGGAAACAGATCAAAGACGAAG
66 G-GTAACAGGTCGAATTCACAGATCTTATCACCCTAAGCAGTAGGGAAACAGATCAAAGACGAAG
40611405 G
130 G
* * * *
40611406 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAGATCTT-GACACCCTAAGCAGTA
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTTACAGACCTTAAAC-CCCTAAGCAGTA
* * * * * * ** * * * * *
40611470 GGGAAACAGATCAAAGGTGA-TGGGCTTTAACCCCCTAAGCAGTAGGGTAACAG-GCTAAATTTA
65 GGGTAACAGGTCGAA-TTCACAGATC-TTATCACCCTAAGCAGTAGGGAAACAGATC-AAA--GA
40611533 C--A-G
125 CGAAGG
** * * * * * * ** * * *
40611536 ATCTTGACACCCTAAGCAGTAGGGAAAC-AGATCAAAGGTGATGGGCTTTAACCCCCTAAGCAGT
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAAG-CCAAA-TTTACAGACCTTAAACCCCTAAGCAGT
* * * * * **
40611600 AGGGTAACAAGCCGAATTTACAGA-CTTA-AACCCCTAAGCAGTAGGGTAACAGGAT-AAATTC-
64 AGGGTAACAGGTCGAATTCACAGATCTTATCA-CCCTAAGCAGTAGGGAAACA-GATCAAAGACG
40611661 ACA-G
127 A-AGG
** ** * * * * * *
40611665 ATCTTGTCACCCTAAGCAGTAGGGAAAC-AGATCAAA--GACGAAGGGCCTTAACCCCCTAAGCA
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAAG-CCAAATTTAC--A-GACCTTAAACCCCTAAGCA
* * * * * *
40611727 GTAGGGTAACAGG-CTAAATTTACAAATCTTAACACCCTAAGCAGTAGAGAAACAGATCGAAG--
62 GTAGGGTAACAGGTC-GAATTCACAGATCTTATCACCCTAAGCAGTAGGGAAACAGATCAAAGAC
40611789 GTAATGG
126 G-AA-GG
* * *
40611796 GCTTTAACCCCCTAAGCAGTAAGGTAACAAGCCGAATTTACAGACCTTAAACCCCTAAGCAGTAG
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTTACAGACCTTAAACCCCTAAGCAGTAG
* * * *
40611861 GGTAACAGGTTGAATTCACAGATCTTATAACCCTAAGCAGTAGGGAAACAGATCGAATG-CGATG
66 GGTAACAGGTCGAATTCACAGATCTTATCACCCTAAGCAGTAGGGAAACAGATC-AAAGACGAAG
*
40611925 A
130 G
*
40611926 GCCTTAACCCCCTAAGTAGTAGGGTAACA
1 GCCTTAACCCCCTAAGCAGTAGGGTAACA
40611955 GGCTAGAAAT
Statistics
Matches: 540, Mismatches: 103, Indels: 71
0.76 0.14 0.10
Matches are distributed among these distances:
126 2 0.00
127 2 0.00
128 1 0.00
129 183 0.34
130 257 0.48
131 87 0.16
132 4 0.01
133 4 0.01
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (130 bp):
GCCTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTTACAGACCTTAAACCCCTAAGCAGTAG
GGTAACAGGTCGAATTCACAGATCTTATCACCCTAAGCAGTAGGGAAACAGATCAAAGACGAAGG
Found at i:40611658 original size:129 final size:130
Alignment explanation
Indices: 40611496--40611773 Score: 425
Period size: 129 Copynumber: 2.1 Consensus size: 130
40611486 GTGATGGGCT
* * *
40611496 TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAGATCTTGACACCCTAAGCAGTAGGGA
1 TTAAACCCCTAAGCAGTAGGGTAACAGGATAAATTCACAGATCTTGACACCCTAAGCAGTAGGGA
** * * * *
40611561 AACAGATCAAAGGTGATGGGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCGAATTTACAGA-C
66 AACAGATCAAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTTACAAATC
*
40611625 TTAAACCCCTAAGCAGTAGGGTAACAGGATAAATTCACAGATCTTGTCACCCTAAGCAGTAGGGA
1 TTAAACCCCTAAGCAGTAGGGTAACAGGATAAATTCACAGATCTTGACACCCTAAGCAGTAGGGA
* *
40611690 AACAGATCAAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAAATC
66 AACAGATCAAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTTACAAATC
40611755 TT-AACACCCTAAGCAGTAG
1 TTAAAC-CCCTAAGCAGTAG
40611774 AGAAACAGAT
Statistics
Matches: 135, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
129 119 0.88
130 16 0.12
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (130 bp):
TTAAACCCCTAAGCAGTAGGGTAACAGGATAAATTCACAGATCTTGACACCCTAAGCAGTAGGGA
AACAGATCAAAGACGAAGGGCCTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTTACAAATC
Found at i:40611745 original size:303 final size:304
Alignment explanation
Indices: 40611282--40611868 Score: 991
Period size: 303 Copynumber: 1.9 Consensus size: 304
40611272 AAGGGTCTTG
40611282 ACCCCCTAAGCAGTAGGGTAACAAGCCGAATTTACAGACCTTAAACCCCTAAGCAGTAGGAGAAC
1 ACCCCCTAAGCAGTAGGGTAACAAGCCGAATTTACAGACCTTAAACCCCTAAGCAGTAGGAGAAC
* * *
40611347 AGGTTGAATTCATAGATCTTATCACCCTAAGCAGTAGGGAAACAGATCAAAGACGAAGGGCCTTA
66 AGGATAAATTCACAGATCTTATCACCCTAAGCAGTAGGGAAACAGATCAAAGACGAAGGGCCTTA
* * *
40611412 ACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAGATCTTGACACCCTAAGCAGTAGGGAAAC
131 ACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAAATCTTAACACCCTAAGCAGTAGAGAAAC
* * * * *
40611477 AGATCAAAGGTGATGGGCTTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAGATCTT-
196 AGATCAAAGGTAATGGGCTTTAACCCCCTAAGCAGTAAGGTAACAAGCCAAATTTACAGACCTTA
*
40611541 GACACCCTAAGCAGTAGGGAAACAGATCAAAGGTGATGGGCTTTA
261 AAC-CCCTAAGCAGTAGGGAAACAGATCAAAGGTGATGGGCTTTA
40611586 ACCCCCTAAGCAGTAGGGTAACAAGCCGAATTTACAGA-CTTAAACCCCTAAGCAGTAGG-GTAA
1 ACCCCCTAAGCAGTAGGGTAACAAGCCGAATTTACAGACCTTAAACCCCTAAGCAGTAGGAG-AA
*
40611649 CAGGATAAATTCACAGATCTTGTCACCCTAAGCAGTAGGGAAACAGATCAAAGACGAAGGGCCTT
65 CAGGATAAATTCACAGATCTTATCACCCTAAGCAGTAGGGAAACAGATCAAAGACGAAGGGCCTT
40611714 AACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAAATCTTAACACCCTAAGCAGTAGAGAAA
130 AACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAAATCTTAACACCCTAAGCAGTAGAGAAA
* *
40611779 CAGATCGAAGGTAATGGGCTTTAACCCCCTAAGCAGTAAGGTAACAAGCCGAATTTACAGACCTT
195 CAGATCAAAGGTAATGGGCTTTAACCCCCTAAGCAGTAAGGTAACAAGCCAAATTTACAGACCTT
*
40611844 AAACCCCTAAGCAGTAGGGTAACAG
260 AAACCCCTAAGCAGTAGGGAAACAG
40611869 GTTGAATTCA
Statistics
Matches: 265, Mismatches: 16, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
302 1 0.00
303 224 0.85
304 40 0.15
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.19
Consensus pattern (304 bp):
ACCCCCTAAGCAGTAGGGTAACAAGCCGAATTTACAGACCTTAAACCCCTAAGCAGTAGGAGAAC
AGGATAAATTCACAGATCTTATCACCCTAAGCAGTAGGGAAACAGATCAAAGACGAAGGGCCTTA
ACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAAATCTTAACACCCTAAGCAGTAGAGAAAC
AGATCAAAGGTAATGGGCTTTAACCCCCTAAGCAGTAAGGTAACAAGCCAAATTTACAGACCTTA
AACCCCTAAGCAGTAGGGAAACAGATCAAAGGTGATGGGCTTTA
Found at i:40611834 original size:87 final size:86
Alignment explanation
Indices: 40611624--40611860 Score: 298
Period size: 87 Copynumber: 2.7 Consensus size: 86
40611614 AATTTACAGA
* * * ** *
40611624 CTTAAACCCCTAAGCAGTAGGGTAACAGGATAAATTCACAGATCTTGTCACCCTAAGCAGTAGGG
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAGATCTTAACACCCTAAGCAGTAGAG
40611689 AAACAGATCAAAGACGAAGGGC
66 AAACAGATCAAAGA-GAAGGGC
*
40611711 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAAATCTTAACACCCTAAGCAGTAGAG
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAGATCTTAACACCCTAAGCAGTAGAG
*
40611776 AAACAGATCGAAG-GTAATGGGC
66 AAACAGATCAAAGAG-AA-GGGC
* * * ** *
40611798 TTTAACCCCCTAAGCAGTAAGGTAACAAGCCGAATTTACAGACCTTAA-ACCCCTAAGCAGTAG
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAGATCTTAACA-CCCTAAGCAGTAG
40611861 GGTAACAGGT
Statistics
Matches: 132, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
85 1 0.01
86 3 0.02
87 128 0.97
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (86 bp):
CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAGATCTTAACACCCTAAGCAGTAGAG
AAACAGATCAAAGAGAAGGGC
Found at i:40612533 original size:17 final size:17
Alignment explanation
Indices: 40612511--40612549 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
40612501 GCCCAAATTA
40612511 AAAGTCCATTTACAAAC
1 AAAGTCCATTTACAAAC
40612528 AAAGTCCATTTACAAAC
1 AAAGTCCATTTACAAAC
40612545 AAAGT
1 AAAGT
40612550 TACCAGCCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.49, C:0.21, G:0.08, T:0.23
Consensus pattern (17 bp):
AAAGTCCATTTACAAAC
Found at i:40613798 original size:3 final size:3
Alignment explanation
Indices: 40613790--40613847 Score: 62
Period size: 3 Copynumber: 18.3 Consensus size: 3
40613780 TTTTTATTTA
* * *
40613790 TAT TAT TAT TAG TAT CAT TAT TAT TAT TAT TAT CTCCAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -T--AT TAT TAT TAT
40613838 TAT TAT TAT T
1 TAT TAT TAT T
40613848 CTCTTGTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
3 42 0.91
4 1 0.02
5 1 0.02
6 2 0.04
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:40613816 original size:21 final size:21
Alignment explanation
Indices: 40613790--40613843 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
40613780 TTTTTATTTA
*
40613790 TATTATTATTAGTAT-CATTAT
1 TATTATTATTA-TATCCATTAC
*
40613811 TATTATTATTATCTCCATTAC
1 TATTATTATTATATCCATTAC
40613832 TATTATTATTAT
1 TATTATTATTAT
40613844 TATTCTCTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.57
Consensus pattern (21 bp):
TATTATTATTATATCCATTAC
Found at i:40613845 original size:15 final size:15
Alignment explanation
Indices: 40613790--40613945 Score: 59
Period size: 15 Copynumber: 10.4 Consensus size: 15
40613780 TTTTTATTTA
*
40613790 TATTATTATTAGTAT
1 TATTATTATTACTAT
* *
40613805 CATTATTATTATTAT
1 TATTATTATTACTAT
**
40613820 TATCT-CCATTACTAT
1 TAT-TATTATTACTAT
*
40613835 TATTATTATTATTCTCT
1 TATTATTATTA--CTAT
*
40613852 TGTTA-TATTACTAT
1 TATTATTATTACTAT
* **
40613866 TATTGTGNTTACTAT
1 TATTATTATTACTAT
* * *
40613881 TCTTGTTA-TATTAT
1 TATTATTATTACTAT
* * * *
40613895 CACTATT-TTTCTTAC
1 TATTATTATTAC-TAT
*
40613910 TATTATTATTACTAC
1 TATTATTATTACTAT
* *
40613925 AACTATTATTACTAT
1 TATTATTATTACTAT
*
40613940 GATTAT
1 TATTAT
40613946 ATTTTCTTTT
Statistics
Matches: 99, Mismatches: 34, Indels: 16
0.66 0.23 0.11
Matches are distributed among these distances:
14 16 0.16
15 67 0.68
16 9 0.09
17 7 0.07
ACGTcount: A:0.28, C:0.12, G:0.04, T:0.56
Consensus pattern (15 bp):
TATTATTATTACTAT
Found at i:40613901 original size:20 final size:21
Alignment explanation
Indices: 40613876--40613915 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
40613866 TATTGTGNTT
*
40613876 ACTATTCTTGTTA-TATTATC
1 ACTATTCTTCTTACTATTATC
*
40613896 ACTATTTTTCTTACTATTAT
1 ACTATTCTTCTTACTATTAT
40613916 TATTACTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.25, C:0.15, G:0.03, T:0.57
Consensus pattern (21 bp):
ACTATTCTTCTTACTATTATC
Found at i:40614151 original size:23 final size:24
Alignment explanation
Indices: 40614125--40614169 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
40614115 TATTAACATA
* *
40614125 ATTTTTTA-CCATATTATTATTTC
1 ATTTTTTATACATATCATTATTTC
40614148 ATTTTTTATACATATCATTATT
1 ATTTTTTATACATATCATTATT
40614170 GATATTAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTTTTTATACATATCATTATTTC
Found at i:40614232 original size:15 final size:15
Alignment explanation
Indices: 40614212--40614242 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
40614202 TATTATTTTC
40614212 TATTTATTACTATTA
1 TATTTATTACTATTA
40614227 TATTTATTACTATTA
1 TATTTATTACTATTA
40614242 T
1 T
40614243 TAATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTATTACTATTA
Found at i:40614249 original size:21 final size:21
Alignment explanation
Indices: 40614216--40614255 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
40614206 ATTTTCTATT
* *
40614216 TATTACTATTATATTTATTAC
1 TATTACTAATATATATATTAC
*
40614237 TATTATTAATATATATATT
1 TATTACTAATATATATATT
40614256 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTACTAATATATATATTAC
Found at i:40614349 original size:15 final size:15
Alignment explanation
Indices: 40614331--40614368 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
40614321 CCCACTTAGC
40614331 TATTATTACTATTAT
1 TATTATTACTATTAT
*
40614346 TATTTTTACTATTAT
1 TATTATTACTATTAT
*
40614361 AATTATTA
1 TATTATTA
40614369 TTAATCTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTATTACTATTAT
Found at i:40622857 original size:20 final size:18
Alignment explanation
Indices: 40622810--40622858 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
40622800 CAAGATAAAC
40622810 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
40622827 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
40622847 ATTAAATTAATA
1 ATTAAATTAATA
40622859 AAATATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:40624443 original size:27 final size:27
Alignment explanation
Indices: 40624405--40624511 Score: 137
Period size: 27 Copynumber: 3.9 Consensus size: 27
40624395 GCCTTAAGAA
40624405 CAGATATATGTGGCAGAGCCACCAGAT
1 CAGATATATGTGGCAGAGCCACCAGAT
*
40624432 CAGATA-ATTGTGGCATAGCCACCAGGA-
1 CAGATATA-TGTGGCAGAGCCACCA-GAT
40624459 CAGATATATGTGGCAGAGCCACCAGAT
1 CAGATATATGTGGCAGAGCCACCAGAT
* * *
40624486 TAGATAAATTGTGGCATAGCCACCAG
1 CAGATATA-TGTGGCAGAGCCACCAG
40624512 TACGCTTCCT
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
26 3 0.04
27 48 0.69
28 19 0.27
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (27 bp):
CAGATATATGTGGCAGAGCCACCAGAT
Found at i:40624467 original size:54 final size:55
Alignment explanation
Indices: 40624404--40624511 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 55
40624394 GGCCTTAAGA
40624404 ACAGATATATGTGGCAGAGCCACCAGATCAGAT-AATTGTGGCATAGCCACCAGG
1 ACAGATATATGTGGCAGAGCCACCAGATCAGATAAATTGTGGCATAGCCACCAGG
*
40624458 ACAGATATATGTGGCAGAGCCACCAGATTAGATAAATTGTGGCATAGCCACCAG
1 ACAGATATATGTGGCAGAGCCACCAGATCAGATAAATTGTGGCATAGCCACCAG
40624512 TACGCTTCCT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
54 32 0.62
55 20 0.38
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.19
Consensus pattern (55 bp):
ACAGATATATGTGGCAGAGCCACCAGATCAGATAAATTGTGGCATAGCCACCAGG
Found at i:40624917 original size:8 final size:8
Alignment explanation
Indices: 40624901--40624930 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
40624891 CTCAAAATAC
40624901 CGGCTTTT
1 CGGCTTTT
*
40624909 CGGCATTT
1 CGGCTTTT
40624917 CGGCTTTT
1 CGGCTTTT
40624925 CGGCTT
1 CGGCTT
40624931 GTGCCGATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.03, C:0.27, G:0.27, T:0.43
Consensus pattern (8 bp):
CGGCTTTT
Found at i:40627612 original size:20 final size:20
Alignment explanation
Indices: 40627587--40627625 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
40627577 AATGCTATAC
*
40627587 AGAGGCACTGAAGTGCAAAA
1 AGAGGCACTAAAGTGCAAAA
40627607 AGAGGCACTAAAGTGCAAA
1 AGAGGCACTAAAGTGCAAA
40627626 CAAAGTCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.15, G:0.28, T:0.10
Consensus pattern (20 bp):
AGAGGCACTAAAGTGCAAAA
Found at i:40633006 original size:47 final size:48
Alignment explanation
Indices: 40632952--40633083 Score: 194
Period size: 47 Copynumber: 2.8 Consensus size: 48
40632942 TCACATCGAT
* *
40632952 AAGTACCTATACCATGGCTCATAGCCAAATCAAGGTAACTTATCTCAG
1 AAGTACCTATACCATGGCTCGTAGCCAAATCAAGGTAACTCATCTCAG
* * *
40633000 -AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCCTCTCTG
1 AAGTACCTATACCATGGCTCGTAGCCAAATCAAGGTAACTCATCTCAG
* *
40633047 AACTACCTATACCATTGCTCGTAGCCAAATCAAGGTA
1 AAGTACCTATACCATGGCTCGTAGCCAAATCAAGGTA
40633084 TAATTCGTAC
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
47 42 0.56
48 33 0.44
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (48 bp):
AAGTACCTATACCATGGCTCGTAGCCAAATCAAGGTAACTCATCTCAG
Found at i:40637186 original size:729 final size:730
Alignment explanation
Indices: 40634775--40637697 Score: 5407
Period size: 730 Copynumber: 4.0 Consensus size: 730
40634765 ACTTGTACGC
*
40634775 AGAACTCCAAAACTGCACCAAGGCTCGGAACAAATGCTTATCCACTCTAATATCTAGCAGGTAGG
1 AGAATTCCAAAACTGCACCAAGGCTCGGAACAAATGCTTATCCACTCTAATATCTAGCAGGTAGG
40634840 ATATGTCACCATAGCTTTGGTAAAACAACTGCTTGATCCCTTCATCCCAACTAGCCCAAATGTCT
66 ATATGTCACCATAGCTTTGGTAAAACAACTGCTTGATCCCTTCATCCCAACTAGCCCAAATGTCT
* *
40634905 CTCAACTCTTGCAGCTCATTCTGTACTACATTGACGCGAATGAAATCTTGCAGCTCCGATACATA
131 CTCAACTCTTGCAGCTCATTCTGTACTACATTGACGCGAGTGAAATCCTGCAGCTCCGATACATA
* *
40634970 CCCTTCTGCCAAGCTATCCCCCCTCTCAGATTGTAGCCTCTCCGACCAAGCACGAACGGTCGCAT
196 CCCTTCTGCCAAGCTATCCCCCCTCTCAGATTGTAGCCTCTCCGACTAAGCACGAACGGCCGCAT
* *
40635035 TATCTTCGACTTTACTAAGAAATTCATTCTCCATGTTAAATTTTCTAACTTAGTAATTGAATGCG
261 TATCCTCGACTTTACTAAGAAATTCATTCTCCATGTCAAATTTTCTAACTTAGTAATTGAATGCG
*
40635100 GATTAACGCCTCCTTTAATATGCAATGTCATGCCAAAAAGATAATCAAAACGAAACACCGGTTAG
326 GATTAACGCCTCCTTTAATATGCAATGTCATGCAAAAAAGATAATCAAAACGAAACACCGGTTAG
* *
40635165 TATCAAATAATAGTGATAAAATGTAAGCATATAAACAATAATTATAGCGCATATACGGGTAAGTA
391 TATCAAATAATAGCGATAAAATGCAAGCATATAAACAATAATTATAGCGCATATACGGGTAAGTA
*
40635230 CTAAGGCTCAACACGGCTCCACCCAAGGATAGCTCCTAAGGTTCACTATATGTGGTTTAGTTCTA
456 CTAAGGCTCGACACGGCTCCACCCAAGGATAGCTCCTAAGGTTCACTATATGTGGTTTAGTTCTA
40635295 GAGATAAGGTACCCGAACCAGCAGATTCCTCAATCCTCACCCATTATAGGGATCATATAGATCGA
521 GAGATAAGGTACCCGAACCAGCAGATTCCTCAATCCTCACCCATTATAGGGATCATATAGATCGA
*
40635360 GTTCGATTCGGAGGGATACATTTCCCTATGACCATGTGGAGATTAAAATCTCACGAAATCATAAG
586 GTTCGATTCGGAGGGATACATTTCCCTATGACCATGCGGAGATTAAAATCTCACGAAATCATAAG
*
40635425 TACGGATGTACCCCGGAAGCAATCCACTAGCCCATGCGGAGGTGAAAACCTCACGAAAGCGTAGC
651 TACGGATGTACCCCGGAAGCAATCCACTAGCCCATGCGGAGGTGAAAACCTCACGAAAGCATAGC
*
40635490 TTCGTACTCCCACTT
716 TTCTTACTCCCACTT
* *
40635505 AGAATTCTAAAACTGCACCAAGGCTCGAAACAAATGCTTATCCACTCTAATATCTAGCAGGTAGG
1 AGAATTCCAAAACTGCACCAAGGCTCGGAACAAATGCTTATCCACTCTAATATCTAGCAGGTAGG
*
40635570 ATATGTCACCATAGCTTTGGTAAAACAACTGCTTGATCCCTTCATCCCAACTAGCCCACATGTCT
66 ATATGTCACCATAGCTTTGGTAAAACAACTGCTTGATCCCTTCATCCCAACTAGCCCAAATGTCT
40635635 CTCAACTCTTGCAGCTCATTCTGTACTACATTGACGCGAGTGAAATCCTGCAGCTCCGATACATA
131 CTCAACTCTTGCAGCTCATTCTGTACTACATTGACGCGAGTGAAATCCTGCAGCTCCGATACATA
* *
40635700 CCCTTCTGCCAAGCTATCCCCCCTCTCAGATTGTAGCCTTTCCGACAAAGCACGAACGGCCGCAT
196 CCCTTCTGCCAAGCTATCCCCCCTCTCAGATTGTAGCCTCTCCGACTAAGCACGAACGGCCGCAT
*
40635765 TATCCTCGACTTTACTAAGAAATTCATTCTCCATGTCAAATTTTCTAACTTAGTAATTGAATACG
261 TATCCTCGACTTTACTAAGAAATTCATTCTCCATGTCAAATTTTCTAACTTAGTAATTGAATGCG
* *
40635830 GATTAACGCCTCCTTTAATATGCAATGTCATGCAAAAAAGATAATCAAAATGAAACACCGATTAG
326 GATTAACGCCTCCTTTAATATGCAATGTCATGCAAAAAAGATAATCAAAACGAAACACCGGTTAG
*
40635895 TGTCAAATAATAGCGATAAAATGCAAGCATATAAACAATAATTATAGCGCATATACGGGTAAGTA
391 TATCAAATAATAGCGATAAAATGCAAGCATATAAACAATAATTATAGCGCATATACGGGTAAGTA
*
40635960 CTAAGGCTCGACGCGGCTCCACCCAAGGATAGCTCCTAAGGTTCACTATATGTGGTTTAGTTCTA
456 CTAAGGCTCGACACGGCTCCACCCAAGGATAGCTCCTAAGGTTCACTATATGTGGTTTAGTTCTA
40636025 GAGATAAGGTACCCGAACCAGCAGATTCCTCAATCCTCACCCATTATAGGGATCATATAGATCGA
521 GAGATAAGGTACCCGAACCAGCAGATTCCTCAATCCTCACCCATTATAGGGATCATATAGATCGA
*
40636090 GTTCGATTCGGAGGGATACATTTCCCTATGACCATGTGGAGATTAAAATCTCACGAAATCATAAG
586 GTTCGATTCGGAGGGATACATTTCCCTATGACCATGCGGAGATTAAAATCTCACGAAATCATAAG
40636155 TACGGATGTACCCCGGAAGCAATCCACTAGCCCATGCGGAGGTGAAAACCTCACGAAAGCATAGC
651 TACGGATGTACCCCGGAAGCAATCCACTAGCCCATGCGGAGGTGAAAACCTCACGAAAGCATAGC
40636220 TTCTTACTCCCACTT
716 TTCTTACTCCCACTT
40636235 AGAATTCCAAAACTGCACCAAGGCTCGGAACAAATGCTTATCCACTCTAATATCTAGCAGGTAGG
1 AGAATTCCAAAACTGCACCAAGGCTCGGAACAAATGCTTATCCACTCTAATATCTAGCAGGTAGG
40636300 ATATGTCACCATAGCTTTGGTAAAACAACTGCTTGATCCCTTCATCCCAACTAGCCCAAATGTCT
66 ATATGTCACCATAGCTTTGGTAAAACAACTGCTTGATCCCTTCATCCCAACTAGCCCAAATGTCT
40636365 CTCAACTCTTGCAGCTCATTCTGTACTACATTGACGCGAGTGAAATCCTGCAGCTCCGATACATA
131 CTCAACTCTTGCAGCTCATTCTGTACTACATTGACGCGAGTGAAATCCTGCAGCTCCGATACATA
** * *
40636430 CCCTTCTGCCAAGCTATCCTTCCTCTCAGATTGTAGCCTCTCCGACTAAGCACGAATGGCCGTAT
196 CCCTTCTGCCAAGCTATCCCCCCTCTCAGATTGTAGCCTCTCCGACTAAGCACGAACGGCCGCAT
40636495 TATCCTCGACTTTACTAAGAAATTCATTCTCCATGTCAAATTTTCTAACTTAGTAATTGAATGCG
261 TATCCTCGACTTTACTAAGAAATTCATTCTCCATGTCAAATTTTCTAACTTAGTAATTGAATGCG
40636560 GATTAACGCCTCCTTTAATATGCAATGTCATGCAAAAAAGATAATCAAAACGAAACACCGGTTAG
326 GATTAACGCCTCCTTTAATATGCAATGTCATGCAAAAAAGATAATCAAAACGAAACACCGGTTAG
* *
40636625 TATCAAATAATAGCGATAAAATGCAAGCATATAAAAAATAATTATAGCGTATATACGGGTAAGTA
391 TATCAAATAATAGCGATAAAATGCAAGCATATAAACAATAATTATAGCGCATATACGGGTAAGTA
*
40636690 CTAAGGCTCGACGCGGCTCCACCCAAGGATAGCTCCTAAGGTTCACTATATGTGGTTTAGTTCTA
456 CTAAGGCTCGACACGGCTCCACCCAAGGATAGCTCCTAAGGTTCACTATATGTGGTTTAGTTCTA
* * * *
40636755 GAGATAAGGTACCCGAACCAGCAGATTCCTCGATCCTCACCCATTATA-GGCTTATATAGATTGA
521 GAGATAAGGTACCCGAACCAGCAGATTCCTCAATCCTCACCCATTATAGGGATCATATAGATCGA
* * *
40636819 GTTCGGTTCGGGGGGATACATTTCCCTATGACCATGCGGAAATTAAAATCTCACGAAATCATAAG
586 GTTCGATTCGGAGGGATACATTTCCCTATGACCATGCGGAGATTAAAATCTCACGAAATCATAAG
*
40636884 TACGGATGTACCCCGGAAGCAATCCACTAGCCCATGCGGAGGTGAAAACCTCAGGAAAGCATAGC
651 TACGGATGTACCCCGGAAGCAATCCACTAGCCCATGCGGAGGTGAAAACCTCACGAAAGCATAGC
40636949 TTCTTACTCCCACTT
716 TTCTTACTCCCACTT
40636964 AGAATTCCAAAACTGCACCAAGGCTCGGAACAAATGCTTATCCACTCTAATATCTAGCAGGTAGG
1 AGAATTCCAAAACTGCACCAAGGCTCGGAACAAATGCTTATCCACTCTAATATCTAGCAGGTAGG
40637029 ATATGTCACCATAGCTTTGGTAAAACAACTGCTTGATCCCTTCATCCCAACTAGCCCAAATGTCT
66 ATATGTCACCATAGCTTTGGTAAAACAACTGCTTGATCCCTTCATCCCAACTAGCCCAAATGTCT
*
40637094 CTCAACTCTTGCAGCTCATTCTGTACTACATTGACGAGAGTGAAATCCTGCAGCTCCGATACATA
131 CTCAACTCTTGCAGCTCATTCTGTACTACATTGACGCGAGTGAAATCCTGCAGCTCCGATACATA
40637159 CCCTTCTGCCAAGCTATCCCCCCTCTCAGATTGTAGCCTCTCCGACTAAGCACGAACGGCCGCAT
196 CCCTTCTGCCAAGCTATCCCCCCTCTCAGATTGTAGCCTCTCCGACTAAGCACGAACGGCCGCAT
40637224 TATCCTCGACTTTACTAAGAAATTCATTCTCCATGTCAAATTTTCTAACTTAGTAATTGAATGCG
261 TATCCTCGACTTTACTAAGAAATTCATTCTCCATGTCAAATTTTCTAACTTAGTAATTGAATGCG
40637289 GATTAACGCCTCCTTTAATATGCAATGTCATGCAAAAAAGATAATCAAAACGAAACACCGGTTAG
326 GATTAACGCCTCCTTTAATATGCAATGTCATGCAAAAAAGATAATCAAAACGAAACACCGGTTAG
*
40637354 TATCAAATAATAGCGATAAAATGCAAGCATATAAACAATAATTATAGCGTATATACGGGTAAGTA
391 TATCAAATAATAGCGATAAAATGCAAGCATATAAACAATAATTATAGCGCATATACGGGTAAGTA
40637419 CTAAGGCTCGACACGGCTCCACCCAAGGATAGCTCCTAAGGTTCACTATATGTGGTTTAGTTCTA
456 CTAAGGCTCGACACGGCTCCACCCAAGGATAGCTCCTAAGGTTCACTATATGTGGTTTAGTTCTA
* *
40637484 GAGATAAGGTATCCGAACCAGCAGATTCCTCAATCCTCACCCATTATAGGGCTCATATAGATCGA
521 GAGATAAGGTACCCGAACCAGCAGATTCCTCAATCCTCACCCATTATAGGGATCATATAGATCGA
* *
40637549 GTTTGATTCGGGGGGATACATTTCCCTATGACCATGCGGAGATTAAAATCTCACGAAATCATAAG
586 GTTCGATTCGGAGGGATACATTTCCCTATGACCATGCGGAGATTAAAATCTCACGAAATCATAAG
**
40637614 TACGGATGTACCCCGGAAGCAATCCACTAGCCCATGCGGAGGTGAAAACCTCACGAAAGTGTAGC
651 TACGGATGTACCCCGGAAGCAATCCACTAGCCCATGCGGAGGTGAAAACCTCACGAAAGCATAGC
40637679 TTCTTACTCCCACTT
716 TTCTTACTCCCACTT
40637694 AGAA
1 AGAA
40637698 GGTGTGACCA
Statistics
Matches: 2129, Mismatches: 63, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
729 712 0.33
730 1417 0.67
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (730 bp):
AGAATTCCAAAACTGCACCAAGGCTCGGAACAAATGCTTATCCACTCTAATATCTAGCAGGTAGG
ATATGTCACCATAGCTTTGGTAAAACAACTGCTTGATCCCTTCATCCCAACTAGCCCAAATGTCT
CTCAACTCTTGCAGCTCATTCTGTACTACATTGACGCGAGTGAAATCCTGCAGCTCCGATACATA
CCCTTCTGCCAAGCTATCCCCCCTCTCAGATTGTAGCCTCTCCGACTAAGCACGAACGGCCGCAT
TATCCTCGACTTTACTAAGAAATTCATTCTCCATGTCAAATTTTCTAACTTAGTAATTGAATGCG
GATTAACGCCTCCTTTAATATGCAATGTCATGCAAAAAAGATAATCAAAACGAAACACCGGTTAG
TATCAAATAATAGCGATAAAATGCAAGCATATAAACAATAATTATAGCGCATATACGGGTAAGTA
CTAAGGCTCGACACGGCTCCACCCAAGGATAGCTCCTAAGGTTCACTATATGTGGTTTAGTTCTA
GAGATAAGGTACCCGAACCAGCAGATTCCTCAATCCTCACCCATTATAGGGATCATATAGATCGA
GTTCGATTCGGAGGGATACATTTCCCTATGACCATGCGGAGATTAAAATCTCACGAAATCATAAG
TACGGATGTACCCCGGAAGCAATCCACTAGCCCATGCGGAGGTGAAAACCTCACGAAAGCATAGC
TTCTTACTCCCACTT
Found at i:40638934 original size:131 final size:131
Alignment explanation
Indices: 40638799--40639042 Score: 364
Period size: 131 Copynumber: 1.9 Consensus size: 131
40638789 AAGATATGAA
* * *
40638799 TGAAATTTTGAAGGGATGCTCGATTACTTTGGA-CAAACGCAAAATTGCAACCCAATACGTTAGG
1 TGAAATTTCGAAGGGATACTCGATTA-TTTGGAGCAAACGCAAAATTGCAACCCAACACGTTAGG
* * **
40638863 GCACGATTCCGCGAATTGCTAAGTATCGAATCTCGTCTTCGTTTTGAAGCATTTTAAACGACGCG
65 GCACGATTCCACGAATTGCCAAACATCGAATCTCGTCTTCGTTTTGAAGCATTTTAAACGACGCG
40638928 CG
130 CG
* * * *
40638930 TGAAATTTCGAAGTGATATTCGATTATTTTGAGCAAACGCGAAATTGCAACCCAACACGTTAGGG
1 TGAAATTTCGAAGGGATACTCGATTATTTGGAGCAAACGCAAAATTGCAACCCAACACGTTAGGG
*
40638995 CACGATTCCACTAATTGCCAAACATCGAATCTCGTCTTCGTTTTGAAG
66 CACGATTCCACGAATTGCCAAACATCGAATCTCGTCTTCGTTTTGAAG
40639043 AACTTTTGAA
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
130 5 0.05
131 95 0.95
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (131 bp):
TGAAATTTCGAAGGGATACTCGATTATTTGGAGCAAACGCAAAATTGCAACCCAACACGTTAGGG
CACGATTCCACGAATTGCCAAACATCGAATCTCGTCTTCGTTTTGAAGCATTTTAAACGACGCGC
G
Found at i:40639635 original size:15 final size:16
Alignment explanation
Indices: 40639601--40639644 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
40639591 GAAAGTTAAC
40639601 AAAATATATGATAGTACA
1 AAAATATATG--AGTACA
40639619 AAAATATATGA-TACA
1 AAAATATATGAGTACA
*
40639634 AAAATACATGA
1 AAAATATATGA
40639645 CAAAAAGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 14 0.56
16 1 0.04
18 10 0.40
ACGTcount: A:0.59, C:0.07, G:0.09, T:0.25
Consensus pattern (16 bp):
AAAATATATGAGTACA
Found at i:40644655 original size:131 final size:131
Alignment explanation
Indices: 40644404--40644733 Score: 319
Period size: 131 Copynumber: 2.5 Consensus size: 131
40644394 TAATTATTCA
* * ** ** ** *
40644404 TTTAAAAACTCTTTAAACCGAAGGCGATGTTCGATATTTGGTAATTCGCGA-AATCATGCCCTGT
1 TTTAAAAACTCTTCAAAACGAAGGAAATACTCGATATTTGACAATTCG-GAGAATCATGCCCTAT
* *** * * *
40644468 CGTGCTT-GGTTACAATTTCTCGTTTGCTCAAAATAATCGAATGTCCCTTTAGAATTTCACTCAT
65 CGTG-TTCAGTTGTGATTTTTCATTTGCTCAAAACAATCGAATGTCCCTTTAGAATTTCACTCAT
*
40644532 G-T
129 GAC
** * ** * * *
40644534 TTTCCAAAAACTCTTTGAAATGAAGGAAATGTTCGATGTTTGGCAATTC-GAGAATCGTGCCCTA
1 TTT--AAAAACTCTTCAAAACGAAGGAAATACTCGATATTTGACAATTCGGAGAATCATGCCCTA
* *
40644598 TCGTGTTCAGTTGTGATTTTTCATTTGTTCAAAACAATCGAA-GATTCCTTTAGAATTTCACTCA
64 TCGTGTTCAGTTGTGATTTTTCATTTGCTCAAAACAATCGAATG-TCCCTTTAGAATTTCACTCA
40644662 TGAC
128 TGAC
* *
40644666 TTTAAAAACTCTTCAAAACGAAGGTAATACTCGATATTTGACAATTCGGGGAATCATGCCCTATC
1 TTTAAAAACTCTTCAAAACGAAGGAAATACTCGATATTTGACAATTCGGAGAATCATGCCCTATC
40644731 GTG
66 GTG
40644734 CTTGTAATAG
Statistics
Matches: 164, Mismatches: 29, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
130 44 0.27
131 80 0.49
132 40 0.24
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (131 bp):
TTTAAAAACTCTTCAAAACGAAGGAAATACTCGATATTTGACAATTCGGAGAATCATGCCCTATC
GTGTTCAGTTGTGATTTTTCATTTGCTCAAAACAATCGAATGTCCCTTTAGAATTTCACTCATGA
C
Found at i:40646274 original size:17 final size:17
Alignment explanation
Indices: 40646252--40646291 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
40646242 GTTATATATA
*
40646252 TATATTTCAAATTATTT
1 TATATTTCAAATTATTG
* *
40646269 TATATTTTAAGTTATTG
1 TATATTTCAAATTATTG
40646286 TATATT
1 TATATT
40646292 ATATATTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (17 bp):
TATATTTCAAATTATTG
Found at i:40646421 original size:27 final size:28
Alignment explanation
Indices: 40646391--40646447 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
40646381 ATCATATATT
* *
40646391 TTAAACTCCT-TATTAATTATTTTTAAA
1 TTAAACTCATATATTAATTATTTTAAAA
* *
40646418 TT-AACTTATATATTATTTATTTTAAAA
1 TTAAACTCATATATTAATTATTTTAAAA
40646445 TTA
1 TTA
40646448 TTCATATATG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (28 bp):
TTAAACTCATATATTAATTATTTTAAAA
Found at i:40646423 original size:26 final size:27
Alignment explanation
Indices: 40646401--40646456 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
40646391 TTAAACTCCT
* *
40646401 TATTAATTATTTTTAAATTAACTTATA
1 TATTAATTATTTTAAAATTAACTCATA
* *
40646428 TATTATTTATTTTAAAATT-ATTCATA
1 TATTAATTATTTTAAAATTAACTCATA
40646454 TAT
1 TAT
40646457 GTCATTCTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (27 bp):
TATTAATTATTTTAAAATTAACTCATA
Found at i:40646538 original size:27 final size:25
Alignment explanation
Indices: 40646508--40646561 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 25
40646498 GCTTTATACA
*
40646508 TTATTTATTTGAAACTTGTTTTATGTG
1 TTATTCATTTGAAA-TTGTTTTAT-TG
*
40646535 TTATTCATTTTAAATTGTTTTATTG
1 TTATTCATTTGAAATTGTTTTATTG
40646560 TT
1 TT
40646562 TACTTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.16
26 9 0.36
27 12 0.48
ACGTcount: A:0.22, C:0.04, G:0.11, T:0.63
Consensus pattern (25 bp):
TTATTCATTTGAAATTGTTTTATTG
Found at i:40647288 original size:29 final size:27
Alignment explanation
Indices: 40647256--40647316 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
40647246 AAGTTGTTTC
40647256 TTTTTTTTATATACACTATGTATATTA
1 TTTTTTTTATATACACTATGTATATTA
*
40647283 TTTTTTTTATATATACTATGTATATTA
1 TTTTTTTTATATACACTATGTATATTA
40647310 TTTTTTT
1 TTTTTTT
40647317 AAAATTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (27 bp):
TTTTTTTTATATACACTATGTATATTA
Found at i:40656217 original size:40 final size:40
Alignment explanation
Indices: 40656162--40656239 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
40656152 AAACATTAAG
40656162 TAAAAAATAAAACAATTAATATTTAGATTCGGATTATAAA
1 TAAAAAATAAAACAATTAATATTTAGATTCGGATTATAAA
* *
40656202 TAAAAAATACAACAATTAATATTTATATTCGGATTATA
1 TAAAAAATAAAACAATTAATATTTAGATTCGGATTATA
40656240 GAAATACAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (40 bp):
TAAAAAATAAAACAATTAATATTTAGATTCGGATTATAAA
Found at i:40656398 original size:19 final size:20
Alignment explanation
Indices: 40656359--40656399 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
40656349 ATCAATACAA
*
40656359 TTCAATTTTACATTGAATAT
1 TTCAATTTTACATTCAATAT
*
40656379 TTCAATTTT-TATTCAATAT
1 TTCAATTTTACATTCAATAT
40656398 TT
1 TT
40656400 GCCTAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTCAATTTTACATTCAATAT
Found at i:40656971 original size:19 final size:20
Alignment explanation
Indices: 40656934--40656972 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
40656924 AATACTTATT
*
40656934 TATTATTTTATACATATGTA
1 TATTATTTTATACACATGTA
40656954 TATTATTTT-TACACATGTA
1 TATTATTTTATACACATGTA
40656973 CACTCAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (20 bp):
TATTATTTTATACACATGTA
Found at i:40657914 original size:38 final size:38
Alignment explanation
Indices: 40657869--40657945 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
40657859 GAATTTGTGA
* * *
40657869 ATAGTCCCGCATACTATCATAGCATAAAGACTTGGTGG
1 ATAGTCCCACAGACTATCATAGCACAAAGACTTGGTGG
* * *
40657907 ATAGTCCCACGGATTGTCATAGCACAAAGACTTGGTGG
1 ATAGTCCCACAGACTATCATAGCACAAAGACTTGGTGG
40657945 A
1 A
40657946 CTTATACATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (38 bp):
ATAGTCCCACAGACTATCATAGCACAAAGACTTGGTGG
Found at i:40657970 original size:29 final size:29
Alignment explanation
Indices: 40657937--40658048 Score: 143
Period size: 29 Copynumber: 3.9 Consensus size: 29
40657927 AGCACAAAGA
* * **
40657937 CTTGGTGGACTTATACATATGGATTCATG
1 CTTGGTGAACTCATACATGCGGATTCATG
*
40657966 CTTGGTGAACTCATACATGCGGACTCATG
1 CTTGGTGAACTCATACATGCGGATTCATG
* *
40657995 CTTGATGAACTCATACATGCAGATTCATG
1 CTTGGTGAACTCATACATGCGGATTCATG
* *
40658024 CTTGGTAAACTCATACATGTGGATT
1 CTTGGTGAACTCATACATGCGGATT
40658049 TATACTCACA
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 71 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (29 bp):
CTTGGTGAACTCATACATGCGGATTCATG
Found at i:40660104 original size:20 final size:20
Alignment explanation
Indices: 40660079--40660121 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
40660069 AGGAGTTAGA
40660079 TTACATTTTAACTTTTTTAC
1 TTACATTTTAACTTTTTTAC
40660099 TTACATTTTAACTTTTTTAC
1 TTACATTTTAACTTTTTTAC
40660119 TTA
1 TTA
40660122 AAAAATAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (20 bp):
TTACATTTTAACTTTTTTAC
Found at i:40660452 original size:21 final size:21
Alignment explanation
Indices: 40660418--40660477 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 21
40660408 TAAATAATTA
*
40660418 TAAAAAATAT-AGAAACTTAT
1 TAAAAATTATAAGAAACTTAT
*
40660438 TAAAAATTATAAG-AATTTAT
1 TAAAAATTATAAGAAACTTAT
*
40660458 TTAAAATCTATTAA-AAACTT
1 TAAAAAT-TA-TAAGAAACTT
40660478 GGACAAACAG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
20 21 0.66
21 4 0.12
22 7 0.22
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (21 bp):
TAAAAATTATAAGAAACTTAT
Found at i:40669457 original size:21 final size:21
Alignment explanation
Indices: 40669431--40669471 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40669421 AGACGAGCAA
* *
40669431 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
40669452 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
40669472 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:40675919 original size:19 final size:19
Alignment explanation
Indices: 40675897--40675933 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
40675887 CCACTATCAC
40675897 CCACCGTAATCAAATTTGA
1 CCACCGTAATCAAATTTGA
*
40675916 CCACTGTAATCAAATTTG
1 CCACCGTAATCAAATTTG
40675934 TTATTAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (19 bp):
CCACCGTAATCAAATTTGA
Found at i:40679365 original size:54 final size:56
Alignment explanation
Indices: 40679278--40679388 Score: 172
Period size: 57 Copynumber: 2.0 Consensus size: 56
40679268 AATTAGGAAT
*
40679278 TAATAAAATAAAATAATTGATTAATTAGG-TAATAATAATTGGATTAATAAAAATC
1 TAATAAAATAAAATAATTAATTAATTAGGATAATAATAATTGGATTAATAAAAATC
*
40679333 TAATAAAAT-AATTAATTAATTAATTAGGTAATAATAATAATTGGATTAATAAAAAT
1 TAATAAAATAAAATAATTAATTAATTAGG--ATAATAATAATTGGATTAATAAAAAT
40679389 ATATTAGTGA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
54 17 0.33
55 9 0.18
57 25 0.49
ACGTcount: A:0.55, C:0.01, G:0.08, T:0.36
Consensus pattern (56 bp):
TAATAAAATAAAATAATTAATTAATTAGGATAATAATAATTGGATTAATAAAAATC
Found at i:40680653 original size:19 final size:19
Alignment explanation
Indices: 40680629--40680681 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
40680619 ACTTGTATGC
*
40680629 ATGTGCGAACCCATAAGCT
1 ATGTGCAAACCCATAAGCT
40680648 ATGTGCAAACCCATAAGCT
1 ATGTGCAAACCCATAAGCT
40680667 ATGTGCAAACCCATA
1 ATGTGCAAACCCATA
40680682 TGAATGTGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (19 bp):
ATGTGCAAACCCATAAGCT
Found at i:40683359 original size:84 final size:84
Alignment explanation
Indices: 40683218--40683386 Score: 302
Period size: 84 Copynumber: 2.0 Consensus size: 84
40683208 ATGATAAGAG
* * *
40683218 AATGATTAAGTCTTATAATTGCATGAGATGTTGAGGGTGTTGGAACACTATTAAAATAAGTTGAA
1 AATGATTAAGTCTTATAATTGCATGAGATGTTGAGGATGTTAGAACACCATTAAAATAAGTTGAA
40683283 AATATAAAAGAAGATAAGT
66 AATATAAAAGAAGATAAGT
*
40683302 AATGATTAAGTCTTATAATTGCATGAGATGTTGAGGATGTTAGAACACCATTAAAATAAGTTGAT
1 AATGATTAAGTCTTATAATTGCATGAGATGTTGAGGATGTTAGAACACCATTAAAATAAGTTGAA
40683367 AATATAAAAGAAGATAAGT
66 AATATAAAAGAAGATAAGT
40683386 A
1 A
40683387 GATTTATTCC
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.31
Consensus pattern (84 bp):
AATGATTAAGTCTTATAATTGCATGAGATGTTGAGGATGTTAGAACACCATTAAAATAAGTTGAA
AATATAAAAGAAGATAAGT
Found at i:40684372 original size:164 final size:164
Alignment explanation
Indices: 40684072--40684402 Score: 448
Period size: 164 Copynumber: 2.0 Consensus size: 164
40684062 TTTATTATTC
*
40684072 AATAGAGGCCCAACATAGACTTAACAAAACATATAAGGTATACGAAAATAGTACAACAATGCACT
1 AATAGAGGCCCAACATAGACTTAACAAAACATATAAGGTATACGAAAATAGTACAACAATGCACC
* * * *
40684137 GAAGTGCAAATATAGAATAAGATGGCACTGAAGTGCATATTCAGAATAGGATAACATTAAAATGC
66 GAAGTGCAAATACAGAACAAGATGGCACCGAAGTGCATATTCAGAATAGGACAACATTAAAATGC
* * **
40684202 GTATTCAGAACAGGGAGTGCGCT-AAATTTTCCTT
131 GTATTCAAAACAGAGAGCACGCTAAAATTTT-CTT
** ** *
40684236 AATAGAGGCCCAAGGTAGACTTAACAAAATGTATAAGGTATACGAAAATAGTACAATAATGCACC
1 AATAGAGGCCCAACATAGACTTAACAAAACATATAAGGTATACGAAAATAGTACAACAATGCACC
* ** * * * * *
40684301 GAAGTGCAAATACAGAACAGGATGGCACCGAAGTGTGTATTCAGAATAGGGCAGCATTGATATGT
66 GAAGTGCAAATACAGAACAAGATGGCACCGAAGTGCATATTCAGAATAGGACAACATTAAAATGC
40684366 GTATTCAAAACAGAGAGCACGCTAAAATTTTCTT
131 GTATTCAAAACAGAGAGCACGCTAAAATTTTCTT
40684400 AAT
1 AAT
40684403 GGCATGCCAT
Statistics
Matches: 144, Mismatches: 22, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
164 137 0.95
165 7 0.05
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23
Consensus pattern (164 bp):
AATAGAGGCCCAACATAGACTTAACAAAACATATAAGGTATACGAAAATAGTACAACAATGCACC
GAAGTGCAAATACAGAACAAGATGGCACCGAAGTGCATATTCAGAATAGGACAACATTAAAATGC
GTATTCAAAACAGAGAGCACGCTAAAATTTTCTT
Found at i:40684592 original size:26 final size:26
Alignment explanation
Indices: 40684563--40684612 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
40684553 CCAACTTTCT
* * *
40684563 TTAATACATATAACATATTTCACTAC
1 TTAATAAAAATAACATAATTCACTAC
*
40684589 TTAATAAAAATTACATAATTCACT
1 TTAATAAAAATAACATAATTCACT
40684613 CTACAACTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.38
Consensus pattern (26 bp):
TTAATAAAAATAACATAATTCACTAC
Found at i:40685865 original size:11 final size:11
Alignment explanation
Indices: 40685849--40685895 Score: 58
Period size: 11 Copynumber: 4.0 Consensus size: 11
40685839 ATTTTAATTG
40685849 AATAAAATATT
1 AATAAAATATT
40685860 AATAAATATATTAT
1 AATAAA-ATA-T-T
*
40685874 AATAAAATAAT
1 AATAAAATATT
40685885 AATAAAATATT
1 AATAAAATATT
40685896 CAACCAATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
11 17 0.55
12 3 0.10
13 4 0.13
14 7 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATAAAATATT
Found at i:40685881 original size:25 final size:24
Alignment explanation
Indices: 40685849--40685895 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
40685839 ATTTTAATTG
*
40685849 AATAAAATATTAATAAATATATTAT
1 AATAAAATAATAATAAA-ATATTAT
40685874 AATAAAATAATAATAAAATATT
1 AATAAAATAATAATAAAATATT
40685896 CAACCAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
AATAAAATAATAATAAAATATTAT
Found at i:40692131 original size:18 final size:19
Alignment explanation
Indices: 40692110--40692145 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
40692100 TTATTTTCAG
40692110 TTATTTTCAATTT-AATTA
1 TTATTTTCAATTTGAATTA
*
40692128 TTATTTTTAATTTGAATT
1 TTATTTTCAATTTGAATT
40692146 TTTTTATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (19 bp):
TTATTTTCAATTTGAATTA
Found at i:40697400 original size:21 final size:21
Alignment explanation
Indices: 40697374--40697414 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40697364 CAACGTGACA
40697374 AGTTAACCGGCCACATCAGCT
1 AGTTAACCGGCCACATCAGCT
**
40697395 AGTTAACTTGCCACATCAGC
1 AGTTAACCGGCCACATCAGC
40697415 GGTCCCGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (21 bp):
AGTTAACCGGCCACATCAGCT
Found at i:40699762 original size:39 final size:39
Alignment explanation
Indices: 40699719--40699819 Score: 105
Period size: 39 Copynumber: 2.6 Consensus size: 39
40699709 ACCAGCTCGA
* *
40699719 AGCCTGCGGGA-CTTTAGCCCGGACATATTTCCAACACAT
1 AGCCTGC-GGACCTTAAGCCCGGACATAATTCCAACACAT
** *
40699758 AGCCTGCGGACCTTAAGCCCGGTTATAATTCCAGCACAT
1 AGCCTGCGGACCTTAAGCCCGGACATAATTCCAACACAT
* * * *
40699797 AGCCCGCGAACCCTAAGTCCGGA
1 AGCCTGCGGACCTTAAGCCCGGA
40699820 TGAACATCAC
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
38 3 0.06
39 48 0.94
ACGTcount: A:0.26, C:0.33, G:0.22, T:0.20
Consensus pattern (39 bp):
AGCCTGCGGACCTTAAGCCCGGACATAATTCCAACACAT
Found at i:40711525 original size:78 final size:78
Alignment explanation
Indices: 40711452--40711624 Score: 231
Period size: 78 Copynumber: 2.2 Consensus size: 78
40711442 ACCAGCTCGA
* * * * * *
40711452 AGCCTGCGGGA-CTTTAGCCCGAACATATTTCTAGCACGTAGCCTGCGGACCTTAAGTCCGATTA
1 AGCCTGC-GGACCTTAAGCCCGAACATAATTCCAGCACATAGCCTGCGGACCCTAAGTCCGAATA
40711516 TAATTCCAGCACAT
65 TAATTCCAGCACAT
* * *
40711530 AGCCTGCGGACCTTAAGTCCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGTCCGAATAT
1 AGCCTGCGGACCTTAAGCCCGAACATAATTCCAGCACATAGCCTGCGGACCCTAAGTCCGAATAT
40711595 AATTCCAGCACAT
66 AATTCCAGCACAT
* *
40711608 AGCCTACGGACCCTAAG
1 AGCCTGCGGACCTTAAG
40711625 TCCGGATGAA
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
77 3 0.04
78 80 0.96
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (78 bp):
AGCCTGCGGACCTTAAGCCCGAACATAATTCCAGCACATAGCCTGCGGACCCTAAGTCCGAATAT
AATTCCAGCACAT
Found at i:40711527 original size:39 final size:38
Alignment explanation
Indices: 40711484--40711628 Score: 227
Period size: 39 Copynumber: 3.7 Consensus size: 38
40711474 ACATATTTCT
* *
40711484 AGCACGTAGCCTGCGGACCTTAAGTCCGATTATAATTCC
1 AGCACATAGCCTGCGGACCCTAAGTCCGA-TATAATTCC
*
40711523 AGCACATAGCCTGCGGACCTTAAGTCCGGATATAATTCC
1 AGCACATAGCCTGCGGACCCTAAGTCC-GATATAATTCC
40711562 AGCACATAGCCTGCGGACCCTAAGTCCGAATATAATTCC
1 AGCACATAGCCTGCGGACCCTAAGTCCG-ATATAATTCC
*
40711601 AGCACATAGCCTACGGACCCTAAGTCCG
1 AGCACATAGCCTGCGGACCCTAAGTCCG
40711629 GATGAACATC
Statistics
Matches: 101, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
38 1 0.01
39 98 0.97
40 2 0.02
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.21
Consensus pattern (38 bp):
AGCACATAGCCTGCGGACCCTAAGTCCGATATAATTCC
Found at i:40711625 original size:78 final size:78
Alignment explanation
Indices: 40711484--40711631 Score: 251
Period size: 78 Copynumber: 1.9 Consensus size: 78
40711474 ACATATTTCT
* * * * *
40711484 AGCACGTAGCCTGCGGACCTTAAGTCCGATTATAATTCCAGCACATAGCCTGCGGACCTTAAGTC
1 AGCACATAGCCTGCGGACCCTAAGTCCGAATATAATTCCAGCACATAGCCTACGGACCCTAAGTC
40711549 CGGATATAATTCC
66 CGGATATAATTCC
40711562 AGCACATAGCCTGCGGACCCTAAGTCCGAATATAATTCCAGCACATAGCCTACGGACCCTAAGTC
1 AGCACATAGCCTGCGGACCCTAAGTCCGAATATAATTCCAGCACATAGCCTACGGACCCTAAGTC
40711627 CGGAT
66 CGGAT
40711632 GAACATCACT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 65 1.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (78 bp):
AGCACATAGCCTGCGGACCCTAAGTCCGAATATAATTCCAGCACATAGCCTACGGACCCTAAGTC
CGGATATAATTCC
Found at i:40714125 original size:23 final size:23
Alignment explanation
Indices: 40714099--40714166 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
40714089 AGTATTGTGA
40714099 TATATGCTTAAATGTTATGTAAT
1 TATATGCTTAAATGTTATGTAAT
40714122 TATATG-----A-G-TATTGTAA-
1 TATATGCTTAAATGTTA-TGTAAT
*
40714138 TATATGCTTAAATGTTATGTGAT
1 TATATGCTTAAATGTTATGTAAT
40714161 TATATG
1 TATATG
40714167 TCTAATGAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 18
0.65 0.02 0.33
Matches are distributed among these distances:
16 8 0.23
17 6 0.17
18 1 0.03
21 1 0.03
22 5 0.14
23 14 0.40
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.47
Consensus pattern (23 bp):
TATATGCTTAAATGTTATGTAAT
Found at i:40714188 original size:39 final size:39
Alignment explanation
Indices: 40713932--40714185 Score: 314
Period size: 39 Copynumber: 6.5 Consensus size: 39
40713922 AACATGTTTT
*
40713932 TGAGT-TTCGTGATATATGCTTGAATGTTATGTAATTATA
1 TGAGTATT-GTGATATATGCTTGAATGTTATGTAACTATA
*
40713971 TGAGTATTGT-ATATATGCTTGAATGTTATGCAACTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTAACTATA
* **
40714009 TGAGTATTGTGATATATGCTTGAATTTTATGCGACTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTAACTATA
* ** *
40714048 TGAGTATTGTGATATATGTTTGAATGTTATGGGACTACA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTAACTATA
* *
40714087 TGAGTATTGTGATATATGCTTAAATGTTATGTAATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTAACTATA
* * * *
40714126 TGAGTATTGTAATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTAACTATA
** * *
40714165 TGTCTAATGAGATATATGCTT
1 TGAGTATTGTGATATATGCTT
40714186 AAAAGTGAGT
Statistics
Matches: 192, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
38 36 0.19
39 154 0.80
40 2 0.01
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTGAATGTTATGTAACTATA
Found at i:40715692 original size:3 final size:3
Alignment explanation
Indices: 40715684--40715790 Score: 56
Period size: 3 Copynumber: 35.7 Consensus size: 3
40715674 TTAATTTTAA
* * * * * * *
40715684 TAT TAT TAT TGT TGT TAT TAG TAA TAT TAT TAA TAT TAT TTT TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
40715732 TAT TAG TAC TAT TTT CTAT T-T TCT ATAT TTT TAT TAT TAG TAT TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
*
40715778 T-T CAT TAT TAT TA
1 TAT TAT TAT TAT TA
40715791 AATTATTGAA
Statistics
Matches: 77, Mismatches: 23, Indels: 8
0.71 0.21 0.07
Matches are distributed among these distances:
2 3 0.04
3 70 0.91
4 4 0.05
ACGTcount: A:0.28, C:0.04, G:0.05, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:40715722 original size:33 final size:33
Alignment explanation
Indices: 40715680--40715744 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
40715670 CTAATTAATT
*
40715680 TTAATATTATTATTGTTGTTATTAGTAATATTA
1 TTAATATTATTATTATTGTTATTAGTAATATTA
* * *
40715713 TTAATATTATTTTTATTTTTATTAGTACTATT
1 TTAATATTATTATTATTGTTATTAGTAATATT
40715745 TTCTATTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.62
Consensus pattern (33 bp):
TTAATATTATTATTATTGTTATTAGTAATATTA
Found at i:40715734 original size:21 final size:22
Alignment explanation
Indices: 40715710--40715753 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
40715700 ATTAGTAATA
*
40715710 TTATTAATATTATTTT-TATTT
1 TTATTAATACTATTTTCTATTT
*
40715731 TTATTAGTACTATTTTCTATTT
1 TTATTAATACTATTTTCTATTT
40715753 T
1 T
40715754 CTATATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (22 bp):
TTATTAATACTATTTTCTATTT
Found at i:40716232 original size:3 final size:3
Alignment explanation
Indices: 40716224--40716633 Score: 192
Period size: 3 Copynumber: 139.0 Consensus size: 3
40716214 TTAATTTTAA
* * * * * * *
40716224 TAT TAT TAT TGT TAT TAT TAG TAA TAT TAT TTT TAT AAT TTT TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * * * *
40716272 TAT TAG TAC TAT TTT CTAT TTT TAC TGT TGT TAT TAA TAG CA- TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
40716317 TAT TAT TCAT ATAT TAT TAT TTT CTAT T-T TTT TAT TAT CAT TAT TGT
1 TAT TAT T-AT -TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
* *
40716364 TAA CA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
40716411 TAT CT-T CTA- TAT TTT TAT TAT TAG TAT TAT T-T CAT TAT TAT TAT
1 TAT -TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
40716455 ATGT TAC TAT TA- CAT TCAT TAT TTT TAT T-T T-T TAT TAA TAT TAT
1 -TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
40716499 TAT TAC TAT TAT TAT TAT TTT TAT TTT TAT T-T T-T TA- TAC TAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
40716544 TA- TAT T-T TCT T-T TAT GT-T TAT CAT TAT TCT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
40716585 CT-T TA- TAT TAT TGT CAT TAT TAGCT TAT CAT TAT TAT TAT AAT TAT
1 -TAT TAT TAT TAT TAT TAT TAT TA--T TAT TAT TAT TAT TAT TAT TAT
40716631 TAT
1 TAT
40716634 AATACTTTCC
Statistics
Matches: 305, Mismatches: 75, Indels: 54
0.70 0.17 0.12
Matches are distributed among these distances:
2 29 0.10
3 257 0.84
4 15 0.05
5 4 0.01
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:40722073 original size:7 final size:8
Alignment explanation
Indices: 40722046--40722086 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
40722036 TAATAATTTA
40722046 TTTTATAAT
1 TTTTA-AAT
40722055 TTTTAAAT
1 TTTTAAAT
40722063 TTTTAAATT
1 TTTTAAA-T
*
40722072 TTTTGAAT
1 TTTTAAAT
40722080 TTTTAAA
1 TTTTAAA
40722087 ATATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 17 0.59
9 12 0.41
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (8 bp):
TTTTAAAT
Found at i:40722074 original size:17 final size:17
Alignment explanation
Indices: 40722054--40722086 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40722044 TATTTTATAA
40722054 TTTTTAAATTTTTAAAT
1 TTTTTAAATTTTTAAAT
*
40722071 TTTTTGAATTTTTAAA
1 TTTTTAAATTTTTAAA
40722087 ATATTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTTTAAATTTTTAAAT
Found at i:40737019 original size:19 final size:19
Alignment explanation
Indices: 40736995--40737035 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
40736985 TGAAAATTTG
*
40736995 AAATCTCTCAAAACCTTCA
1 AAATCTCCCAAAACCTTCA
40737014 AAATCTCCCAAAACCTTCA
1 AAATCTCCCAAAACCTTCA
40737033 AAA
1 AAA
40737036 ATATCATAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (19 bp):
AAATCTCCCAAAACCTTCA
Found at i:40737556 original size:19 final size:19
Alignment explanation
Indices: 40737534--40737572 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
40737524 TTAACTGTAA
*
40737534 TTTATTGCTGTAAATTATT
1 TTTATTACTGTAAATTATT
*
40737553 TTTATTACTGTAATTTATT
1 TTTATTACTGTAAATTATT
40737572 T
1 T
40737573 AGTTTAAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.62
Consensus pattern (19 bp):
TTTATTACTGTAAATTATT
Found at i:40737585 original size:121 final size:121
Alignment explanation
Indices: 40737445--40737717 Score: 528
Period size: 121 Copynumber: 2.3 Consensus size: 121
40737435 TCTAATTAAG
40737445 TTTATTTAGTTTAAGATTCATTGATTTATTGTTGTAATTTTTGCTTATTTTTATTTGTTGTCAAA
1 TTTATTTAGTTTAAGATTCATTGATTTATTGTTGTAATTTTTGCTTATTTTTATTTGTTGTCAAA
40737510 GGTAAATTATCCTATTAACTGTAATTTATTGCTGTAAATTATTTTTATTACTGTAA
66 GGTAAATTATCCTATTAACTGTAATTTATTGCTGTAAATTATTTTTATTACTGTAA
40737566 TTTATTTAGTTTAAGATTCATTGATTTATTGTTGTAATTTTTGCTTATTTTTATTTGTTGTCAAA
1 TTTATTTAGTTTAAGATTCATTGATTTATTGTTGTAATTTTTGCTTATTTTTATTTGTTGTCAAA
40737631 GGTAAATTATCCTATTAACTGTAATTTATTGCTGTAAATTATTTTTATTACTGTAA
66 GGTAAATTATCCTATTAACTGTAATTTATTGCTGTAAATTATTTTTATTACTGTAA
* *
40737687 TTTATTTAGTTTAAGATTAATTGATTCATTG
1 TTTATTTAGTTTAAGATTCATTGATTTATTG
40737718 AGATTTGTAT
Statistics
Matches: 150, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 150 1.00
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (121 bp):
TTTATTTAGTTTAAGATTCATTGATTTATTGTTGTAATTTTTGCTTATTTTTATTTGTTGTCAAA
GGTAAATTATCCTATTAACTGTAATTTATTGCTGTAAATTATTTTTATTACTGTAA
Found at i:40737677 original size:19 final size:19
Alignment explanation
Indices: 40737655--40737693 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
40737645 TTAACTGTAA
*
40737655 TTTATTGCTGTAAATTATT
1 TTTATTACTGTAAATTATT
*
40737674 TTTATTACTGTAATTTATT
1 TTTATTACTGTAAATTATT
40737693 T
1 T
40737694 AGTTTAAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.62
Consensus pattern (19 bp):
TTTATTACTGTAAATTATT
Found at i:40739379 original size:16 final size:16
Alignment explanation
Indices: 40739358--40739390 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
40739348 AGATAGAGTG
40739358 CAAGAAGATGTTGTGT
1 CAAGAAGATGTTGTGT
40739374 CAAGAAGATGTTGTGT
1 CAAGAAGATGTTGTGT
40739390 C
1 C
40739391 TTGATGTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.30
Consensus pattern (16 bp):
CAAGAAGATGTTGTGT
Found at i:40740550 original size:22 final size:22
Alignment explanation
Indices: 40740519--40740563 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
40740509 TGAAAGGTAT
*
40740519 CTTACTATCTTATTC-TTGTTAA
1 CTTACAATC-TATTCATTGTTAA
40740541 CTTACAATCTATTCATTTGTTAA
1 CTTACAATCTATTCA-TTGTTAA
40740564 TATTATTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 8 0.40
23 7 0.35
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.51
Consensus pattern (22 bp):
CTTACAATCTATTCATTGTTAA
Found at i:40740614 original size:18 final size:19
Alignment explanation
Indices: 40740574--40740616 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
40740564 TATTATTTGA
40740574 TTTTTT-TTAAATGCGTAT
1 TTTTTTATTAAATGCGTAT
* *
40740592 ATTTTTATTAAATG-TTAT
1 TTTTTTATTAAATGCGTAT
40740610 TTTTTTA
1 TTTTTTA
40740617 CACATGTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.65
Consensus pattern (19 bp):
TTTTTTATTAAATGCGTAT
Found at i:40740957 original size:9 final size:9
Alignment explanation
Indices: 40740943--40740976 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
40740933 TTTTGTTTTT
40740943 GTTAATTCA
1 GTTAATTCA
40740952 GTTAATTCA
1 GTTAATTCA
40740961 GTTAATTCA
1 GTTAATTCA
40740970 GTTAATT
1 GTTAATT
40740977 TGGTTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (9 bp):
GTTAATTCA
Found at i:40741328 original size:26 final size:26
Alignment explanation
Indices: 40741299--40741348 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
40741289 TCTTACAATA
*
40741299 GATTAA-ATCTAGCATGGGATATAATT
1 GATTAATAT-TAGCATGGGAGATAATT
40741325 GATTAATATTAGCATGGGAGATAA
1 GATTAATATTAGCATGGGAGATAA
40741349 GCTTCAGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (26 bp):
GATTAATATTAGCATGGGAGATAATT
Found at i:40745284 original size:42 final size:42
Alignment explanation
Indices: 40745217--40745298 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
40745207 ATGAGTTTCC
* * *
40745217 GTTTAACCCTAATGGGTTTCAATTCAGCTATTTTGAGCTTTA
1 GTTTAACCCTAACGGGTTTCAATTCAACTATTATGAGCTTTA
* *
40745259 GTTTAACCCTTACGGGTTTTC-ATTCAACTCTTATGAGCTT
1 GTTTAACCCTAACGGG-TTTCAATTCAACTATTATGAGCTT
40745299 CCGTTCAACT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 30 0.88
43 4 0.12
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.43
Consensus pattern (42 bp):
GTTTAACCCTAACGGGTTTCAATTCAACTATTATGAGCTTTA
Found at i:40747818 original size:40 final size:40
Alignment explanation
Indices: 40747729--40747825 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
40747719 AAAGATATTT
* * * **
40747729 GGCACTAAGTGTGCGATTGAAACTAGCTTTGGCTATTTGG
1 GGCACTAAGTGTGCGATTGAAACTAGCTTCGACTATATAA
* * * *
40747769 GGCATTAAGTGTGCGATTTAAATTATCTTCGACTATATAA
1 GGCACTAAGTGTGCGATTGAAACTAGCTTCGACTATATAA
40747809 GGCACTAAGTGTGCGAT
1 GGCACTAAGTGTGCGAT
40747826 ACTAACTTAG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (40 bp):
GGCACTAAGTGTGCGATTGAAACTAGCTTCGACTATATAA
Found at i:40750895 original size:37 final size:37
Alignment explanation
Indices: 40750834--40750979 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
40750824 TACGTATGAT
* *
40750834 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
40750869 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
40750906 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
40750943 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
40750980 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:40750996 original size:46 final size:46
Alignment explanation
Indices: 40750943--40751211 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
40750933 TAAGTGTAGC
* **
40750943 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
40750989 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
40751035 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
40751087 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
40751133 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
40751185 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
40751212 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:40751062 original size:52 final size:52
Alignment explanation
Indices: 40750986--40751205 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
40750976 TAGCTAAAGC
* *
40750986 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
40751039 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
40751091 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
40751137 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
40751189 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
40751206 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:40751108 original size:98 final size:98
Alignment explanation
Indices: 40750943--40751211 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
40750933 TAAGTGTAGC
* * *
40750943 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
40751008 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
40751042 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
40751107 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
40751140 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
40751205 GATCAGA
66 GATCAGA
40751212 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:40757657 original size:4 final size:4
Alignment explanation
Indices: 40757648--40757672 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
40757638 GCAAATCGTG
40757648 AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA A
40757673 TAGAAAAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:40758499 original size:47 final size:47
Alignment explanation
Indices: 40758435--40758545 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
40758425 GACATTGAGT
* *
40758435 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTATTC
* * *
40758482 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTATTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTATTC
40758529 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
40758546 CTTATCCCGG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 51 0.93
48 4 0.07
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTATTC
Found at i:40762713 original size:45 final size:45
Alignment explanation
Indices: 40762609--40762777 Score: 144
Period size: 45 Copynumber: 3.7 Consensus size: 45
40762599 AGTTCGCACG
* * * * * * *
40762609 TATAAGTCTGCCATATCTATAAATTTTCTTCTCTAAATTCGCA-A
1 TATAAGTCTACCATATCTATGAATCTTCTTCTATGAAGTCACATA
* * * * *
40762653 GTATAAGACCACCATAACTATGAATCTGCTTCTATGAA-TCTGCATA
1 -TATAAGTCTACCATATCTATGAATCTTCTTCTATGAAGTC-ACATA
* * ** *
40762699 TATAAGTTTGCCATATCTATGAATCTTCTTAAATGAAGTCACATT
1 TATAAGTCTACCATATCTATGAATCTTCTTCTATGAAGTCACATA
40762744 TATAAGTCTACCATATCTATGAATTCTTCTTCTA
1 TATAAGTCTACCATATCTATGAA-TCTTCTTCTA
40762778 CGAGTTCACA
Statistics
Matches: 97, Mismatches: 23, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
44 2 0.02
45 84 0.87
46 11 0.11
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (45 bp):
TATAAGTCTACCATATCTATGAATCTTCTTCTATGAAGTCACATA
Found at i:40767637 original size:17 final size:19
Alignment explanation
Indices: 40767617--40767653 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
40767607 ATAAAAAATG
40767617 ATTTTTTAT-ATTTT-ATA
1 ATTTTTTATAATTTTAATA
40767634 A-TTTTTATAATTTTAATA
1 ATTTTTTATAATTTTAATA
40767652 AT
1 AT
40767654 AATAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
16 7 0.41
17 6 0.35
18 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTTTTATAATTTTAATA
Found at i:40767652 original size:18 final size:18
Alignment explanation
Indices: 40767619--40767685 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 18
40767609 AAAAAATGAT
40767619 TTTTTAT-ATTTT-ATAA
1 TTTTTATAATTTTAATAA
40767635 TTTTTATAATTTTAATAA
1 TTTTTATAATTTTAATAA
** *
40767653 TAATAATAAATTATTTAATAA
1 TTTTTAT-AA-T-TTTAATAA
40767674 TTTTTA-AATTTT
1 TTTTTATAATTTT
40767686 TAACTATGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
16 7 0.17
17 8 0.20
18 9 0.22
19 4 0.10
20 1 0.03
21 11 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTTATAATTTTAATAA
Found at i:40767687 original size:18 final size:18
Alignment explanation
Indices: 40767627--40767688 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 18
40767617 ATTTTTTATA
40767627 TTTT-ATAATTTTTATAA-
1 TTTTAATAATTTTTA-AAT
**
40767644 TTTTAATAATAATAATAAAT
1 TTTTAATAAT--TTTTAAAT
40767664 TATTTAATAATTTTTAAAT
1 T-TTTAATAATTTTTAAAT
40767683 TTTTAA
1 TTTTAA
40767689 CTATGAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
17 4 0.11
18 10 0.28
19 9 0.25
20 4 0.11
21 9 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAATAATTTTTAAAT
Found at i:40769066 original size:9 final size:9
Alignment explanation
Indices: 40769038--40769081 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
40769028 AATTTATTTA
40769038 ATAATTTTT
1 ATAATTTTT
*
40769047 ACAATTTTT
1 ATAATTTTT
40769056 ATAATTTTT
1 ATAATTTTT
40769065 AT--TTTTT
1 ATAATTTTT
*
40769072 TTAATTTTT
1 ATAATTTTT
40769081 A
1 A
40769082 AATATTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 6 0.21
9 23 0.79
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (9 bp):
ATAATTTTT
Found at i:40769076 original size:16 final size:16
Alignment explanation
Indices: 40769051--40769081 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40769041 ATTTTTACAA
40769051 TTTTTATAATTTTTAT
1 TTTTTATAATTTTTAT
*
40769067 TTTTTTTAATTTTTA
1 TTTTTATAATTTTTA
40769082 AATATTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTATAATTTTTAT
Found at i:40771883 original size:20 final size:20
Alignment explanation
Indices: 40771860--40771917 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
40771850 TACCCCTAAC
40771860 TGCACTCTGGTGCCCCTGAT
1 TGCACTCTGGTGCCCCTGAT
* * *
40771880 TGCACACTCGTGCTCCTGAT
1 TGCACTCTGGTGCCCCTGAT
*
40771900 TGCACTTTGGTGCCCCTG
1 TGCACTCTGGTGCCCCTG
40771918 TTTTTCCATG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.10, C:0.34, G:0.24, T:0.31
Consensus pattern (20 bp):
TGCACTCTGGTGCCCCTGAT
Found at i:40772782 original size:54 final size:54
Alignment explanation
Indices: 40772723--40772845 Score: 140
Period size: 54 Copynumber: 2.3 Consensus size: 54
40772713 CTATGTGTCT
* * *
40772723 CAAGTCAGTGAGTTACACGGGCTAGCACACG-GCCTGCGACATGGCCGTATGAGC
1 CAAGTCAGTGAGTTACAAGGGCTAGCACA-GAGCCTGCGACACGGCCGTATGAAC
*** * * * *
40772777 CAAGTCAAAAAGTTACAAGGGCTAGCATAGAGTCTGTGACACGGTCGTATGAAC
1 CAAGTCAGTGAGTTACAAGGGCTAGCACAGAGCCTGCGACACGGCCGTATGAAC
40772831 CAAGTCAGTGAGTTA
1 CAAGTCAGTGAGTTA
40772846 TACAATCTAT
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
53 1 0.02
54 54 0.98
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.20
Consensus pattern (54 bp):
CAAGTCAGTGAGTTACAAGGGCTAGCACAGAGCCTGCGACACGGCCGTATGAAC
Found at i:40775619 original size:23 final size:22
Alignment explanation
Indices: 40775541--40775623 Score: 71
Period size: 21 Copynumber: 3.8 Consensus size: 22
40775531 ATCAGTATAC
* *
40775541 GACACATAAAGTGCCT-AAAAC
1 GACACACAAAGTGCCTGAAAAT
* * *
40775562 GACACACGAGGTGCCTG-ACAT
1 GACACACAAAGTGCCTGAAAAT
* *
40775583 GACACACGAGGTGCCTGAAATAT
1 GACACACAAAGTGCCTGAAA-AT
*
40775606 GACACATAAAGTGCCTGA
1 GACACACAAAGTGCCTGA
40775624 TCGGTAAAGC
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
21 32 0.64
22 1 0.02
23 17 0.34
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.16
Consensus pattern (22 bp):
GACACACAAAGTGCCTGAAAAT
Found at i:40788590 original size:72 final size:72
Alignment explanation
Indices: 40788514--40788934 Score: 610
Period size: 72 Copynumber: 5.8 Consensus size: 72
40788504 CTGTTTCAAA
*
40788514 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
*
40788579 TGTTGTC
66 TGTTTTC
*
40788586 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
40788651 TCTGTTTTC
64 TCTGTTTTC
*
40788660 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
40788725 TGTTTTC
66 TGTTTTC
* * * ** * *
40788732 AAAATTCAACTCATATTGTGATAAATGAGTTGAGCCTCAAGG-CACGTTGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTAATTTCAATTT
*
40788796 TTGTCTTTC
65 CTGT-TTTC
*
40788805 AAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
*
40788870 TCTGTTGTTAA
64 TCTGTT-TT-C
** *
40788881 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA
40788935 NNNNNNNNNN
Statistics
Matches: 314, Mismatches: 26, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
72 128 0.41
73 6 0.02
74 123 0.39
75 57 0.18
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (72 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
TGTTTTC
Found at i:40788590 original size:74 final size:74
Alignment explanation
Indices: 40788500--40788934 Score: 641
Period size: 74 Copynumber: 5.9 Consensus size: 74
40788490 TGATGTTTTT
*
40788500 ATTTCTG-TTTCAAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
1 ATTTCTGTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
40788564 GGTAATTTCA
65 GGTAATTTCA
* *
40788574 ATTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAG
1 ATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
40788639 GTAATTTCA
66 GTAATTTCA
*
40788648 ATTTCTGTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAG
1 ATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
40788711 GTAATTTCA
66 GTAATTTCA
* * * ** *
40788720 ATTTCTGTTTTC--AAAATTCAACTCATATTGTGATAAATGAGTTGAGCCTCAAGG-CACGTTGA
1 ATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGACACGCTGA
*
40788782 GGTATTTTCA
65 GGTAATTTCA
* *
40788792 ATTTTTGTCTTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
1 ATTTCTGT-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
40788857 GGTAATTTCA
65 GGTAATTTCA
** *
40788867 ATTTCTGTTGTT-AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGA
1 ATTTCTGTT-TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
40788931 GGTA
65 GGTA
40788935 NNNNNNNNNN
Statistics
Matches: 328, Mismatches: 26, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
72 128 0.39
73 6 0.02
74 134 0.41
75 60 0.18
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (74 bp):
ATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
GTAATTTCA
Found at i:40791512 original size:15 final size:15
Alignment explanation
Indices: 40791462--40791514 Score: 81
Period size: 15 Copynumber: 3.6 Consensus size: 15
40791452 CATATATATT
40791462 ATATAA-TTCAATCA
1 ATATAATTTCAATCA
*
40791476 ATATAAATTCAATCA
1 ATATAATTTCAATCA
*
40791491 AAATAATTTCAATCA
1 ATATAATTTCAATCA
40791506 ATATAATTT
1 ATATAATTT
40791515 TAATAAATTC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
14 6 0.17
15 29 0.83
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATAATTTCAATCA
Found at i:40791903 original size:51 final size:51
Alignment explanation
Indices: 40791827--40791944 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 51
40791817 CCCAAATTTT
* * *
40791827 CTTCATACTTCATCCGGAATTATTACTTTGTTGTTCTAGCTTCAACAAGAA
1 CTTCATATTTCATCCGGAATTATTACTTTATTGCTCTAGCTTCAACAAGAA
* *
40791878 CTTCATATTTCATCCGG-ATATATTACTTTATTGCTCTAGTTTCAACAAGAG
1 CTTCATATTTCATCCGGAAT-TATTACTTTATTGCTCTAGCTTCAACAAGAA
40791929 CTTCATATTTCATCCG
1 CTTCATATTTCATCCG
40791945 AATAACTTAG
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 2 0.03
51 59 0.97
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (51 bp):
CTTCATATTTCATCCGGAATTATTACTTTATTGCTCTAGCTTCAACAAGAA
Found at i:40792393 original size:13 final size:14
Alignment explanation
Indices: 40792375--40792410 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
40792365 TTTAAATTTC
40792375 CCTTTCTTTCTT-T
1 CCTTTCTTTCTTCT
40792388 CCTTTCTTT-TTCT
1 CCTTTCTTTCTTCT
40792401 CC-TTCTTTCT
1 CCTTTCTTTCT
40792411 CCCCTGTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (14 bp):
CCTTTCTTTCTTCT
Found at i:40796834 original size:20 final size:20
Alignment explanation
Indices: 40796809--40796847 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
40796799 ATTAAGTGGA
40796809 TTTAATATT-GTCATATTTTT
1 TTTAATATTCGT-ATATTTTT
40796829 TTTAATATTCGTATATTTT
1 TTTAATATTCGTATATTTT
40796848 ATATTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (20 bp):
TTTAATATTCGTATATTTTT
Found at i:40800528 original size:94 final size:93
Alignment explanation
Indices: 40800339--40800554 Score: 256
Period size: 94 Copynumber: 2.3 Consensus size: 93
40800329 AGTCATTTGT
* *
40800339 GAGCTAGTGTAAGACATGTCTGGGACATGAATCGGCCACATTATGAGAGCCAGTGTAAGACCATG
1 GAGCTAGTGTAAGACATGTCTGGGACATGAATCGGCCACATGAT-AGAGCCAGTGTAAGACCAGG
* * **
40800404 TCTGGGACATGGCATCGGTATTGAGATGA
65 TCTAGGACATGGCATCGGCACGGAGATGA
* * * *
40800433 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-GAT-GTGTCAGTGTAAGACCAGG
1 GAGCTAGTGTAAGACATGTCTGGGACATGAATCGGCCAC-ATGATAGAGCCAGTGTAAGACCAGG
*
40800496 TCTAGGACATGGCATCGGCACGGATATGTGA
65 TCTAGGACATGGCATCGGCACGGAGA--TGA
* *
40800527 GAGCTAATGTAAGACCATGTCTAGGACA
1 GAGCTAGTGTAAGA-CATGTCTGGGACA
40800555 AGGCGTCGGT
Statistics
Matches: 105, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
92 37 0.35
94 55 0.52
95 13 0.12
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.23
Consensus pattern (93 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGAATCGGCCACATGATAGAGCCAGTGTAAGACCAGGT
CTAGGACATGGCATCGGCACGGAGATGA
Found at i:40800648 original size:47 final size:48
Alignment explanation
Indices: 40800338--40800661 Score: 232
Period size: 47 Copynumber: 6.8 Consensus size: 48
40800328 AAGTCATTTG
* *
40800338 TGAGCTAGTGTAAGA-CATGTCTGGGACAT-GAATCGGCCACATT-ATGA
1 TGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CAC-TTGATGA
*
40800385 -GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGTA-TTGA-GA
1 TGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTTGATGA
*
40800430 TGAGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTAC--GA-GA
1 T--GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACTTGATGA
* * * *
40800476 TGTGTCAGTGTAAGACCAGGTCTAGGACATGGCATCGGCACGGATATG-TGA
1 TGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC---T-TGATGA
* * * * * * *
40800527 -GAGCTAATGTAAGACCATGTCTAGGACAAGGCGTCGG-TCTCGATCGCGA
1 TGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTTGAT---GA
* * *
40800576 -AAGTCAGTGTAAGACCATGTTTGGGACATGGCATC-G-ACTTGATGTA
1 TGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTTGATG-A
* *
40800622 TGAGCCAGTGTAAGATCATGTCTGGGACACGGCATCGGCA
1 TGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
40800662 TTCTACCCTA
Statistics
Matches: 218, Mismatches: 34, Indels: 48
0.73 0.11 0.16
Matches are distributed among these distances:
44 11 0.05
45 20 0.09
46 37 0.17
47 60 0.28
48 26 0.12
49 31 0.14
50 30 0.14
51 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (48 bp):
TGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTTGATGA
Found at i:40801233 original size:14 final size:16
Alignment explanation
Indices: 40801209--40801241 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
40801199 ATTTTTTGTG
40801209 TTTATTATGTGT-GAA
1 TTTATTATGTGTGGAA
40801224 TTTA-TATGTGTGGAA
1 TTTATTATGTGTGGAA
40801239 TTT
1 TTT
40801242 TCATGCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (16 bp):
TTTATTATGTGTGGAA
Found at i:40802850 original size:16 final size:16
Alignment explanation
Indices: 40802829--40802862 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
40802819 ACATTCGGCC
40802829 ATATAATAATAAGTGT
1 ATATAATAATAAGTGT
40802845 ATATAATAATAAGTGT
1 ATATAATAATAAGTGT
40802861 AT
1 AT
40802863 GTATAAGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (16 bp):
ATATAATAATAAGTGT
Found at i:40818813 original size:38 final size:38
Alignment explanation
Indices: 40818765--40818844 Score: 110
Period size: 38 Copynumber: 2.1 Consensus size: 38
40818755 ATGAGATGAT
*
40818765 ATAT-TATAAGATATGTTCT-AACATGAAATTTGATATG
1 ATATGTATAAGATATGTTCTGAA-ATGAAATCTGATATG
*
40818802 ATATGTATAAGATATGTTCTGAAATGGAATCTGATATG
1 ATATGTATAAGATATGTTCTGAAATGAAATCTGATATG
*
40818840 CTATG
1 ATATG
40818845 ATACGTTCTG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 4 0.11
38 32 0.84
39 2 0.05
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (38 bp):
ATATGTATAAGATATGTTCTGAAATGAAATCTGATATG
Found at i:40822596 original size:17 final size:19
Alignment explanation
Indices: 40822562--40822598 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
40822552 TTTAAAAATG
*
40822562 AAAATGAAAAAACCTTTAA
1 AAAATGAAAAAACATTTAA
40822581 AAAAT-AAAAAA-ATTTAA
1 AAAATGAAAAAACATTTAA
40822598 A
1 A
40822599 GTTCATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 6 0.35
19 5 0.29
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.22
Consensus pattern (19 bp):
AAAATGAAAAAACATTTAA
Found at i:40823782 original size:26 final size:26
Alignment explanation
Indices: 40823738--40823856 Score: 104
Period size: 26 Copynumber: 4.7 Consensus size: 26
40823728 ACACCCTGTA
40823738 GCTCTT-ATGAG-TATCCCGA-TAAATG
1 GCTCTTCATGAGCT-TCCCGATTAAA-G
*
40823763 GCTCTTCACGAGCTTCCCGATTAAAG
1 GCTCTTCATGAGCTTCCCGATTAAAG
* ** * *
40823789 GCTTTTTGTGAGCTTCCCTATTAAAT
1 GCTCTTCATGAGCTTCCCGATTAAAG
**
40823815 GCTCTTTGTGAGCTTCCCG-TTAAAG
1 GCTCTTCATGAGCTTCCCGATTAAAG
*
40823840 GTTCTTCA-GAGCTTCCC
1 GCTCTTCATGAGCTTCCC
40823857 AATATTGGCT
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
24 9 0.12
25 16 0.21
26 48 0.62
27 5 0.06
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.35
Consensus pattern (26 bp):
GCTCTTCATGAGCTTCCCGATTAAAG
Found at i:40835795 original size:21 final size:21
Alignment explanation
Indices: 40835769--40835808 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40835759 CAAGGGCAAA
*
40835769 AGAAACCGAAGCAAAAATAGT
1 AGAAACAGAAGCAAAAATAGT
*
40835790 AGAAACAGAAGCAACAATA
1 AGAAACAGAAGCAAAAATA
40835809 TCGACAAAAT
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:0.60, C:0.15, G:0.17, T:0.07
Consensus pattern (21 bp):
AGAAACAGAAGCAAAAATAGT
Found at i:40838967 original size:18 final size:18
Alignment explanation
Indices: 40838944--40838997 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
40838934 ACAAGTGGTG
40838944 GTGGAGAAGGTGTGGCTA
1 GTGGAGAAGGTGTGGCTA
40838962 GT-G-G-A-GT-TGG-TA
1 GTGGAGAAGGTGTGGCTA
*
40838974 GTGGAAAAGGTGTGGCTA
1 GTGGAGAAGGTGTGGCTA
40838992 GTGGAG
1 GTGGAG
40838998 TTGGTGGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 4 0.14
13 4 0.14
14 2 0.07
15 2 0.07
16 3 0.11
17 4 0.14
18 9 0.32
ACGTcount: A:0.22, C:0.04, G:0.50, T:0.24
Consensus pattern (18 bp):
GTGGAGAAGGTGTGGCTA
Found at i:40838978 original size:30 final size:30
Alignment explanation
Indices: 40838939--40839473 Score: 1034
Period size: 30 Copynumber: 17.8 Consensus size: 30
40838929 TAGGTACAAG
*
40838939 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
40838969 TGGTAGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
40838999 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
40839029 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
40839059 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
40839089 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
40839119 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
40839149 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
40839179 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
40839209 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
40839239 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
40839269 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
40839299 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
40839329 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
40839359 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
40839389 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
* *
40839419 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
40839449 TGGTGGTGGAAAAGGTGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGT
40839474 TGAGAAAAGT
Statistics
Matches: 498, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 498 1.00
ACGTcount: A:0.20, C:0.03, G:0.50, T:0.27
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:40840359 original size:77 final size:77
Alignment explanation
Indices: 40840184--40840584 Score: 639
Period size: 77 Copynumber: 5.2 Consensus size: 77
40840174 ATGTGAACCC
* * * * * *
40840184 AAGGCTCAACTCACATCTCGCAACATGAGTTGA-T-TTTTGAAAAACAGAAATTTAAAAATACCT
1 AAGGCTCAACTCACCTCTCACAATATGAGTTGATTCTTTTGAAAAGCAGAAA-TTGAAAATAGCT
* ** *
40840247 CAG--TGTGTCCT
65 CAGCACGTGAGCA
* * *
40840258 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTGAAAATAGCTC
1 AAGGCTCAACTCACCTCTCACAATATGAGTTGATTCTTTTGAAAAGCAGAAATTGAAAATAGCTC
40840323 AGCACGTGAGCA
66 AGCACGTGAGCA
40840335 AAGGCTCAACTCACCTCTCACAATATGAGTTGATTCTTTTGAAAAGCAGAAATTGAAAATAGCTC
1 AAGGCTCAACTCACCTCTCACAATATGAGTTGATTCTTTTGAAAAGCAGAAATTGAAAATAGCTC
40840400 AGCACGTGAGCA
66 AGCACGTGAGCA
40840412 AAGGCTCAACTCACCTCTCACAATATGAGTTGATTCTTTTGAAAAGCAGAAATTGAAAATAGCTC
1 AAGGCTCAACTCACCTCTCACAATATGAGTTGATTCTTTTGAAAAGCAGAAATTGAAAATAGCTC
40840477 AGCACGTGAGCA
66 AGCACGTGAGCA
40840489 AAGGCTCAACTCACCTCTCACAATATGAGTTGATTCTTTTGAAAAGCAGAAATTGAAAATAGCTC
1 AAGGCTCAACTCACCTCTCACAATATGAGTTGATTCTTTTGAAAAGCAGAAATTGAAAATAGCTC
40840554 AGCACGTGAGCA
66 AGCACGTGAGCA
*
40840566 AAGGCTCAACTCACTTCTC
1 AAGGCTCAACTCACCTCTC
40840585 GCAAAAGTAG
Statistics
Matches: 309, Mismatches: 14, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
74 30 0.10
75 14 0.05
76 15 0.05
77 250 0.81
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (77 bp):
AAGGCTCAACTCACCTCTCACAATATGAGTTGATTCTTTTGAAAAGCAGAAATTGAAAATAGCTC
AGCACGTGAGCA
Found at i:40840712 original size:14 final size:14
Alignment explanation
Indices: 40840679--40840712 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40840669 ATAAATTGAA
*
40840679 AAAAAACAGAAATT
1 AAAAAGCAGAAATT
*
40840693 GAAAAGCAGAAATT
1 AAAAAGCAGAAATT
40840707 AAAAAG
1 AAAAAG
40840713 ACCTCAGCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.06, G:0.15, T:0.12
Consensus pattern (14 bp):
AAAAAGCAGAAATT
Found at i:40840850 original size:75 final size:75
Alignment explanation
Indices: 40840691--40840932 Score: 308
Period size: 76 Copynumber: 3.2 Consensus size: 75
40840681 AAAACAGAAA
* * ** * *
40840691 TTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCCACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTAAAAATACCTCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATAT
*
40840756 GAGTT-A-ATTT
64 GAGTTGATTTTT
* * * *
40840766 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTCGCAATATGA
1 TTGAAAAACAGAAATTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
40840831 GTTGATTTTT
66 GTTGATTTTT
*
40840841 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAA-TTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
40840906 AGTTGATTTTT
65 AGTTGATTTTT
* **
40840917 TTTACGAACAGAAATT
1 TTGAAAAACAGAAATT
40840933 GAAGAACAGA
Statistics
Matches: 145, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
73 33 0.23
74 1 0.01
75 43 0.30
76 68 0.47
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (75 bp):
TTGAAAAACAGAAATTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTT
Found at i:40840941 original size:14 final size:14
Alignment explanation
Indices: 40840922--40840949 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40840912 TTTTTTTTAC
40840922 GAACAGAAATTGAA
1 GAACAGAAATTGAA
40840936 GAACAGAAATTGAA
1 GAACAGAAATTGAA
40840950 AAGACCTCAG
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:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:40841064 original size:73 final size:74
Alignment explanation
Indices: 40840931--40841099 Score: 223
Period size: 73 Copynumber: 2.3 Consensus size: 74
40840921 CGAACAGAAA
* *
40840931 TTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAAGACCTCAGCA-GTGACCCGAGGCTCAACTCACCTCTCGCAATAT
40840996 GAGTTAATGT
65 GAGTTAATGT
* ** * *
40841006 TTGACAAACAGAAATTGAAATTACCTCAGC-GTGTCCCGAGGCTCAACTCACCTTTCGCAATATG
1 TTGAAAAACAGAAATTGAAAAGACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
* *
40841070 AGTTGATTT
66 AGTTAATGT
* *
40841079 TTGAAAAATATAAATTGAAAA
1 TTGAAAAACAGAAATTGAAAA
40841100 AACAGAAATT
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
73 55 0.68
75 26 0.32
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (74 bp):
TTGAAAAACAGAAATTGAAAAGACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
AGTTAATGT
Found at i:40841098 original size:14 final size:14
Alignment explanation
Indices: 40841079--40841128 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
40841069 GAGTTGATTT
* *
40841079 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
40841093 TTGAAAAAACAGAAA
1 TTG-AAAAACAGAAA
*
40841108 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
40841122 TT-AAAAA
1 TTGAAAAA
40841129 GACCTCAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
15 12 0.39
ACGTcount: A:0.64, C:0.04, G:0.12, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:40841238 original size:78 final size:75
Alignment explanation
Indices: 40841108--40841349 Score: 307
Period size: 78 Copynumber: 3.2 Consensus size: 75
40841098 AAAACAGAAA
* * * *
40841108 TTGAAAAGCAGAAATT-AAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACAATA
1 TTGAAAAACAGAAATTGAAAAACACCTCAGCATGT-AGCC-AGGCTCAACTCACCTCTCGCAATA
40841172 TGAGTTGATTTTT
64 TGAGTTGA-TTTT
* * * *
40841185 TTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAGGCTCAACTCACCTTTCGCAATA
1 TTGAAAAACAGAAATTGAAAAACACCTCAGCATGT-AGCC-AGGCTCAACTCACCTCTCGCAATA
40841250 TGAGTTGATTTT
64 TGAGTTGATTTT
*
40841262 TTGAAAAATAGAAATTG-AAAACACCTCAGCATGT-G--AGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTGAAAAACACCTCAGCATGTAGCCAGGCTCAACTCACCTCTCGCAATATG
40841323 AGTTGA-TTT
66 AGTTGATTTT
*
40841332 TTGAAAAACATAAATTGA
1 TTGAAAAACAGAAATTGA
40841350 GCAGAAATTG
Statistics
Matches: 147, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
70 18 0.12
71 31 0.21
74 1 0.01
76 15 0.10
77 33 0.22
78 49 0.33
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (75 bp):
TTGAAAAACAGAAATTGAAAAACACCTCAGCATGTAGCCAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTT
Found at i:40841301 original size:417 final size:407
Alignment explanation
Indices: 40840598--40841488 Score: 1211
Period size: 417 Copynumber: 2.1 Consensus size: 407
40840588 AAAGTAGATT
* * *
40840598 TTGAAAATACCTCGACATGTGAACCCAAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTG
1 TTGAAAATACCTC-A-ACGTG-ACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
40840663 AAAAATATAAATTGAAAAAAAACAGAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAG
63 AAAAATATAAATTG-AAAAAAACAGAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAG
* * *
40840728 CCGAGACTCCACTCACCTCTCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTC
127 CCGAGACTCAACTCACCTCTCACAATATGAGTTAATTTTTGACAAACAGAAATTGAAAATACCTC
*
40840793 AGCGTGTCCCGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTT
192 AGCGTGTCCCAAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTT
* * * **
40840858 AAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACG
257 AAAAACACCTCAGCATG--CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAA
*
40840923 AACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAG-C-CGAGGCTCAACTCACCT
318 AACAGAAATTG-AG--CAGAAATTGAAAAGACCTCA--ACG-G-GTCTCGAGGCTCAACTCACCT
40840986 CTCGCAATATGAGTT-AATGTTTGACAAACAGAAA
376 CTCGCAATATGAGTTGAATGTTTG---AACAGAAA
* * * *
40841020 TTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGAAA
1 TTGAAAATACCTCAACGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
40841085 AATATAAATTG-AAAAAACAGAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGA
66 AATATAAATTGAAAAAAACAGAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGA
*
40841149 GACTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGACAAACAGAAATTGAAAAATACCTCA
131 GACTCAACTCACCTCTCACAATATGAGTT-A-ATTTTTGACAAACAGAAATTG-AAAATACCTCA
* *
40841214 GCGTGTAAGCCAAGGCTCAACTCACCTTTCGCAATATGAGTTGA-TTTTTTGAAAAATAGAAA-T
193 GCGTGT--CCCAAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATT
*
40841277 TGAAAACACCTCAGCATG-TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
256 TAAAAACACCTCAGCATGCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
* * * *
40841341 ATAAATTGAGCAGAAATTGAAAATACCTCAACGGGTCTTGAGGTTCAACTCACCTCTCGCAATAT
321 AGAAATTGAGCAGAAATTGAAAAGACCTCAACGGGTCTCGAGGCTCAACTCACCTCTCGCAATAT
* * ** *
40841406 GAGTTGATTTTTTGATGATAAA
386 GAGTTGAATGTTTGAACAGAAA
* ** * *
40841428 TTGAAAATACCTCAATGTGACTTGAGGTTCAACTCACCTCTCACAATATGAGTTGATTTTT
1 TTGAAAATACCTCAACGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
40841489 TGAATTAAAA
Statistics
Matches: 422, Mismatches: 39, Indels: 30
0.86 0.08 0.06
Matches are distributed among these distances:
408 58 0.14
409 2 0.00
410 32 0.08
411 6 0.01
412 19 0.05
414 2 0.00
415 16 0.04
417 114 0.27
418 1 0.00
419 73 0.17
420 35 0.08
421 18 0.04
422 46 0.11
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (407 bp):
TTGAAAATACCTCAACGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
AATATAAATTGAAAAAAACAGAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGA
GACTCAACTCACCTCTCACAATATGAGTTAATTTTTGACAAACAGAAATTGAAAATACCTCAGCG
TGTCCCAAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAA
ACACCTCAGCATGCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
TTGAGCAGAAATTGAAAAGACCTCAACGGGTCTCGAGGCTCAACTCACCTCTCGCAATATGAGTT
GAATGTTTGAACAGAAA
Found at i:40841317 original size:71 final size:71
Alignment explanation
Indices: 40841108--40841513 Score: 309
Period size: 71 Copynumber: 5.3 Consensus size: 71
40841098 AAAACAGAAA
* * * *
40841108 TTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACAATAT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCATGTGA---G-G-CTCAACTCACCTCTCGCAATAT
40841173 GAGTTGATTTTT
61 GAGTTGA-TTTT
* * *
40841185 TTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAGGCTCAACTCACCTTTCGCAATA
1 TTGAAAAACAGAAATTG-AAAATACCTCAGCATGT--G---AGGCTCAACTCACCTCTCGCAATA
40841250 TGAGTTGATTTT
60 TGAGTTGATTTT
* *
40841262 TTGAAAAATAGAAATTGAAAACACCTCAGCATGTGAGGCTCAACTCACCTCTCGCAATATGAGTT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCATGTGAGGCTCAACTCACCTCTCGCAATATGAGTT
40841327 GA-TTT
66 GATTTT
** * *
40841332 TTGAAAAACATAAATTGAGCAGAAATTGAAAATACCTCAACGGGTCTTGAGGTTCAACTCACCTC
1 TTG------A-AAA---A-CAGAAATTGAAAATACCTC-A-GCAT-GTGAGGCTCAACTCACCTC
40841397 TCGCAATATGAGTTGATTTT
52 TCGCAATATGAGTTGATTTT
** * * * *
40841417 TTG---ATGATAAATTGAAAATACCTCAATGTGACT-TGAGGTTCAACTCACCTCTCACAATATG
1 TTGAAAAACAGAAATTGAAAATACCTC-A-G-CA-TGTGAGGCTCAACTCACCTCTCGCAATATG
40841478 AGTTGATTTT
62 AGTTGATTTT
40841488 TTGAATTAAAACAGAAATTGAAAATA
1 TTG-A--AAAACAGAAATTGAAAATA
40841514 GAAATGGAAA
Statistics
Matches: 273, Mismatches: 27, Indels: 58
0.76 0.08 0.16
Matches are distributed among these distances:
70 6 0.02
71 91 0.33
72 1 0.00
73 1 0.00
74 1 0.00
75 1 0.00
76 16 0.06
77 50 0.18
78 42 0.15
79 1 0.00
80 3 0.01
81 17 0.06
82 1 0.00
83 3 0.01
84 33 0.12
85 6 0.02
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (71 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCATGTGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTT
Found at i:40841454 original size:155 final size:156
Alignment explanation
Indices: 40841230--40841582 Score: 441
Period size: 155 Copynumber: 2.2 Consensus size: 156
40841220 AAGCCAAGGC
*
40841230 TCAACTCACCTTTCGCAATATGAGTTGATTTTTTGAAAAATAGAAATTGAAAACACCTCAGCATG
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATA-AAATTGAAAACACCTCAGCATG
* * *
40841295 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG-A-AAAACATAAATTG-AGCAGAA
65 TGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTGAATAAAACAGAAATTGAAACAGAA
* * *
40841356 ATTGAAAATACCTCAACGGGTCTTGAGGT
130 ATGGAAAACACCTC-A-GCGTCTTGAGGT
** * *
40841385 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-ATGAT-AAATTGAAAATACCTCAATGTGA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAAAATTGAAAACACCTC-A-G-CA
*
40841448 CT-TGAGGTTCAACTCACCTCTCACAATATGAGTTGATTTTTTGAATTAAAACAGAAATTGAAAA
63 -TGTGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTGAA-TAAAACAGAAATTG-AAA
*
40841512 TAGAAATGGAAAACACCTCAGCGTCTTGAGGT
125 CAGAAATGGAAAACACCTCAGCGTCTTGAGGT
*
40841544 TCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAA
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA
40841583 CACATAAATT
Statistics
Matches: 171, Mismatches: 15, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
152 15 0.09
153 1 0.01
154 4 0.02
155 67 0.39
156 7 0.04
157 1 0.01
159 50 0.29
160 8 0.05
161 18 0.11
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (156 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAAAATTGAAAACACCTCAGCATGT
GAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTGAATAAAACAGAAATTGAAACAGAAA
TGGAAAACACCTCAGCGTCTTGAGGT
Done.