Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 35 of 345
Found at i:10610713 original size:15 final size:15
Alignment explanation
Indices: 10610693--10610722 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10610683 TACAAATATA
10610693 TATATATATATGTGT
1 TATATATATATGTGT
*
10610708 TATATATGTATGTGT
1 TATATATATATGTGT
10610723 AATGGAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (15 bp):
TATATATATATGTGT
Found at i:10613094 original size:40 final size:40
Alignment explanation
Indices: 10613003--10613206 Score: 243
Period size: 40 Copynumber: 5.2 Consensus size: 40
10612993 AATGATACCC
* *
10613003 GGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATA-CCG
1 GGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATCCG
* *
10613042 GGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCG
1 GGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATCCG
* *
10613082 GGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATATCCG
1 GGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATATCCG
* * ** *
10613122 GGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCCG
1 GGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATCCG
* * * *
10613162 GGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCC-
1 GGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATCCG
10613201 GGCTAA
1 GGCTAA
10613207 ATTCCGAAGA
Statistics
Matches: 142, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
39 42 0.30
40 98 0.69
41 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
GGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATCCG
Found at i:10621266 original size:40 final size:40
Alignment explanation
Indices: 10621211--10621422 Score: 221
Period size: 40 Copynumber: 5.3 Consensus size: 40
10621201 CATTCGAATG
*
10621211 ATACCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATACCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATT
*
10621251 ATACCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATACCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATT
* ** *
10621291 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TT
1 ATACCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATT
* * * * **
10621331 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACC
1 ATACCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATT
* * * * * * *
10621371 AAATCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATACCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATT
*
10621411 ATATCC-GGCTAA
1 ATACCCGGGCTAA
10621423 ATTCCGAAGA
Statistics
Matches: 149, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
39 6 0.04
40 141 0.95
41 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
ATACCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATT
Found at i:10622946 original size:24 final size:24
Alignment explanation
Indices: 10622835--10622970 Score: 200
Period size: 24 Copynumber: 5.7 Consensus size: 24
10622825 CGGATTTAAG
*
10622835 TGGCACTATGTGTGCATATTTGTA
1 TGGCACTATGTGTGCGTATTTGTA
10622859 TGGCACTATGTGTGCGTATTTGTA
1 TGGCACTATGTGTGCGTATTTGTA
10622883 TGGCACTATGTGTGCGTATTTGTA
1 TGGCACTATGTGTGCGTATTTGTA
*
10622907 TGGCACTATGTGTGCGTATATGTA
1 TGGCACTATGTGTGCGTATTTGTA
* * * * *
10622931 AGGCACTATGTGTGCGGAATTATT
1 TGGCACTATGTGTGCGTATTTGTA
*
10622955 TGGCACTAAGTGTGCG
1 TGGCACTATGTGTGCG
10622971 GAGTTGAATC
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 102 1.00
ACGTcount: A:0.20, C:0.13, G:0.29, T:0.38
Consensus pattern (24 bp):
TGGCACTATGTGTGCGTATTTGTA
Found at i:10629266 original size:46 final size:46
Alignment explanation
Indices: 10629216--10629754 Score: 846
Period size: 46 Copynumber: 11.7 Consensus size: 46
10629206 GATAGAAAGT
10629216 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
*
10629262 GTGTAAGACCATGGTTGAAAGATACCATAGCAACCTGATATGAAAC
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
10629308 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
*
10629354 GTGTAAGACCATGGTTGAAAGATACCATAGCAACCTGATATGAAAC
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
*
10629400 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
10629446 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
10629492 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
* *
10629538 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATTTGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
* * *
10629584 GTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
* *** *
10629630 GTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACGGGGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA-TATGAAAC
** * * * *
10629677 GAATAAGACCATGGTTGAATGATACCATGGCAACATGACA-GAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG-AAAC
* * * *
10629723 GAGTAAGACCATAGTTGAAAGACACTATGGCA
1 GTGTAAGACCATGGTTGAAAGATACCATGGCA
10629755 TCATGTCGAA
Statistics
Matches: 466, Mismatches: 25, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
45 1 0.00
46 426 0.91
47 39 0.08
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (46 bp):
GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
Found at i:10629969 original size:19 final size:18
Alignment explanation
Indices: 10629934--10629972 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
10629924 GAAATAATTT
10629934 ATAAGATAGATAAATGAA
1 ATAAGATAGATAAATGAA
* *
10629952 ATAAGTATAGGTACATGAA
1 ATAAG-ATAGATAAATGAA
10629971 AT
1 AT
10629973 TTAAATTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.54, C:0.03, G:0.18, T:0.26
Consensus pattern (18 bp):
ATAAGATAGATAAATGAA
Found at i:10634337 original size:24 final size:23
Alignment explanation
Indices: 10634310--10634435 Score: 112
Period size: 24 Copynumber: 5.3 Consensus size: 23
10634300 TTACTAGATA
10634310 TGCGGATTTAAGTGGCACTATGTG
1 TGCGGATTTAA-TGGCACTATGTG
* *
10634334 TGCGTATTCGT-ATGGCACTATGTA
1 TGCGGATT--TAATGGCACTATGTG
* *
10634358 TGCGTATTTGTATGGCACTATGTG
1 TGCGGATTT-AATGGCACTATGTG
*
10634382 TGCGTATATGTAA-GGCACTATGTG
1 TGCGGAT-T-TAATGGCACTATGTG
* *
10634406 TGCGGAATTATTTGGCACTATGTG
1 TGCGGATTTA-ATGGCACTATGTG
10634430 TGCGGA
1 TGCGGA
10634436 GTTGAATCGT
Statistics
Matches: 87, Mismatches: 7, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
22 3 0.03
23 1 0.01
24 78 0.90
25 3 0.03
26 2 0.02
ACGTcount: A:0.21, C:0.13, G:0.30, T:0.36
Consensus pattern (23 bp):
TGCGGATTTAATGGCACTATGTG
Found at i:10634379 original size:48 final size:48
Alignment explanation
Indices: 10634308--10634433 Score: 157
Period size: 48 Copynumber: 2.6 Consensus size: 48
10634298 GGTTACTAGA
* *
10634308 TATGCGGATTTA-AGTGGCACTATGTGTGCGTAT-TCGTATGGCACTATG
1 TATGCGGAATTATA-TGGCACTATGTGTGCGTATAT-GTAAGGCACTATG
* * *
10634356 TATGCGTATTTGTATGGCACTATGTGTGCGTATATGTAAGGCACTATG
1 TATGCGGAATTATATGGCACTATGTGTGCGTATATGTAAGGCACTATG
* *
10634404 TGTGCGGAATTATTTGGCACTATGTGTGCG
1 TATGCGGAATTATATGGCACTATGTGTGCG
10634434 GAGTTGAATC
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
48 66 0.97
49 2 0.03
ACGTcount: A:0.21, C:0.13, G:0.29, T:0.37
Consensus pattern (48 bp):
TATGCGGAATTATATGGCACTATGTGTGCGTATATGTAAGGCACTATG
Found at i:10635678 original size:15 final size:15
Alignment explanation
Indices: 10635658--10635687 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10635648 AAAATTGCAC
10635658 AATTACATAATACGA
1 AATTACATAATACGA
*
10635673 AATTACGTAATACGA
1 AATTACATAATACGA
10635688 GTAATCTCCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (15 bp):
AATTACATAATACGA
Found at i:10638484 original size:25 final size:25
Alignment explanation
Indices: 10638456--10638535 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
10638446 TTACATATAA
10638456 GAATGCTATATACATTAAGGATGTG
1 GAATGCTATATACATTAAGGATGTG
** * * * **
10638481 GAATTATAGATAATATTACA-TAT-AA
1 GAATGCTATAT-ACATTA-AGGATGTG
10638506 GAATGCTATATACATTAAGGATGTG
1 GAATGCTATATACATTAAGGATGTG
10638531 GAATG
1 GAATG
10638536 GAGAGGAGGA
Statistics
Matches: 37, Mismatches: 14, Indels: 8
0.63 0.24 0.14
Matches are distributed among these distances:
23 1 0.03
24 7 0.19
25 21 0.57
26 7 0.19
27 1 0.03
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (25 bp):
GAATGCTATATACATTAAGGATGTG
Found at i:10638487 original size:50 final size:50
Alignment explanation
Indices: 10638428--10638534 Score: 214
Period size: 50 Copynumber: 2.1 Consensus size: 50
10638418 GATGTAAATA
10638428 GTGGAATTATAGATAATATTACATATAAGAATGCTATATACATTAAGGAT
1 GTGGAATTATAGATAATATTACATATAAGAATGCTATATACATTAAGGAT
10638478 GTGGAATTATAGATAATATTACATATAAGAATGCTATATACATTAAGGAT
1 GTGGAATTATAGATAATATTACATATAAGAATGCTATATACATTAAGGAT
10638528 GTGGAAT
1 GTGGAAT
10638535 GGAGAGGAGG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 57 1.00
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.34
Consensus pattern (50 bp):
GTGGAATTATAGATAATATTACATATAAGAATGCTATATACATTAAGGAT
Found at i:10642583 original size:22 final size:22
Alignment explanation
Indices: 10642535--10642578 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
10642525 TAGTTGATTG
*
10642535 ATAAATTTAGATATTTAACCAT
1 ATAAATTGAGATATTTAACCAT
10642557 ATAAATTGA-ATATTTAA-CAT
1 ATAAATTGAGATATTTAACCAT
10642577 AT
1 AT
10642579 TTAAAAGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (22 bp):
ATAAATTGAGATATTTAACCAT
Found at i:10646404 original size:18 final size:18
Alignment explanation
Indices: 10646364--10646423 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
10646354 TTAAAATTTA
*
10646364 AAAAATTA-AAAAAAATAT
1 AAAAATTATTAAAAAAT-T
**
10646382 AAAAAATTATTTTAAAATT
1 -AAAAATTATTAAAAAATT
10646401 AAAAATTATTAAAAAATT
1 AAAAATTATTAAAAAATT
10646419 AAAAA
1 AAAAA
10646424 GCAATTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 21 0.60
19 9 0.26
20 5 0.14
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAATTATTAAAAAATT
Found at i:10646415 original size:39 final size:38
Alignment explanation
Indices: 10646352--10646451 Score: 114
Period size: 39 Copynumber: 2.5 Consensus size: 38
10646342 AATTAATATT
10646352 TTTTAAAATTTAAAAAATTAAAAAAAATATAAAA-AATTA
1 TTTTAAAA-TTAAAAAATTAAAAAAAATA-AAAACAATTA
* *
10646391 TTTTAAAATT-AAAAATTATTAAAAAATTAAAAAGCAATTT
1 TTTTAAAATTAAAAAATTA--AAAAAAATAAAAA-CAATTA
10646431 TTTTAAAATTAAAATAATTAA
1 TTTTAAAATTAAAA-AATTAA
10646452 TTAGATAATG
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
37 8 0.15
38 6 0.11
39 16 0.30
40 15 0.28
41 3 0.06
42 5 0.09
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (38 bp):
TTTTAAAATTAAAAAATTAAAAAAAATAAAAACAATTA
Found at i:10646435 original size:40 final size:38
Alignment explanation
Indices: 10646350--10646451 Score: 118
Period size: 40 Copynumber: 2.6 Consensus size: 38
10646340 TGAATTAATA
10646350 TTTTTTAAAATTTAAAAAATTAAAAAAAATATAAAAAAT
1 TTTTTTAAAA-TTAAAAAATTAAAAAAAATATAAAAAAT
* *
10646389 TATTTTAAAATT-AAAAATTATTAAAAAAT-TAAAAAGCAAT
1 TTTTTTAAAATTAAAAAATTA-AAAAAAATAT-AAAA--AAT
10646429 TTTTTTAAAATTAAAATAATTAA
1 TTTTTTAAAATTAAAA-AATTAA
10646452 TTAGATAATG
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
37 9 0.17
38 13 0.25
39 9 0.17
40 14 0.26
41 3 0.06
42 5 0.09
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (38 bp):
TTTTTTAAAATTAAAAAATTAAAAAAAATATAAAAAAT
Found at i:10662000 original size:16 final size:18
Alignment explanation
Indices: 10661968--10662014 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
10661958 GAATACTGTT
*
10661968 GAGAAAGAGAAATTTTG-G
1 GAGAAAGAG-GATTTTGTG
*
10661986 GAGAAA-AGGATTTTGTT
1 GAGAAAGAGGATTTTGTG
10662003 GAGAAAGAGGAT
1 GAGAAAGAGGAT
10662015 AAAAGAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 6 0.24
17 8 0.32
18 11 0.44
ACGTcount: A:0.43, C:0.00, G:0.34, T:0.23
Consensus pattern (18 bp):
GAGAAAGAGGATTTTGTG
Found at i:10664292 original size:33 final size:33
Alignment explanation
Indices: 10664250--10664373 Score: 230
Period size: 33 Copynumber: 3.8 Consensus size: 33
10664240 TTTCTTCTTG
*
10664250 ACATTCCAGCTACTGTCCAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
10664283 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
*
10664316 ACATTCCAGCTCCCGTCCAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
10664349 ACATTCCAGCTCCTGTCCAGCAACC
1 ACATTCCAGCTCCTGTCCAGCAACC
10664374 TGAAACAGAG
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.30, C:0.43, G:0.10, T:0.18
Consensus pattern (33 bp):
ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
Found at i:10683766 original size:46 final size:46
Alignment explanation
Indices: 10683716--10683891 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
10683706 TGGTTGAGCA
10683716 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
10683762 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
10683807 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
10683855 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
10683892 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:10683872 original size:93 final size:93
Alignment explanation
Indices: 10683713--10683884 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
10683703 GGATGGTTGA
* *
10683713 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
10683778 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
10683806 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
10683871 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
10683885 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:10688220 original size:30 final size:27
Alignment explanation
Indices: 10688179--10688245 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
10688169 AATAAAATTA
*
10688179 TTTTTACTTTTAGAAATTT-ATTCCTTTATT
1 TTTTTAATTTTA-AAATTTAATT-C--TATT
*
10688209 TTTTTAATTTTAAATTTTAATTCTATT
1 TTTTTAATTTTAAAATTTAATTCTATT
10688236 TTTTTAATTT
1 TTTTTAATTT
10688246 ATTGGTGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 14 0.41
29 6 0.18
30 14 0.41
ACGTcount: A:0.25, C:0.06, G:0.01, T:0.67
Consensus pattern (27 bp):
TTTTTAATTTTAAAATTTAATTCTATT
Found at i:10689710 original size:27 final size:27
Alignment explanation
Indices: 10689650--10689711 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
10689640 TAAATAAAAG
*
10689650 TTAAAATAAATACTCAGCTAAAAATTA
1 TTAAAATAAATACTCAGCTAAAAATAA
* * ** *
10689677 TTTAAATAAATACTCATCTTTATATAA
1 TTAAAATAAATACTCAGCTAAAAATAA
10689704 TTAAAATA
1 TTAAAATA
10689712 TTCATATTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.37
Consensus pattern (27 bp):
TTAAAATAAATACTCAGCTAAAAATAA
Found at i:10691759 original size:23 final size:25
Alignment explanation
Indices: 10691711--10691760 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 25
10691701 CAAGACGCGC
*
10691711 ACAAAGAGCCATTATTCGGGAAGCTT
1 ACAAAGAGCCA-TATTCAGGAAGCTT
10691737 ACAAAGAGCC-TA-TCAGGAAGCTT
1 ACAAAGAGCCATATTCAGGAAGCTT
10691760 A
1 A
10691761 TCCGGACTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 2 0.09
26 10 0.43
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (25 bp):
ACAAAGAGCCATATTCAGGAAGCTT
Found at i:10693337 original size:15 final size:15
Alignment explanation
Indices: 10693317--10693382 Score: 55
Period size: 15 Copynumber: 4.1 Consensus size: 15
10693307 ATACTACAAA
10693317 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
10693332 ATATTTATAATTTTAAT
1 ATATTTAT--TATTAAT
10693349 AAATATTTATTATTGAA-
1 --ATATTTATTATT-AAT
10693366 ATATTTA-TATTTAAT
1 ATATTTATTA-TTAAT
10693381 AT
1 AT
10693383 TTTTCAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
14 4 0.10
15 19 0.45
17 9 0.21
18 2 0.05
19 8 0.19
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:10693358 original size:34 final size:32
Alignment explanation
Indices: 10693315--10693381 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 32
10693305 ATATACTACA
10693315 AAATATTTATTATT-AATATATTTATAATTTTAAT
1 AAATATTTATTATTGAA-ATATTTAT-A-TTTAAT
10693349 AAATATTTATTATTGAAATATTTATATTTAAT
1 AAATATTTATTATTGAAATATTTATATTTAAT
10693381 A
1 A
10693382 TTTTTCAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 7 0.22
33 1 0.03
34 22 0.69
35 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (32 bp):
AAATATTTATTATTGAAATATTTATATTTAAT
Found at i:10693368 original size:19 final size:17
Alignment explanation
Indices: 10693315--10693362 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
10693305 ATATACTACA
10693315 AAATATTTATTATTAAT
1 AAATATTTATTATTAAT
*
10693332 --ATATTTATAATTTTAAT
1 AAATATTTAT--TATTAAT
10693349 AAATATTTATTATT
1 AAATATTTATTATT
10693363 GAAATATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
15 8 0.32
17 9 0.36
19 8 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATATTTATTATTAAT
Found at i:10693504 original size:13 final size:13
Alignment explanation
Indices: 10693476--10693514 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
10693466 TAAAATAATA
10693476 AATTATATTA-AT-
1 AATT-TATTATATG
10693488 AATTTATTATATG
1 AATTTATTATATG
10693501 AATTTATTATATG
1 AATTTATTATATG
10693514 A
1 A
10693515 TTCGGTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 5 0.20
12 6 0.24
13 14 0.56
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (13 bp):
AATTTATTATATG
Found at i:10695899 original size:25 final size:27
Alignment explanation
Indices: 10695848--10695912 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 27
10695838 CATGTTATAT
* *
10695848 TATATATAATATTTTATTAATAATTTTG
1 TATATATAATATTATATTAAT-ATTTTA
*
10695876 TATAT-TAATATTATATTGAT-TTTTA
1 TATATATAATATTATATTAATATTTTA
10695901 TAT-TATAATATT
1 TATATATAATATT
10695913 GCAATTAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
24 1 0.03
25 14 0.42
27 13 0.39
28 5 0.15
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (27 bp):
TATATATAATATTATATTAATATTTTA
Found at i:10699332 original size:30 final size:31
Alignment explanation
Indices: 10699296--10699374 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 31
10699286 TTTTTTTAAA
*
10699296 ATTATTTAAATAATGAAAAATAATATTTTT-
1 ATTATTTAAATAATGAAAAACAATATTTTTC
*
10699326 ATTATTT-AAT--TGAAATAACATTATTTTTC
1 ATTATTTAAATAATGAAA-AACAATATTTTTC
*
10699355 ATTATTTAAATAATTAAAAA
1 ATTATTTAAATAATGAAAAA
10699375 AACTTATCTA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
27 5 0.12
28 10 0.24
29 10 0.24
30 10 0.24
31 2 0.05
32 4 0.10
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTATTTAAATAATGAAAAACAATATTTTTC
Found at i:10700549 original size:20 final size:21
Alignment explanation
Indices: 10700517--10700555 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
10700507 CTATTTATAT
10700517 TTAATAATATTT-ATAAATAA
1 TTAATAATATTTAATAAATAA
10700537 TTAAT-ATATTTTAATAAAT
1 TTAATAATA-TTTAATAAAT
10700556 TATTTAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 8 0.47
21 6 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAATAATATTTAATAAATAA
Found at i:10712758 original size:4 final size:4
Alignment explanation
Indices: 10712749--10712776 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
10712739 GCCATTAACA
10712749 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
10712777 GTTAGGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:10715325 original size:42 final size:42
Alignment explanation
Indices: 10715266--10715352 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
10715256 CCAAAAAGTG
10715266 CATTGATGGAGTCTCATGGGAGGCAAGAAGAACATCCTGGTC
1 CATTGATGGAGTCTCATGGGAGGCAAGAAGAACATCCTGGTC
10715308 CATTGATGGAGTCTCATGGGAGGCAAGAAGAACATCCTGGTC
1 CATTGATGGAGTCTCATGGGAGGCAAGAAGAACATCCTGGTC
10715350 CAT
1 CAT
10715353 CAGAAACATC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.22
Consensus pattern (42 bp):
CATTGATGGAGTCTCATGGGAGGCAAGAAGAACATCCTGGTC
Found at i:10720064 original size:21 final size:21
Alignment explanation
Indices: 10720040--10720087 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
10720030 CATCTTAAAG
10720040 GCTGCAGAACAGTTTGTCATC
1 GCTGCAGAACAGTTTGTCATC
*
10720061 GCTGCGGAACAGTTTGTCATC
1 GCTGCAGAACAGTTTGTCATC
*
10720082 ACTGCA
1 GCTGCA
10720088 AAGAAGCTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (21 bp):
GCTGCAGAACAGTTTGTCATC
Found at i:10723776 original size:31 final size:31
Alignment explanation
Indices: 10723736--10723806 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
10723726 GCTTTTTTTA
* *
10723736 AGTTAAATTT-GGTATTCAATATTTTAAAAAG
1 AGTTAAATTTAAGTATT-AACATTTTAAAAAG
* *
10723767 AGTTGAATTTAATTATTAACATTTTAAAAAG
1 AGTTAAATTTAAGTATTAACATTTTAAAAAG
*
10723798 AGTTCAATT
1 AGTTAAATT
10723807 GATATTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 30 0.88
32 4 0.12
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.42
Consensus pattern (31 bp):
AGTTAAATTTAAGTATTAACATTTTAAAAAG
Found at i:10724716 original size:12 final size:12
Alignment explanation
Indices: 10724699--10724724 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10724689 CTTTTCCTCT
10724699 TTTGTTCATTTA
1 TTTGTTCATTTA
10724711 TTTGTTCATTTA
1 TTTGTTCATTTA
10724723 TT
1 TT
10724725 ATTAAATTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (12 bp):
TTTGTTCATTTA
Found at i:10726348 original size:16 final size:16
Alignment explanation
Indices: 10726329--10726361 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
10726319 TACCATTTGT
10726329 TAAAAGTTTGTGGAGA
1 TAAAAGTTTGTGGAGA
10726345 TAAAAGTTTGTGGAGA
1 TAAAAGTTTGTGGAGA
10726361 T
1 T
10726362 GGATTTTGCT
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:0.36, C:0.00, G:0.30, T:0.33
Consensus pattern (16 bp):
TAAAAGTTTGTGGAGA
Found at i:10728254 original size:31 final size:31
Alignment explanation
Indices: 10728196--10728281 Score: 127
Period size: 31 Copynumber: 2.6 Consensus size: 31
10728186 CGTTCGTCTA
10728196 TTTATTTATTTATTTATTCTCAAATCCCCATATTTG
1 TTTATTTA-TTA-TTATT-TC--ATCCCCATATTTG
10728232 TTTATTTATTATTATTTCATCCCCATATTTG
1 TTTATTTATTATTATTTCATCCCCATATTTG
10728263 TTTATTTATTATTATTTCA
1 TTTATTTATTATTATTTCA
10728282 CTTCTCATAA
Statistics
Matches: 50, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
31 32 0.64
33 2 0.04
34 5 0.10
35 3 0.06
36 8 0.16
ACGTcount: A:0.24, C:0.14, G:0.02, T:0.59
Consensus pattern (31 bp):
TTTATTTATTATTATTTCATCCCCATATTTG
Found at i:10728347 original size:3 final size:3
Alignment explanation
Indices: 10728339--10728446 Score: 85
Period size: 3 Copynumber: 34.3 Consensus size: 3
10728329 TGTCTTTCTC
* * *
10728339 ATT ATT ATT ATT GTT ATT AGT ATT ATT TTT ATT -TT ATT CATT AGTCT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT A-T-T
* * *
10728386 ACTT GGTT ATCT ATT CATT -TG CTT ATT ATT ATT ATT ATT ATT ATT ATT
1 A-TT -ATT AT-T ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
10728434 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
10728447 AATTGTCTTG
Statistics
Matches: 85, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
2 3 0.04
3 66 0.78
4 13 0.15
5 3 0.04
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:10729462 original size:127 final size:127
Alignment explanation
Indices: 10729281--10729757 Score: 539
Period size: 127 Copynumber: 3.7 Consensus size: 127
10729271 ATGGAATTTC
**
10729281 AAAAGGATATTCTGTATTTTAGTCGAATGAAAAATTGAAACCCAGCACGATTGGGCACGACCTCC
1 AAAAGGATATTCCATATTTTAGTCGAATGAAAAATTGAAACCCAGCACGATTGGGCACGACCTCC
*
10729346 CAAACTTCCAAGCACGAAATATTACCTCGTTTTATTTTAAGAAAGCGTGGATGAAATTTTAA
66 CAAACTTCCAAACACGAAATATTACCTCGTTTTATTTTAAGAAAGCGTGGATGAAATTTTAA
* * * * *
10729408 AAAAGGATATTCCATATTTTAGTCGAGTGGAAAATTGAAGCCCAGCACAATTGGGCACGACTTCC
1 AAAAGGATATTCCATATTTTAGTCGAATGAAAAATTGAAACCCAGCACGATTGGGCACGACCTCC
* * * * *
10729473 CAAACTTCCAAACACGAAATATTGCCTCGTTTTATGTTAAGAAAACGCGGATGAATTTTTAAAAA
66 CAAACTTCCAAACACGAAATATTACCTCGTTTTATTTTAAGAAAGCGTGGATGAAATTTT---AA
* ** * * *
10729538 AAAAGGATATTCTATA-TTTAGTCGAATGAATAAAACGAAACTCAGCACGATTAGGCACGATCTC
1 AAAAGGATATTCCATATTTTAGTCGAATGAA-AAATTGAAACCCAGCACGATTGGGCACGACCTC
* * * * * * ** *
10729602 TCAAACTCCCCAAATATGAAATATTGCCTCCTTTTAATTCTTTAA-AAAGTATGGACGAAA-TTT
65 CCAAACT-TCCAAACACGAAATATTACCTCGTTTT-A-T-TTTAAGAAAGCGTGGATGAAATTTT
*
10729665 -C
126 AA
* * * * *
10729666 CAAAGGATATTCCGTATTTTAGCCGAATGGAAAATTGAAGCCCAGCACGATTGGGCACGACCTCC
1 AAAAGGATATTCCATATTTTAGTCGAATGAAAAATTGAAACCCAGCACGATTGGGCACGACCTCC
*
10729731 CAAACTTCCCAACACGAAATATTACCT
66 CAAACTTCCAAACACGAAATATTACCT
10729758 TATGCTGAGA
Statistics
Matches: 287, Mismatches: 54, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
127 128 0.45
128 46 0.16
129 24 0.08
130 48 0.17
131 23 0.08
132 4 0.01
133 10 0.03
134 4 0.01
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (127 bp):
AAAAGGATATTCCATATTTTAGTCGAATGAAAAATTGAAACCCAGCACGATTGGGCACGACCTCC
CAAACTTCCAAACACGAAATATTACCTCGTTTTATTTTAAGAAAGCGTGGATGAAATTTTAA
Found at i:10729699 original size:258 final size:257
Alignment explanation
Indices: 10729281--10729753 Score: 657
Period size: 258 Copynumber: 1.8 Consensus size: 257
10729271 ATGGAATTTC
* ** *
10729281 AAAAGGATATTCTGTATTTTAGTCGAATGAAAAATTGAAACCCAGCACGATTGGGCACGACCTCC
1 AAAAGGATATTCTATATTTTAGTCGAATGAAAAAACGAAACCCAGCACGATTAGGCACGACCTCC
* * * * *
10729346 CAAACTTCCAAGCACGAAATATTACCTCGTTTTATTTTAAGAAAGCGTGGATGAAATTTTAAAAA
66 CAAACTCCCAAACACGAAATATTACCTCCTTTTATTTTAAGAAAGCATGGACGAAATTTTAAAAA
* * *
10729411 AGGATATTCCATATTTTAGTCGAGTGGAAAATTGAAGCCCAGCACAATTGGGCACGACTTCCCAA
131 AGGATATTCCATATTTTAGCCGAATGGAAAATTGAAGCCCAGCACAATTGGGCACGACCTCCCAA
10729476 ACTTCCAAACACGAAATATTGCCTCGTTTTATGTTAAGAAAACGCGGATGAATTTTTAAAAA
196 ACTTCCAAACACGAAATATTGCCTCGTTTTATGTTAAGAAAACGCGGATGAATTTTTAAAAA
* *
10729538 AAAAGGATATTCTATA-TTTAGTCGAATGAATAAAACGAAACTCAGCACGATTAGGCACGATCTC
1 AAAAGGATATTCTATATTTTAGTCGAATGAA-AAAACGAAACCCAGCACGATTAGGCACGACCTC
* * * * *
10729602 TCAAACTCCCCAAATATGAAATATTGCCTCCTTTTAATTCTTTAA-AAAGTATGGACGAAA-TTT
65 CCAAACT-CCCAAACACGAAATATTACCTCCTTTT-A-T-TTTAAGAAAGCATGGACGAAATTTT
** * *
10729665 -CCAAAGGATATTCCGTATTTTAGCCGAATGGAAAATTGAAGCCCAGCACGATTGGGCACGACCT
126 AAAAAAGGATATTCCATATTTTAGCCGAATGGAAAATTGAAGCCCAGCACAATTGGGCACGACCT
*
10729729 CCCAAACTTCCCAACACGAAATATT
191 CCCAAACTTCCAAACACGAAATATT
10729754 ACCTTATGCT
Statistics
Matches: 187, Mismatches: 24, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
256 14 0.07
257 49 0.26
258 102 0.55
259 4 0.02
260 13 0.07
261 5 0.03
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (257 bp):
AAAAGGATATTCTATATTTTAGTCGAATGAAAAAACGAAACCCAGCACGATTAGGCACGACCTCC
CAAACTCCCAAACACGAAATATTACCTCCTTTTATTTTAAGAAAGCATGGACGAAATTTTAAAAA
AGGATATTCCATATTTTAGCCGAATGGAAAATTGAAGCCCAGCACAATTGGGCACGACCTCCCAA
ACTTCCAAACACGAAATATTGCCTCGTTTTATGTTAAGAAAACGCGGATGAATTTTTAAAAA
Found at i:10731843 original size:45 final size:45
Alignment explanation
Indices: 10731764--10732250 Score: 344
Period size: 45 Copynumber: 10.9 Consensus size: 45
10731754 AAGATCTGTA
* * *
10731764 ATTTTCAGTCTGCTTC-CTGCAACTTCAGGAAGATAATACTTGCC
1 ATTTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCC
* * **
10731808 GTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTT
1 ATTTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCC
** * * **
10731853 ATTTTC-GATCTGCTCCA-TAGTTGA-TACATGGAGATAAGA-TCTGTA
1 ATTTTCAG-TCTGCTCCACT-G-CAACTTCAGGGAGATAAGACT-TGCC
* *
10731898 ATTTTCAGTCTGCTTC-CTGCAACTTCAGGAAGATAAGACTTGCC
1 ATTTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCC
* * * *
10731942 GTCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTTGTC
1 ATTTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCC
* * * * **
10731987 ATTTTTTA-TCTGCTCCA-TAGCCGA-TACATGGAGATAAGA-TCTGTA
1 A-TTTTCAGTCTGCTCCACT-G-CAACTTCAGGGAGATAAGACT-TGCC
* * * *
10732032 ACTTTT-AGTCTGCTTC-CTGCATCTTCAGGAAGATAAGACTTGCT
1 A-TTTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCC
* *
10732076 GTTTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTC
1 ATTTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCC
* * * **
10732121 ATTTTC-GATCTGCTCCA-TAGCCGA-TACATGGAGATAAGA-TCTGTA
1 ATTTTCAG-TCTGCTCCACT-G-CAACTTCAGGGAGATAAGACT-TGCC
* * *
10732166 ACTTTT-AGTCTGCTTC-CTGCAACTTCAGGAAGATAAGACTTGCT
1 A-TTTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCC
* * *
10732210 ATCTACAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACT
1 ATTTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACT
10732251 AGTGGCTAAA
Statistics
Matches: 346, Mismatches: 66, Indels: 61
0.73 0.14 0.13
Matches are distributed among these distances:
43 10 0.03
44 99 0.29
45 222 0.64
46 15 0.04
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (45 bp):
ATTTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCC
Found at i:10731966 original size:134 final size:134
Alignment explanation
Indices: 10731726--10732292 Score: 888
Period size: 134 Copynumber: 4.2 Consensus size: 134
10731716 GATGGCCAAA
*
10731726 ATCTGCTCCATAGTCGATACATGGAGATAAGATCTGTAA-TTTTCAGTCTGCTTCCTGCAACTTC
1 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAACTTTT-AGTCTGCTTCCTGCAACTTC
* *
10731790 AGGAAGATAATACTTGCCGTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTAT
65 AGGAAGATAAGACTTGCCGTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCAT
10731855 TTTCG
130 TTTCG
**
10731860 ATCTGCTCCATAGTTGATACATGGAGATAAGATCTGTAA-TTTTCAGTCTGCTTCCTGCAACTTC
1 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAACTTTT-AGTCTGCTTCCTGCAACTTC
*
10731924 AGGAAGATAAGACTTGCCGTCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTTGTCAT
65 AGGAAGATAAGACTTGCCGTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCAT
**
10731989 TTTTT
130 TTTCG
*
10731994 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAACTTTTAGTCTGCTTCCTGCATCTTCA
1 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAACTTTTAGTCTGCTTCCTGCAACTTCA
* *
10732059 GGAAGATAAGACTTGCTGTTTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCATT
66 GGAAGATAAGACTTGCCGTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCATT
10732124 TTCG
131 TTCG
10732128 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAACTTTTAGTCTGCTTCCTGCAACTTCA
1 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAACTTTTAGTCTGCTTCCTGCAACTTCA
** * * * ***
10732193 GGAAGATAAGACTTGCTATCTACAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACTAGT-GGC
66 GGAAGATAAGACTTGCCGTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCATT
***
10732257 TAAA
131 TTCG
*
10732261 ATCTGCTCCATAGCCGGTACATGGAGATAAGA
1 ATCTGCTCCATAGCCGATACATGGAGATAAGA
10732293 CTCGCCATTT
Statistics
Matches: 405, Mismatches: 27, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
133 32 0.08
134 369 0.91
135 4 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (134 bp):
ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAACTTTTAGTCTGCTTCCTGCAACTTCA
GGAAGATAAGACTTGCCGTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCATT
TTCG
Found at i:10732356 original size:45 final size:43
Alignment explanation
Indices: 10731727--10732357 Score: 203
Period size: 45 Copynumber: 14.1 Consensus size: 43
10731717 ATGGCCAAAA
* * *
10731727 TCTGCTCCATAGTCGATACATGGAGATAAGATCTGTAATTTTCAG
1 TCTGCTCCATAG-CAATTCATGGAGATAAGA-CTGTAATTTTTAG
* *** * *
10731772 TCTGCTTCC-T-GCAACTTCA-GGAAGATAATACTTGCCGTCTTCAG
1 TCTGC-TCCATAGCAA-TTCATGG-AGATAAGAC-TGTAATTTTTAG
* * *
10731816 TCTGCTCCACT-GCAACTTCAGGGAGATAAGACTTGTTA-TTTTCG
1 TCTGCTCCA-TAGCAA-TTCATGGAGATAAGAC-TGTAATTTTTAG
** * *
10731860 ATCTGCTCCATAGTTGATACATGGAGATAAGATCTGTAATTTTCAG
1 -TCTGCTCCATAG-CAATTCATGGAGATAAGA-CTGTAATTTTTAG
*** * *
10731906 TCTGCTTCC-T-GCAACTTCA-GGAAGATAAGACTTGCCGTCTTCAG
1 TCTGC-TCCATAGCAA-TTCATGG-AGATAAGAC-TGTAATTTTTAG
* *
10731950 TCTGCTCCACTA-CAACTTCAGGGAGATAAGACTTGTCATTTTTTA-
1 TCTGCTCCA-TAGCAA-TTCATGGAGATAAGAC-TGT-AATTTTTAG
* * *
10731995 TCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAACTTTTAG
1 TCTGCTCCATAG-CAATTCATGGAGATAAGA-CTGTAATTTTTAG
* * *
10732040 TCTGCTTCC-T-GCATCTTCA-GGAAGATAAGACTTGCT-GTTTTCAG
1 TCTGC-TCCATAGCA-ATTCATGG-AGATAAGAC-TG-TAATTTTTAG
* * *
10732084 TCTGCTCCACT-GCAACTTCAGGGAGATAAGACTTGTCA-TTTTCG
1 TCTGCTCCA-TAGCAA-TTCATGGAGATAAGAC-TGTAATTTTTAG
* * *
10732128 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAACTTTTAG
1 -TCTGCTCCATAG-CAATTCATGGAGATAAGA-CTGTAATTTTTAG
* **
10732174 TCTGCTTCC-T-GCAACTTCA-GGAAGATAAGACTTGCT-ATCTACAG
1 TCTGC-TCCATAGCAA-TTCATGG-AGATAAGAC-TG-TAATTTTTAG
*** ** *
10732218 TCTGCTCCACT-GCAACTTCA-GGAAGATAAGACTAGT-GGCTAAAA
1 TCTGCTCCA-TAGCAA-TTCATGG-AGATAAGACT-GTAATTTTTAG
** * ** *
10732262 TCTGCTCCATAGCCGGTACATGGAGATAAGACTCGCCATTTCT-G
1 TCTGCTCCATAG-CAATTCATGGAGATAAGACT-GTAATTTTTAG
* *
10732306 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTTAG
1 -TCTGCTCCATAG-CAATTCATGGAGATAAGA-CTGTAATTTTTAG
10732352 TCTGCT
1 TCTGCT
10732358 TCCTACAACT
Statistics
Matches: 453, Mismatches: 78, Indels: 110
0.71 0.12 0.17
Matches are distributed among these distances:
43 31 0.07
44 144 0.32
45 236 0.52
46 42 0.09
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (43 bp):
TCTGCTCCATAGCAATTCATGGAGATAAGACTGTAATTTTTAG
Found at i:10732560 original size:64 final size:64
Alignment explanation
Indices: 10732449--10732572 Score: 162
Period size: 64 Copynumber: 1.9 Consensus size: 64
10732439 TCATGTATCT
* *
10732449 ATGCTTATGCCAAATAACTAGGATGCTATGATCAAAATAATCCAAGTGCTCCTAGTTAGACGTG
1 ATGCTTATACCAAATAACTAGGATGCTATGATCAAAATAATCCAAGTGCTCCTAGCTAGACGTG
* * * *
10732513 ATGCTTATATCAAATAATTAGGATGCTATGA-CTAGAATGAAT-GAAGTGCTCCTAGCTAGA
1 ATGCTTATACCAAATAACTAGGATGCTATGATC-AAAAT-AATCCAAGTGCTCCTAGCTAGA
10732573 TGTATTATGA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
63 1 0.02
64 48 0.92
65 3 0.06
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (64 bp):
ATGCTTATACCAAATAACTAGGATGCTATGATCAAAATAATCCAAGTGCTCCTAGCTAGACGTG
Found at i:10743976 original size:127 final size:127
Alignment explanation
Indices: 10743800--10744275 Score: 485
Period size: 127 Copynumber: 3.7 Consensus size: 127
10743790 ATGGAATTTC
** * *
10743800 AAAAGGATATTCTGTATTTTAGTCGAATGAAAAATTAAAACCCAGCACGATTAGGCACGACCTCC
1 AAAAGGATATTCCATATTTTAGTCGAATGAAAAATTGAAACCCAGCACGATTGGGCACGACCTCC
* * * * *
10743865 CAAACTTCCAAGCATGAAATATTACCTTGTTTTATTTTAAGAAAGCGTGAATGAAATTTTAA
66 CAAACTTCCAAACACGAAATATTGCCTCGTTTTATTTTAAGAAAGCGTGGATGAAATTTTAA
* * * * *
10743927 AAAAGGATATTCCATATTTTAGTCGAGTGGAAAATTGAAGCCTAGCACGATTGGGCACGACTTCC
1 AAAAGGATATTCCATATTTTAGTCGAATGAAAAATTGAAACCCAGCACGATTGGGCACGACCTCC
* * * *
10743992 CAAACTTTCAAACACGAAATATTGCCTCGTTTTATTTTAAGAAAACGCGGATG-AATTTAAAAAA
66 CAAACTTCCAAACACGAAATATTGCCTCGTTTTATTTTAAGAAAGCGTGGATGAAATTT---TAA
* ** * * *
10744056 AAAAAGATATTCCATA-TTTAGTCGAATGAACAAAACGAAACCCAGCACGATTGGACACAATCTC
1 AAAAGGATATTCCATATTTTAGTCGAATGAA-AAATTGAAACCCAGCACGATTGGGCACGACCTC
* * * * * * *
10744120 TCAAACTCCCCAAATACTAAATATTGCCTCATTTTAATTTTTTAA-AAAGCATGGACGAAA-TTT
65 CCAAACT-TCCAAACACGAAATATTGCCTCGTTTT-A--TTTTAAGAAAGCGTGGATGAAATTTT
*
10744183 -C
126 AA
* * * * * *
10744184 CAAAGGATATTCCGTATTTTAGCCGAATGGAAAATTGAAGCCCAGCACGATTGGGCACGATCTCC
1 AAAAGGATATTCCATATTTTAGTCGAATGAAAAATTGAAACCCAGCACGATTGGGCACGACCTCC
* *
10744249 CAAATTTCCCAACACGAAATATTGCCT
66 CAAACTTCCAAACACGAAATATTGCCT
10744276 TATGCTGAGA
Statistics
Matches: 282, Mismatches: 57, Indels: 20
0.79 0.16 0.06
Matches are distributed among these distances:
126 5 0.02
127 118 0.42
128 58 0.21
129 60 0.21
130 22 0.08
131 1 0.00
132 10 0.04
133 8 0.03
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (127 bp):
AAAAGGATATTCCATATTTTAGTCGAATGAAAAATTGAAACCCAGCACGATTGGGCACGACCTCC
CAAACTTCCAAACACGAAATATTGCCTCGTTTTATTTTAAGAAAGCGTGGATGAAATTTTAA
Found at i:10747746 original size:23 final size:23
Alignment explanation
Indices: 10747710--10747781 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
10747700 CCGGCCTAAA
* *
10747710 TATATATATTTTTTATTTTTAAT
1 TATATATATATTTTAATTTTAAT
*
10747733 TATATTTATATTTTAATTTTAAT
1 TATATATATATTTTAATTTTAAT
* * * *
10747756 TTTA-ATATA-ATCAATTTTTAT
1 TATATATATATTTTAATTTTAAT
10747777 TATAT
1 TATAT
10747782 TTTTCAAATT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
21 12 0.31
22 4 0.10
23 23 0.59
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (23 bp):
TATATATATATTTTAATTTTAAT
Found at i:10747822 original size:41 final size:41
Alignment explanation
Indices: 10747771--10747858 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 41
10747761 TATAATCAAT
*
10747771 TTTTATTATATTTTTCAAATTGTGTATTGTTTTAAGAATTG
1 TTTTAATATATTTTTCAAATTGTGTATTGTTTTAAGAATTG
** * * * * *
10747812 TTTTAATATATTTTTTTATTTGTTTCTTGTTTTAATATTTG
1 TTTTAATATATTTTTCAAATTGTGTATTGTTTTAAGAATTG
10747853 TTTTAA
1 TTTTAA
10747859 ATGTATTTGA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.24, C:0.02, G:0.09, T:0.65
Consensus pattern (41 bp):
TTTTAATATATTTTTCAAATTGTGTATTGTTTTAAGAATTG
Found at i:10751835 original size:25 final size:25
Alignment explanation
Indices: 10751798--10751867 Score: 94
Period size: 25 Copynumber: 3.0 Consensus size: 25
10751788 AGAATTAATA
*
10751798 TATA-ATTTCACTAATTTATTAAGT
1 TATAGATTTCACTAATTTATTAAAT
10751822 TATAGATTTCACTAATTTATTAAAT
1 TATAGATTTCACTAATTTATTAAAT
*
10751847 TATAG-TTTTA-TAATTT-TTAAA
1 TATAGATTTCACTAATTTATTAAA
10751868 AAATTAAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.12
23 6 0.14
24 8 0.19
25 24 0.56
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (25 bp):
TATAGATTTCACTAATTTATTAAAT
Found at i:10757224 original size:40 final size:40
Alignment explanation
Indices: 10757177--10757265 Score: 126
Period size: 40 Copynumber: 2.2 Consensus size: 40
10757167 TTTTCAGGTC
* *
10757177 AAATCCTATTTGCCTTAAGTTA-CAGTAGTGAATCAGGAAT
1 AAATCCTATTCGCCTTAAATTACCA-TAGTGAATCAGGAAT
* *
10757217 AAATCCTATTCGCTTTAAATTACCATAGTGAATCAGTAAT
1 AAATCCTATTCGCCTTAAATTACCATAGTGAATCAGGAAT
10757257 AAATCCTAT
1 AAATCCTAT
10757266 CCACTTTGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 42 0.95
41 2 0.05
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (40 bp):
AAATCCTATTCGCCTTAAATTACCATAGTGAATCAGGAAT
Found at i:10757285 original size:40 final size:40
Alignment explanation
Indices: 10757202--10757313 Score: 134
Period size: 40 Copynumber: 2.8 Consensus size: 40
10757192 TAAGTTACAG
* * *
10757202 TAGTGAATCAGGAATAAATCCTATTCGCTTTAAATTACCA
1 TAGTGAATCAGGAATAAATCCTATCCACTTTAAAGTACCA
* * * **
10757242 TAGTGAATCAGTAATAAATCCTATCCACTTTGAGGTATTA
1 TAGTGAATCAGGAATAAATCCTATCCACTTTAAAGTACCA
**
10757282 TAGTGAATCAGGAACGAATCCTATCCACTTTA
1 TAGTGAATCAGGAATAAATCCTATCCACTTTA
10757314 TATTCTCGAG
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (40 bp):
TAGTGAATCAGGAATAAATCCTATCCACTTTAAAGTACCA
Found at i:10758955 original size:2 final size:2
Alignment explanation
Indices: 10758948--10758981 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10758938 GATGGATGAG
10758948 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
10758982 TTTCCACACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:10773000 original size:46 final size:46
Alignment explanation
Indices: 10772943--10773254 Score: 399
Period size: 46 Copynumber: 7.0 Consensus size: 46
10772933 AGTGTGGTCT
10772943 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
10772989 CTGAGATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
10773035 C-----TG---TGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
10773073 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
10773119 TTGATATGAGATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * ** * * *
10773165 GTGACATGAAAAGAATAAAACCATGATTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
10773211 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
10773255 TCACGTCAAA
Statistics
Matches: 237, Mismatches: 20, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
38 36 0.15
41 2 0.01
43 2 0.01
45 1 0.00
46 196 0.83
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:10773095 original size:84 final size:87
Alignment explanation
Indices: 10772953--10773208 Score: 365
Period size: 84 Copynumber: 2.9 Consensus size: 87
10772943 CTGATATGAA
*
10772953 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGATGAAATGTGTAAGACCATGGTTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGTGTAAGACCATGGTTG
*
10773018 AAAGATACCATGGCAAC-CT-G
66 AAAGATACCATGGCAACTATAG
*
10773038 -TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGTGTAAGACCATGGTTG
10773102 AAAGATACCATGGCAACTTGATATGAG
66 AAAGATACCATGGCAAC----TAT-AG
* * ** * *
10773129 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAAACCATGATTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGTGTAAGACCATGGTTG
10773194 AAAGATACCATGGCA
66 AAAGATACCATGGCA
10773209 GCATGACAGA
Statistics
Matches: 154, Mismatches: 9, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
84 80 0.52
89 1 0.01
91 1 0.01
92 72 0.47
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.23
Consensus pattern (87 bp):
ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGTGTAAGACCATGGTTG
AAAGATACCATGGCAACTATAG
Found at i:10777302 original size:3 final size:3
Alignment explanation
Indices: 10777294--10777583 Score: 201
Period size: 3 Copynumber: 97.0 Consensus size: 3
10777284 TAGTACCATG
* *
10777294 ATA ATA ATA AGA ATA ATA ATA ATA A-A ATA ATA A-A AGTA AGA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
* * * * * *
10777337 ATG TTA CTA ACA ATA ATA ATAA ATAA ATA ATG TTA ATA A-A TATA TATA
1 ATA ATA ATA ATA ATA ATA AT-A AT-A ATA ATA ATA ATA ATA -ATA -ATA
* *
10777385 A-A ATA ATA GTA ACA ATA ATA A-A ATA A-A TATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
* * * *
10777428 ATA ATA ATA ATA ATA ATA ATA A-A GATA ATA A-C ATG TTA CTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA
* * *
10777472 ATA ATA ATA ATA AGTA ATA ATA TATA ATA ATA ACA GTA ATA AAA ATA
1 ATA ATA ATA ATA A-TA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
10777519 AAA ATA ATGA ATA CA-A ATG ATA ATA A-A ATA ATA ATA ATA ATA ATA
1 ATA ATA AT-A ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
10777564 ATTA AT- TTA ATA ATA A-A ATA
1 A-TA ATA ATA ATA ATA ATA ATA
10777584 GCAAAAATAA
Statistics
Matches: 228, Mismatches: 36, Indels: 46
0.74 0.12 0.15
Matches are distributed among these distances:
2 20 0.09
3 179 0.79
4 29 0.13
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:10782479 original size:15 final size:16
Alignment explanation
Indices: 10782452--10782481 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10782442 TTTTATATAA
10782452 TTTTAAAATTTATTTT
1 TTTTAAAATTTATTTT
10782468 TTTTAAAA-TTATTT
1 TTTTAAAATTTATTT
10782482 ATGTATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTAAAATTTATTTT
Found at i:10782773 original size:18 final size:18
Alignment explanation
Indices: 10782747--10782781 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10782737 GTTGTATACA
10782747 TATAAACTATTAATATAT
1 TATAAACTATTAATATAT
* *
10782765 TATATACTATTTATATA
1 TATAAACTATTAATATA
10782782 ATACAATAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (18 bp):
TATAAACTATTAATATAT
Found at i:10784544 original size:28 final size:27
Alignment explanation
Indices: 10784513--10784575 Score: 63
Period size: 29 Copynumber: 2.2 Consensus size: 27
10784503 CAAATTTTAA
10784513 AATGATAAGAAATGAATTTAAAATGAAT
1 AATG-TAAGAAATGAATTTAAAATGAAT
* * * *
10784541 AATGTGAAAAAAAGAAATTTAATATCAAT
1 AATGT-AAGAAATG-AATTTAAAATGAAT
10784570 AATGTA
1 AATGTA
10784576 CAAAACAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 1 0.03
28 11 0.38
29 17 0.59
ACGTcount: A:0.57, C:0.02, G:0.13, T:0.29
Consensus pattern (27 bp):
AATGTAAGAAATGAATTTAAAATGAAT
Found at i:10784603 original size:29 final size:27
Alignment explanation
Indices: 10784567--10784622 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
10784557 ATTTAATATC
10784567 AATAATGTACAAAACAATTTAAAAATAG
1 AATAATGTACAAAA-AATTTAAAAATAG
* * *
10784595 AATATATGTATAAGAAATTTTAAAATAG
1 AATA-ATGTACAAAAAATTTAAAAATAG
10784623 GTAATATAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (27 bp):
AATAATGTACAAAAAATTTAAAAATAG
Found at i:10784646 original size:26 final size:26
Alignment explanation
Indices: 10784608--10784683 Score: 64
Period size: 26 Copynumber: 2.8 Consensus size: 26
10784598 ATATGTATAA
* **
10784608 GAAATTTTAAAATAGGTAATATA-GG
1 GAAAGTTTAAAATAAATAATATACGG
*
10784633 CGAAAGTTTGAAATAAATAATATACGG
1 -GAAAGTTTAAAATAAATAATATACGG
* *
10784660 GAAAGAGTTTAAAATGAACAATAT
1 G-AA-AGTTTAAAATAAATAATAT
10784684 GTAAAAAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 20 0.50
27 4 0.10
28 16 0.40
ACGTcount: A:0.50, C:0.04, G:0.18, T:0.28
Consensus pattern (26 bp):
GAAAGTTTAAAATAAATAATATACGG
Found at i:10784819 original size:26 final size:23
Alignment explanation
Indices: 10784789--10784859 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
10784779 TATATATAAA
*
10784789 AAATAGATAAAACAATTTGAAATT
1 AAATA-ATAAAACAATTTAAAATT
* * *
10784813 GATAATATATATAA-AATTTTAAAGT
1 -A-AATA-ATAAAACAATTTAAAATT
10784838 AAATAATAAAACAATTTAAAAT
1 AAATAATAAAACAATTTAAAAT
10784860 GAATAATGCA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
22 5 0.14
23 12 0.32
24 1 0.03
25 10 0.27
26 9 0.24
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (23 bp):
AAATAATAAAACAATTTAAAATT
Found at i:10784866 original size:22 final size:23
Alignment explanation
Indices: 10784790--10784864 Score: 55
Period size: 22 Copynumber: 3.2 Consensus size: 23
10784780 ATATATAAAA
*
10784790 AATAGATAAAACAATTTGAAATTG
1 AATAGATAAAACAATTT-AAAATG
* * * *
10784814 ATAATATATATAAA-ATTTTAAAGTA
1 --AATAGATA-AAACAATTTAAAATG
10784839 AATA-ATAAAACAATTTAAAATG
1 AATAGATAAAACAATTTAAAATG
10784861 AATA
1 AATA
10784865 ATGCATAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
21 3 0.08
22 15 0.38
23 4 0.10
25 4 0.10
26 11 0.28
27 3 0.08
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.32
Consensus pattern (23 bp):
AATAGATAAAACAATTTAAAATG
Found at i:10787101 original size:45 final size:45
Alignment explanation
Indices: 10787035--10787283 Score: 171
Period size: 44 Copynumber: 5.6 Consensus size: 45
10787025 TTAATTTGTT
*
10787035 CCACTACAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTGCC
1 CCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTGCC
* * * * * *
10787080 CCACTGCAATTTCAGGTAAATAAGACTTG-TAACTTTAACCTGCC
1 CCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTGCC
** * * ***
10787124 CCACTGCAACTTCAGGGGGATAAGGTTTGCTATCTTCGATCTATT
1 CCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTGCC
* * * * * * *
10787169 TCACTGCAACTTTAGGGAGATAAGATCTG-TAACTTCAATCTACT
1 CCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTGCC
** * * * * * * * * *
10787213 CTTCTGTAACTTTAAGGAGATAAGATTCGCGA-CTTGAATCTACT
1 CCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTGCC
* *
10787257 CCACTGCAACTTCAGGGAGACAAGATT
1 CCACTGCAACTTCAGGGAAATAAGATT
10787284 CGCCATGGTG
Statistics
Matches: 159, Mismatches: 43, Indels: 5
0.77 0.21 0.02
Matches are distributed among these distances:
44 101 0.64
45 58 0.36
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (45 bp):
CCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTGCC
Found at i:10787174 original size:89 final size:89
Alignment explanation
Indices: 10787035--10787203 Score: 207
Period size: 89 Copynumber: 1.9 Consensus size: 89
10787025 TTAATTTGTT
* *
10787035 CCACTACAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTGCCCCACTGCAA-TTTCAGGTAA
1 CCACTACAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTACCCCACTGCAACTTT-AGGGAA
10787099 ATAAGA-CTTGTAACTTTAACCTGCC
65 ATAAGATC-TGTAACTTTAACCTGCC
* ** * * *** *
10787124 CCACTGCAACTTCAGGGGGATAAGGTTTGCTATCTTCGATCTATTTCACTGCAACTTTAGGGAGA
1 CCACTACAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTACCCCACTGCAACTTTAGGGAAA
10787189 TAAGATCTGTAACTT
66 TAAGATCTGTAACTT
10787204 CAATCTACTC
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
89 63 0.94
90 4 0.06
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (89 bp):
CCACTACAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTACCCCACTGCAACTTTAGGGAAA
TAAGATCTGTAACTTTAACCTGCC
Found at i:10789000 original size:46 final size:46
Alignment explanation
Indices: 10788940--10789168 Score: 370
Period size: 46 Copynumber: 5.0 Consensus size: 46
10788930 TTTGACATGA
* * * * * *
10788940 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
10788986 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
10789032 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
10789078 TGCCATGGTATCTTTCCAACCATGATCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTT-CAACCATGGTCTTACACATTTCATATCAGGT
10789125 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
10789169 AGAGCACACT
Statistics
Matches: 173, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
45 4 0.02
46 124 0.72
47 45 0.26
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:10789136 original size:93 final size:92
Alignment explanation
Indices: 10788940--10789168 Score: 370
Period size: 93 Copynumber: 2.5 Consensus size: 92
10788930 TTTGACATGA
* * * * * *
10788940 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTATCTTTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTATCTTTCAA
*
10789004 CCATGGTCTTACACATTTCATATCAGGT
65 CCATGATCTTACACATTTCATATCAGGT
10789032 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTT-CAA
10789097 CCATGATCTTACACATTTCATATCAGGT
65 CCATGATCTTACACATTTCATATCAGGT
10789125 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
10789169 AGAGCACACT
Statistics
Matches: 128, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
91 4 0.03
92 50 0.39
93 74 0.58
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.38
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
CATGATCTTACACATTTCATATCAGGT
Found at i:10791623 original size:30 final size:29
Alignment explanation
Indices: 10791589--10791646 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
10791579 CACCCTTAAA
* *
10791589 ATATTTTCACTATTAGTCCTT-AAACTTTTC
1 ATATTTACACT-TTAATCCTTCAAA-TTTTC
10791619 ATATTTACACTTTAATCCTTCAAATTTT
1 ATATTTACACTTTAATCCTTCAAATTTT
10791647 GTGTATTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.29, C:0.19, G:0.02, T:0.50
Consensus pattern (29 bp):
ATATTTACACTTTAATCCTTCAAATTTTC
Found at i:10796344 original size:12 final size:13
Alignment explanation
Indices: 10796329--10796358 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
10796319 TCCCTTTTTA
10796329 TTTTCTTTCCCT-
1 TTTTCTTTCCCTG
10796341 TTTTCTTTCCCTG
1 TTTTCTTTCCCTG
10796354 TTTTC
1 TTTTC
10796359 ATTTTGTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.00, C:0.30, G:0.03, T:0.67
Consensus pattern (13 bp):
TTTTCTTTCCCTG
Found at i:10796741 original size:15 final size:14
Alignment explanation
Indices: 10796723--10796753 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
10796713 TTAATTTATT
10796723 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
10796738 TAATAATAATCTAA
1 TAATAATAATCTAA
10796752 TA
1 TA
10796754 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:10796764 original size:21 final size:20
Alignment explanation
Indices: 10796740--10796808 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
10796730 AATGCTAATA
10796740 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
** **
10796761 ATAA-CGTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
10796780 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
10796801 ATAATAAT
1 ATAATAAT
10796809 AATCATTATA
Statistics
Matches: 36, Mismatches: 8, Indels: 9
0.68 0.15 0.17
Matches are distributed among these distances:
18 3 0.08
19 10 0.28
20 2 0.06
21 18 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.09, G:0.01, T:0.35
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:10804485 original size:30 final size:31
Alignment explanation
Indices: 10804425--10804485 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
10804415 TTCTAGAGCC
**
10804425 TAGGGGCAAAAGTGTAATTATTTTCAAAGTT
1 TAGGGGCAAAAGTGTAATTATTGCCAAAGTT
10804456 TAGGGGCAAAA-TGGTAATT-TTGCCAAAGTT
1 TAGGGGCAAAAGT-GTAATTATTGCCAAAGTT
10804486 CGTATCAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.33
Consensus pattern (31 bp):
TAGGGGCAAAAGTGTAATTATTGCCAAAGTT
Found at i:10804980 original size:47 final size:47
Alignment explanation
Indices: 10804911--10805081 Score: 172
Period size: 47 Copynumber: 3.7 Consensus size: 47
10804901 TGAACATCCA
* *
10804911 AACTCGTTGAGTTGAGTCCGAGTTCCCTTATAGATGTGAAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGTGAAACGTCCG
* * *
10804958 AACTCGTTGAGTTGAGTCCGAGTT--CGT-GAGATGT-AACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGTGAA--A--CGTCCG
* ** *
10805005 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACG-AACGTCGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGTGAAACGTCCG
* *
10805051 AGCTCGTTGAGTTGAGTTCGAGTTCACTTAT
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTAT
10805082 GGGCGGGTTA
Statistics
Matches: 103, Mismatches: 13, Indels: 17
0.77 0.10 0.13
Matches are distributed among these distances:
43 2 0.02
44 6 0.06
45 3 0.03
46 33 0.32
47 52 0.50
48 1 0.01
49 2 0.02
50 4 0.04
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (47 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGTGAAACGTCCG
Found at i:10806602 original size:35 final size:35
Alignment explanation
Indices: 10806563--10806635 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
10806553 ACACATTCTT
10806563 TATTCTCGTCAGATCAATCTCACATAAATAATATA
1 TATTCTCGTCAGATCAATCTCACATAAATAATATA
10806598 TATTCTCGTCAGATCAATCTCACATAAATAATATA
1 TATTCTCGTCAGATCAATCTCACATAAATAATATA
10806633 TAT
1 TAT
10806636 ATCACATACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (35 bp):
TATTCTCGTCAGATCAATCTCACATAAATAATATA
Found at i:10810226 original size:12 final size:13
Alignment explanation
Indices: 10810211--10810240 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
10810201 TCTCTTTTTA
10810211 TTTTCTTTCCCT-
1 TTTTCTTTCCCTG
10810223 TTTTCTTTCCCTG
1 TTTTCTTTCCCTG
10810236 TTTTC
1 TTTTC
10810241 GTTTTGTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.00, C:0.30, G:0.03, T:0.67
Consensus pattern (13 bp):
TTTTCTTTCCCTG
Found at i:10810282 original size:14 final size:14
Alignment explanation
Indices: 10810258--10810290 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
10810248 TCCGTGCTTC
10810258 GTTTCTGTTTCTTTT
1 GTTTCTGTTTC-TTT
10810273 GTTT-TGTTTCTTT
1 GTTTCTGTTTCTTT
10810286 GTTTC
1 GTTTC
10810291 CTTAATTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.41
14 6 0.35
15 4 0.24
ACGTcount: A:0.00, C:0.12, G:0.15, T:0.73
Consensus pattern (14 bp):
GTTTCTGTTTCTTT
Found at i:10810623 original size:15 final size:14
Alignment explanation
Indices: 10810605--10810635 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
10810595 TTAATTTATT
10810605 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
10810620 TAATAATAATCTAA
1 TAATAATAATCTAA
10810634 TA
1 TA
10810636 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:10810646 original size:21 final size:20
Alignment explanation
Indices: 10810622--10810690 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
10810612 AATGCTAATA
10810622 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
10810643 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
10810662 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
10810683 ATAATAAT
1 ATAATAAT
10810691 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:10818292 original size:35 final size:35
Alignment explanation
Indices: 10818241--10818313 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
10818231 CACTATCCTA
* *
10818241 TACAGAGGTGAAGACCTCACGAATGAATAGTTTCT
1 TACAAAGGTGAAGACCTCACGAAGGAATAGTTTCT
10818276 TACAAAGGTGAAGACCTCACGAAGGAATAGTTTCT
1 TACAAAGGTGAAGACCTCACGAAGGAATAGTTTCT
10818311 TAC
1 TAC
10818314 TCTCACTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (35 bp):
TACAAAGGTGAAGACCTCACGAAGGAATAGTTTCT
Found at i:10819510 original size:28 final size:27
Alignment explanation
Indices: 10819479--10819541 Score: 63
Period size: 29 Copynumber: 2.2 Consensus size: 27
10819469 CAAATTTTAA
10819479 AATGATAAGAAATGAATTTAAAATAAAT
1 AATG-TAAGAAATGAATTTAAAATAAAT
* * * *
10819507 AATGTGAAAAAAAGAAATTTAATATCAAT
1 AATGT-AAGAAATG-AATTTAAAATAAAT
10819536 AATGTA
1 AATGTA
10819542 CAAAACAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 1 0.03
28 11 0.38
29 17 0.59
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.29
Consensus pattern (27 bp):
AATGTAAGAAATGAATTTAAAATAAAT
Found at i:10819569 original size:29 final size:27
Alignment explanation
Indices: 10819533--10819588 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
10819523 ATTTAATATC
10819533 AATAATGTACAAAACAATTTAAAAATAG
1 AATAATGTACAAAA-AATTTAAAAATAG
* * *
10819561 AATATATGTATAAGAAATTTTAAAATAG
1 AATA-ATGTACAAAAAATTTAAAAATAG
10819589 GTAATATAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (27 bp):
AATAATGTACAAAAAATTTAAAAATAG
Found at i:10819612 original size:26 final size:26
Alignment explanation
Indices: 10819574--10819650 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 26
10819564 ATATGTATAA
* **
10819574 GAAATTTTAAAATAGGTAATATA-GG
1 GAAAGTTTAAAATAAATAATATACGG
*
10819599 CGAAAGTTTGAAATAAATAATATACGG
1 -GAAAGTTTAAAATAAATAATATACGG
* *
10819626 GAAAGAGTTTAAAATGAACAATATA
1 G-AA-AGTTTAAAATAAATAATATA
10819651 TAAAAAAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
26 20 0.49
27 4 0.10
28 17 0.41
ACGTcount: A:0.51, C:0.04, G:0.18, T:0.27
Consensus pattern (26 bp):
GAAAGTTTAAAATAAATAATATACGG
Found at i:10819696 original size:26 final size:25
Alignment explanation
Indices: 10819603--10819707 Score: 75
Period size: 26 Copynumber: 4.0 Consensus size: 25
10819593 TATAGGCGAA
* *
10819603 AGTTTGAAATAAATAATATACGGGAAAG
1 AGTTTAAAATAAATAATATA---TAAAG
* * *
10819631 AGTTTAAAATGAACAATATATAAAAAA
1 AGTTTAAAATAAATAATATAT--AAAG
* *
10819658 ATTTTAAGATAAATAATATATAAATG
1 AGTTTAAAATAAATAATATATAAA-G
* *
10819684 AGTTTAAAATAAATATTATGTAAA
1 AGTTTAAAATAAATAATATATAAA
10819708 AAGAAACTTG
Statistics
Matches: 60, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
25 3 0.05
26 20 0.33
27 20 0.33
28 17 0.28
ACGTcount: A:0.55, C:0.02, G:0.11, T:0.31
Consensus pattern (25 bp):
AGTTTAAAATAAATAATATATAAAG
Found at i:10819873 original size:27 final size:23
Alignment explanation
Indices: 10819812--10819893 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 23
10819802 TATATAAAAT
10819812 TTTAAAATAAATAAT-AAAACAA
1 TTTAAAATAAATAATGAAAACAA
* *
10819834 TTTAAAATGAATAATGCATAAAGCGAG
1 TTTAAAATAAATAATG-A-AAA-C-AA
*
10819861 TTTAAAATAAATAATGTAAAAGAA
1 TTTAAAATAAATAATG-AAAACAA
10819885 TTTTAAAAT
1 -TTTAAAAT
10819894 CTATATTACA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
22 14 0.29
24 2 0.04
25 11 0.23
26 4 0.08
27 17 0.35
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (23 bp):
TTTAAAATAAATAATGAAAACAA
Found at i:10821218 original size:29 final size:31
Alignment explanation
Indices: 10821156--10821219 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
10821146 CTATGTCTAT
* *
10821156 TCTTTGTCTGTTTCTTCATTGTTTTTTTTTC
1 TCTTTGTCTGTTTCTTCATTGTTTTTTGTCC
10821187 TCTTTGT-TGTTTGC-T-ATTGTTTTTTGTCC
1 TCTTTGTCTGTTT-CTTCATTGTTTTTTGTCC
10821216 TCTT
1 TCTT
10821220 GTTCGTTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 16 0.53
30 6 0.20
31 8 0.27
ACGTcount: A:0.03, C:0.16, G:0.12, T:0.69
Consensus pattern (31 bp):
TCTTTGTCTGTTTCTTCATTGTTTTTTGTCC
Found at i:10822353 original size:14 final size:15
Alignment explanation
Indices: 10822336--10822365 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
10822326 TTATATAAAA
10822336 ATAAAAATAT-ATTT
1 ATAAAAATATAATTT
10822350 ATAAAAATATAATTT
1 ATAAAAATATAATTT
10822365 A
1 A
10822366 ATTTTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAAAATATAATTT
Found at i:10822650 original size:100 final size:101
Alignment explanation
Indices: 10822510--10822698 Score: 310
Period size: 100 Copynumber: 1.9 Consensus size: 101
10822500 AAATGCATGA
* * * *
10822510 ATATATATTTAATTAATCTTATATATAAAAAATGGTACCTTAGGATTATGTAGAGTGTATAATTG
1 ATATATACTTAATTAATCTTAAATATAAAAAATGGTACCTTAGAATTATGTAGAGTGTAGAATTG
*
10822575 GATGGGTAGTCGAAATTCATCGATAAATACATAAAT
66 AATGGGTAGTCGAAATTCATCGATAAATACATAAAT
10822611 ATATATACTTAATT-ATCTTAAATA-AAAATAATGGTACCTTAGAATTATGTAGAGTGTAGAATT
1 ATATATACTTAATTAATCTTAAATATAAAA-AATGGTACCTTAGAATTATGTAGAGTGTAGAATT
10822674 GAATGGGTAGTCGAAATTCATCGAT
65 GAATGGGTAGTCGAAATTCATCGAT
10822699 TCTCCAATGT
Statistics
Matches: 82, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
99 4 0.05
100 65 0.79
101 13 0.16
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.36
Consensus pattern (101 bp):
ATATATACTTAATTAATCTTAAATATAAAAAATGGTACCTTAGAATTATGTAGAGTGTAGAATTG
AATGGGTAGTCGAAATTCATCGATAAATACATAAAT
Found at i:10823103 original size:15 final size:15
Alignment explanation
Indices: 10823083--10823114 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
10823073 ATTTTTGCTT
10823083 TAATATATTTGGGCG
1 TAATATATTTGGGCG
10823098 TAATATATTTGGGCG
1 TAATATATTTGGGCG
10823113 TA
1 TA
10823115 GTGAAGGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.41
Consensus pattern (15 bp):
TAATATATTTGGGCG
Found at i:10825063 original size:18 final size:18
Alignment explanation
Indices: 10825035--10825071 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
10825025 AAAACTATTT
10825035 TTAAAAATAT-AAAATTA
1 TTAAAAATATAAAAATTA
10825052 TTAAAAAGTATAAAAATTA
1 TTAAAAA-TATAAAAATTA
10825071 T
1 T
10825072 AAATTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
TTAAAAATATAAAAATTA
Found at i:10825077 original size:7 final size:7
Alignment explanation
Indices: 10825065--10825090 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
10825055 AAAAGTATAA
10825065 AAATTAT
1 AAATTAT
10825072 AAATTAT
1 AAATTAT
10825079 AAATTAT
1 AAATTAT
10825086 AAATT
1 AAATT
10825091 TTTAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATTAT
Found at i:10827818 original size:3 final size:3
Alignment explanation
Indices: 10827810--10827946 Score: 59
Period size: 3 Copynumber: 44.3 Consensus size: 3
10827800 TAAAACATAT
* * * *
10827810 ATA ATA AT- ATG ACA ATA ATA ACA ACA ATA ATA ATAA ATAA ATAA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A AT-A AT-A AT-A
* * * *
10827858 ATA ATA ATA ATA AAA ATA ATT GTA A-A GAAA ATA A-A GATA A-A ATTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA -ATA ATA A-TA
* * *
10827903 ATA ATG ATA CTA ACGA AT- ATA AGTA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA A-TA ATA ATA A-TA ATA ATA ATA ATA ATA ATA A
10827947 ATATTTTAAA
Statistics
Matches: 105, Mismatches: 18, Indels: 22
0.72 0.12 0.15
Matches are distributed among these distances:
2 8 0.08
3 73 0.70
4 24 0.23
ACGTcount: A:0.64, C:0.04, G:0.05, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:10828089 original size:3 final size:3
Alignment explanation
Indices: 10828060--10828190 Score: 167
Period size: 3 Copynumber: 44.3 Consensus size: 3
10828050 TAAAAATAGT
* * * * * * *
10828060 ATA ATA ATG ATA AT- ATG ATA GTA ATA ATA ACA AT- ATA GTG ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
10828106 GTA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
10828154 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
10828191 AACAACAAGT
Statistics
Matches: 113, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
2 4 0.04
3 109 0.96
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:10828341 original size:8 final size:7
Alignment explanation
Indices: 10828279--10828343 Score: 53
Period size: 7 Copynumber: 9.1 Consensus size: 7
10828269 GTTAATAAGG
10828279 ATAAT-A
1 ATAATAA
*
10828285 ATAATAG
1 ATAATAA
10828292 ATAATAA
1 ATAATAA
*
10828299 TTAAT-A
1 ATAATAA
*
10828305 ATACTAA
1 ATAATAA
*
10828312 ATTAATTA
1 A-TAATAA
10828320 ATAATAA
1 ATAATAA
10828327 AGTAATAA
1 A-TAATAA
10828335 ATAAATAA
1 AT-AATAA
10828343 A
1 A
10828344 CACAAAAAGA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
6 9 0.20
7 19 0.41
8 18 0.39
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (7 bp):
ATAATAA
Found at i:10829072 original size:25 final size:25
Alignment explanation
Indices: 10829019--10829072 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
10829009 CGATCTCAAG
* *
10829019 CCAGGAATCCGGCCTAGGTTTTCGG
1 CCAGGAATCCGGCCTAGGTTTCCGA
*
10829044 CCAGGAATCCGGCTTAGGTTTCCGA
1 CCAGGAATCCGGCCTAGGTTTCCGA
10829069 CCAG
1 CCAG
10829073 TCGCCACCGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.19, C:0.30, G:0.30, T:0.22
Consensus pattern (25 bp):
CCAGGAATCCGGCCTAGGTTTCCGA
Found at i:10829948 original size:21 final size:21
Alignment explanation
Indices: 10829922--10829965 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
10829912 ATTATGTATC
10829922 AATAA-TATGAAAAAATTATTA
1 AATAATTATGAAAAAATT-TTA
* *
10829943 AATAATTATTAAATAATTTTA
1 AATAATTATGAAAAAATTTTA
10829964 AA
1 AA
10829966 AAAATCATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AATAATTATGAAAAAATTTTA
Found at i:10829951 original size:11 final size:11
Alignment explanation
Indices: 10829922--10829965 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
10829912 ATTATGTATC
*
10829922 AATAA-TATGA
1 AATAATTATTA
*
10829932 AAAAATTATTA
1 AATAATTATTA
10829943 AATAATTATTA
1 AATAATTATTA
10829954 AATAATT-TTA
1 AATAATTATTA
10829964 AA
1 AA
10829966 AAAATCATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
10 9 0.30
11 21 0.70
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
AATAATTATTA
Found at i:10831375 original size:25 final size:25
Alignment explanation
Indices: 10831308--10831383 Score: 98
Period size: 25 Copynumber: 3.0 Consensus size: 25
10831298 TTTTAAATAA
10831308 ATTTAAAGTTTTTAAAAATAAAAATT
1 ATTTAAA-TTTTTAAAAATAAAAATT
* * *
10831334 ATATAAATTATGAAAAATAAAAATT
1 ATTTAAATTTTTAAAAATAAAAATT
*
10831359 ATTTAAATTTTTTAAAATATAAAAT
1 ATTTAAATTTTTAAAAATA-AAAAT
10831384 ATAAAAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
25 31 0.74
26 11 0.26
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTTAAATTTTTAAAAATAAAAATT
Found at i:10832365 original size:13 final size:13
Alignment explanation
Indices: 10832347--10832385 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
10832337 TTTACTCTCG
*
10832347 ATTTTACAAAAAT
1 ATTTTACTAAAAT
10832360 ATTTTACTAAAAT
1 ATTTTACTAAAAT
*
10832373 ACTTTACTAAAAT
1 ATTTTACTAAAAT
10832386 TACAATTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (13 bp):
ATTTTACTAAAAT
Found at i:10832643 original size:26 final size:25
Alignment explanation
Indices: 10832607--10832661 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
10832597 TTACTAAGGG
* *
10832607 TGAAATGAATTAAAATATTAAT-AT
1 TGAAATGAATTAAAAAATAAATAAT
10832631 TGAAATTGAAATTAAAAAATAAATAAT
1 TGAAA-TG-AATTAAAAAATAAATAAT
10832658 TGAA
1 TGAA
10832662 CATGTGGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 5 0.19
25 2 0.08
26 13 0.50
27 6 0.23
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (25 bp):
TGAAATGAATTAAAAAATAAATAAT
Found at i:10837298 original size:21 final size:21
Alignment explanation
Indices: 10837272--10837312 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10837262 ATCTGCTCAA
* *
10837272 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
10837293 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
10837313 TCGCTCGTCT
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:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:10841811 original size:43 final size:43
Alignment explanation
Indices: 10841750--10841835 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
10841740 AATGTGCGAG
10841750 AAAGAAATCAAACTCCGCAACCTCCTCCCCCTATCTCAACATC
1 AAAGAAATCAAACTCCGCAACCTCCTCCCCCTATCTCAACATC
10841793 AAAGAAATCAAACTCCGCAACCTCCTCCCCCTATCTCAACATC
1 AAAGAAATCAAACTCCGCAACCTCCTCCCCCTATCTCAACATC
10841836 GGTAGTACCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.35, C:0.42, G:0.05, T:0.19
Consensus pattern (43 bp):
AAAGAAATCAAACTCCGCAACCTCCTCCCCCTATCTCAACATC
Found at i:10846902 original size:52 final size:53
Alignment explanation
Indices: 10846846--10846984 Score: 156
Period size: 52 Copynumber: 2.6 Consensus size: 53
10846836 TACATGATTT
*
10846846 CGTATAAGACTATAGCCGGGCTATGGCATCGGTACCATGTGATT-CGT-ATCCC
1 CGTATAAGACCATAGCCGGGCTATGGCATCGGTACCATGTGATTACGTGAT-CC
* * *** * *
10846898 CGTATAAGACCATAGCTGGGCTATGGTATCGGTGTGATGTGATTATGTGATTC
1 CGTATAAGACCATAGCCGGGCTATGGCATCGGTACCATGTGATTACGTGATCC
* * *
10846951 TGTATAAGACCATATCCGGGATATGGCATCGGTA
1 CGTATAAGACCATAGCCGGGCTATGGCATCGGTA
10846985 TGATATGTGG
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
52 38 0.54
53 31 0.44
54 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.29
Consensus pattern (53 bp):
CGTATAAGACCATAGCCGGGCTATGGCATCGGTACCATGTGATTACGTGATCC
Found at i:10848795 original size:3 final size:3
Alignment explanation
Indices: 10848773--10848950 Score: 97
Period size: 3 Copynumber: 60.3 Consensus size: 3
10848763 GCGGAGAGTG
* *
10848773 TTA TTT TTA ATA TT- TTA TTA TTA TTA -TA TT- TTA TTA CTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
* *
10848816 TTA TTA -TA TTA -CA TTTA TT- TTA TTA CTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* ** *
10848858 -TA TATA TTTA CTA CCA TTA TTTA TTTA TTTA TTA TTA TTA TTA GTA
1 TTA T-TA -TTA TTA TTA TTA -TTA -TTA -TTA TTA TTA TTA TTA TTA
** * * * *
10848904 ACA -TA CTG TTA TTT TTA TTA TT- TTA TTA TTA TTA TTT TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
10848950 T
1 T
10848951 CATGGTACTA
Statistics
Matches: 137, Mismatches: 23, Indels: 30
0.72 0.12 0.16
Matches are distributed among these distances:
2 18 0.13
3 99 0.72
4 19 0.14
5 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:10850194 original size:20 final size:21
Alignment explanation
Indices: 10850164--10850202 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
10850154 TAGTTTCGAC
10850164 AAATATTATATAAATTTTAAA
1 AAATATTATATAAATTTTAAA
10850185 AAAT-TTATATAAATTTTA
1 AAATATTATATAAATTTTA
10850203 TATTTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATATTATATAAATTTTAAA
Found at i:10850204 original size:11 final size:11
Alignment explanation
Indices: 10850164--10850205 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
10850154 TAGTTTCGAC
*
10850164 AAATATTATAT
1 AAATTTTATAT
10850175 AAATTTTA-A-
1 AAATTTTATAT
*
10850184 AAAATTTATAT
1 AAATTTTATAT
10850195 AAATTTTATAT
1 AAATTTTATAT
10850206 TTTATAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 7 0.27
10 2 0.08
11 17 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AAATTTTATAT
Found at i:10851001 original size:24 final size:24
Alignment explanation
Indices: 10850967--10851028 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 24
10850957 GAAAAATATC
10850967 ATTTTTCAAAAATAATTATCAAAAT-
1 ATTTTT-AAAAATAATTAT-AAAATA
10850992 ATTTTTAAAAAT--TTATAAAATA
1 ATTTTTAAAAATAATTATAAAATA
* *
10851014 ATATTCAAAAATAAT
1 ATTTTTAAAAATAAT
10851029 AAAATAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 5 0.16
22 14 0.44
24 7 0.22
25 6 0.19
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (24 bp):
ATTTTTAAAAATAATTATAAAATA
Found at i:10858247 original size:42 final size:42
Alignment explanation
Indices: 10858188--10858276 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 42
10858178 TCTTAATGGG
*
10858188 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAATATAAAA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAA
*
10858230 GAAAATAGTTCTCTTATTCTAATAAACTACTAAAAGATAAAA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAA
*
10858272 TAAAA
1 GAAAA
10858277 AATTTCTAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (42 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAA
Found at i:10858322 original size:19 final size:18
Alignment explanation
Indices: 10858300--10858339 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
10858290 TGAATAAAAC
10858300 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAA-AT
10858319 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
10858337 TTA
1 TTA
10858340 AAATATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:10862196 original size:42 final size:42
Alignment explanation
Indices: 10862137--10862225 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 42
10862127 TCCTAATTGG
*
10862137 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAATATAAAA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAA
*
10862179 GAAAATAGTTTCCTTATTCTAATAAACTACTAAAAGATAAAA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAA
*
10862221 TAAAA
1 GAAAA
10862226 AAATTCCTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (42 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAA
Found at i:10862272 original size:19 final size:18
Alignment explanation
Indices: 10862250--10862289 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
10862240 TGAATAAAAC
10862250 TTATCTACCGAAATAAGAT
1 TTATCTACCGAAATAA-AT
*
10862269 TTATCTACCTAAATAAAT
1 TTATCTACCGAAATAAAT
10862287 TTA
1 TTA
10862290 AAATATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (18 bp):
TTATCTACCGAAATAAAT
Found at i:10862318 original size:15 final size:15
Alignment explanation
Indices: 10862298--10862326 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10862288 TAAAATATAT
10862298 ATACATATTTCAACA
1 ATACATATTTCAACA
10862313 ATACATATTTCAAC
1 ATACATATTTCAAC
10862327 TATCTACTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (15 bp):
ATACATATTTCAACA
Found at i:10863977 original size:29 final size:29
Alignment explanation
Indices: 10863945--10864001 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
10863935 CTCACATTGC
* *
10863945 AATTAATATAATATTTTTTATTTTTTATG
1 AATTAATATAATATTTTTAAATTTTTATG
**
10863974 AATTGTTATAATATTTTTAAATTTTTAT
1 AATTAATATAATATTTTTAAATTTTTAT
10864002 TATTTTTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (29 bp):
AATTAATATAATATTTTTAAATTTTTATG
Found at i:10870765 original size:16 final size:16
Alignment explanation
Indices: 10870738--10870779 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
10870728 TGGATTATTT
10870738 TTTAATGGAACATATAA
1 TTTAA-GGAACATATAA
10870755 TTTAAGGAACATATAA
1 TTTAAGGAACATATAA
*
10870771 TTTAGGGAA
1 TTTAAGGAA
10870780 AATAATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.33
Consensus pattern (16 bp):
TTTAAGGAACATATAA
Found at i:10878980 original size:25 final size:26
Alignment explanation
Indices: 10878945--10878995 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
10878935 TTCATGTTAT
10878945 TTTTTCTTAAT-TTTTATTAACTTTTA
1 TTTTTCTTAATATTTTA-TAACTTTTA
*
10878971 TTTTT-TTAATATTTTATAATTTTTA
1 TTTTTCTTAATATTTTATAACTTTTA
10878996 AATCATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (26 bp):
TTTTTCTTAATATTTTATAACTTTTA
Found at i:10879457 original size:9 final size:9
Alignment explanation
Indices: 10879443--10879474 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
10879433 TTATTTCAGT
10879443 TTTTTAAAA
1 TTTTTAAAA
10879452 TTTTTAAAA
1 TTTTTAAAA
10879461 TTTTATAAAA
1 TTTT-TAAAA
10879471 TTTT
1 TTTT
10879475 AAATTAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:10879469 original size:10 final size:10
Alignment explanation
Indices: 10879442--10879475 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
10879432 TTTATTTCAG
*
10879442 TTTTTTAAAA
1 TTTTATAAAA
10879452 TTTT-TAAAA
1 TTTTATAAAA
10879461 TTTTATAAAA
1 TTTTATAAAA
10879471 TTTTA
1 TTTTA
10879476 AATTAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTTATAAAA
Found at i:10879495 original size:15 final size:16
Alignment explanation
Indices: 10879454--10879495 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
10879444 TTTTAAAATT
*
10879454 TTTAAAATTTTATAAAA
1 TTTAAAA-TTAATAAAA
*
10879471 TTTTAAATTAATAAAA
1 TTTAAAATTAATAAAA
10879487 -TTAAAATTA
1 TTTAAAATTA
10879496 CACTTTGACC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 8 0.36
16 8 0.36
17 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTAAAATTAATAAAA
Found at i:10880697 original size:17 final size:18
Alignment explanation
Indices: 10880677--10880711 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
10880667 ATAAATTTTA
10880677 TTAAA-TTATAATTATTT
1 TTAAATTTATAATTATTT
10880694 TTAAATTTATAATTATTT
1 TTAAATTTATAATTATTT
10880712 AATAATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAAATTTATAATTATTT
Found at i:10883710 original size:19 final size:19
Alignment explanation
Indices: 10883669--10883712 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
10883659 GCAATTAATT
* *
10883669 TTTTTTATAATTTTATACT
1 TTTTTAATAATTTTATACA
10883688 TTTTTAATAATTTTA-ACGA
1 TTTTTAATAATTTTATAC-A
10883707 TTTTTA
1 TTTTTA
10883713 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTTAATAATTTTATACA
Found at i:10887847 original size:13 final size:14
Alignment explanation
Indices: 10887819--10887845 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10887809 TAAAGAGCTA
10887819 AAAATATTTTTTTT
1 AAAATATTTTTTTT
10887833 AAAATATTTTTTT
1 AAAATATTTTTTT
10887846 AATTTCTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AAAATATTTTTTTT
Found at i:10892751 original size:31 final size:31
Alignment explanation
Indices: 10892713--10892775 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
10892703 AACATTGATG
10892713 AAATTAGGTTAAGTGGGTTAGCCAAATTATT
1 AAATTAGGTTAAGTGGGTTAGCCAAATTATT
10892744 AAATTAGGTTAAGTGGGTTAGCCAAATTATT
1 AAATTAGGTTAAGTGGGTTAGCCAAATTATT
10892775 A
1 A
10892776 CTGAAAAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (31 bp):
AAATTAGGTTAAGTGGGTTAGCCAAATTATT
Found at i:10892983 original size:35 final size:35
Alignment explanation
Indices: 10892944--10893020 Score: 97
Period size: 35 Copynumber: 2.2 Consensus size: 35
10892934 CATGCTCACG
10892944 ATTTGAGT-GAAATTTTCTT-CAACAAATTTATAAAA
1 ATTTGA-TAGAAATTTT-TTGCAACAAATTTATAAAA
* *
10892979 ATTTGATAGAAATTTTTTGTAACAAGTTTATAAAA
1 ATTTGATAGAAATTTTTTGCAACAAATTTATAAAA
10893014 A-TTGATA
1 ATTTGATA
10893021 TTAAAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
34 9 0.24
35 29 0.76
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.42
Consensus pattern (35 bp):
ATTTGATAGAAATTTTTTGCAACAAATTTATAAAA
Found at i:10899993 original size:47 final size:47
Alignment explanation
Indices: 10899924--10900017 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
10899914 AAAGATAGAT
* * *
10899924 TCTAACAGTCCATTAATTCAATTAATCTATCCGGTTAGATTAAATAA
1 TCTAACAGTCCATCAATTCAATTAATCTATCCGGTTAAAATAAATAA
* *
10899971 TCTAACAGTTCATCAATTCAATTAATCTATTCGGTTAAAATAAATAA
1 TCTAACAGTCCATCAATTCAATTAATCTATCCGGTTAAAATAAATAA
10900018 ATTATTATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.36
Consensus pattern (47 bp):
TCTAACAGTCCATCAATTCAATTAATCTATCCGGTTAAAATAAATAA
Done.