Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 53 of 195
Found at i:11078929 original size:44 final size:44
Alignment explanation
Indices: 11078881--11078975 Score: 138
Period size: 44 Copynumber: 2.2 Consensus size: 44
11078871 AAAATCATAC
* *
11078881 AAAAATATCATAATAGA-ATCATGCAATAATATCATTAATCATGG
1 AAAAATATAATAATA-ATATCATGCAATAATATCATCAATCATGG
* *
11078925 AAAAATATAATAATAATGTCATGCAATAATATCATCAATCATGT
1 AAAAATATAATAATAATATCATGCAATAATATCATCAATCATGG
11078969 AAAAATA
1 AAAAATA
11078976 AATGATTCAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 1 0.02
44 45 0.98
ACGTcount: A:0.53, C:0.11, G:0.07, T:0.29
Consensus pattern (44 bp):
AAAAATATAATAATAATATCATGCAATAATATCATCAATCATGG
Found at i:11078975 original size:20 final size:19
Alignment explanation
Indices: 11078897--11078975 Score: 50
Period size: 20 Copynumber: 3.8 Consensus size: 19
11078887 ATCATAATAG
* *
11078897 AATCATGCAATAATATCATT
1 AATCATGTAAAAATATCA-T
* *
11078917 AATCATGGAAAAATATAAT
1 AATCATGTAAAAATATCAT
*
11078936 AATAATGTCATGCAATAATATCAT
1 AATCATGT-A---AA-AATATCAT
11078960 CAATCATGTAAAAATA
1 -AATCATGTAAAAATA
11078976 AATGATTCAT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
19 7 0.15
20 20 0.43
21 2 0.04
23 2 0.04
24 8 0.17
25 7 0.15
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (19 bp):
AATCATGTAAAAATATCAT
Found at i:11079011 original size:26 final size:25
Alignment explanation
Indices: 11078982--11079049 Score: 61
Period size: 24 Copynumber: 2.8 Consensus size: 25
11078972 AATAAATGAT
11078982 TCATTCAAATAAAATCCATAAAAACA
1 TCATTCAAATAAAATCCATAAAAA-A
* * * *
11079008 TCATCCAAA-AATAT-AATAATAAA
1 TCATTCAAATAAAATCCATAAAAAA
11079031 TC-TTGCAAATAAAATCCAT
1 TCATT-CAAATAAAATCCAT
11079050 GCAAAATATC
Statistics
Matches: 32, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
22 1 0.03
23 7 0.22
24 10 0.31
25 6 0.19
26 8 0.25
ACGTcount: A:0.54, C:0.18, G:0.01, T:0.26
Consensus pattern (25 bp):
TCATTCAAATAAAATCCATAAAAAA
Found at i:11079267 original size:19 final size:20
Alignment explanation
Indices: 11079245--11079296 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
11079235 ACTAAAACAA
* *
11079245 AAAATAAGAAGTAA-AAAAT
1 AAAATAAAAAATAAGAAAAT
* *
11079264 AAAACAAAAAATAAGAAATT
1 AAAATAAAAAATAAGAAAAT
11079284 AAAATAAAAAATA
1 AAAATAAAAAATA
11079297 CAAATAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (20 bp):
AAAATAAAAAATAAGAAAAT
Found at i:11079270 original size:26 final size:25
Alignment explanation
Indices: 11079237--11079317 Score: 103
Period size: 26 Copynumber: 3.2 Consensus size: 25
11079227 AAAAAAATAC
*
11079237 TAAAACAAAAAATAAGAAGTAAAAAA
1 TAAAACAAAAAATAAGAAAT-AAAAA
*
11079263 TAAAACAAAAAATAAGAAATTAAAA
1 TAAAACAAAAAATAAGAAATAAAAA
11079288 TAAAA-AATACAAATAA-AAATAAAAA
1 TAAAACAA-A-AAATAAGAAATAAAAA
11079313 TAAAA
1 TAAAA
11079318 TGAAAATGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
24 2 0.04
25 23 0.46
26 25 0.50
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.15
Consensus pattern (25 bp):
TAAAACAAAAAATAAGAAATAAAAA
Found at i:11079328 original size:6 final size:6
Alignment explanation
Indices: 11079244--11079317 Score: 69
Period size: 6 Copynumber: 11.7 Consensus size: 6
11079234 TACTAAAACA
* *
11079244 AAAAAT AAGAAGT AAAAAAT AAAACA- AAAAAT AAGAAAT TAAAAT AAAAAAT
1 AAAAAT AA-AAAT -AAAAAT AAAA-AT AAAAAT AA-AAAT AAAAAT -AAAAAT
*
11079296 ACAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAA
11079318 TGAAAATGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
5 1 0.02
6 36 0.64
7 17 0.30
8 2 0.04
ACGTcount: A:0.78, C:0.03, G:0.04, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:11080785 original size:11 final size:11
Alignment explanation
Indices: 11080769--11080799 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
11080759 TGAGTTTTTT
11080769 CATTATGCTTC
1 CATTATGCTTC
11080780 CATTATGCTTC
1 CATTATGCTTC
11080791 CATTATGCT
1 CATTATGCT
11080800 ATGTTAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.26, G:0.10, T:0.45
Consensus pattern (11 bp):
CATTATGCTTC
Found at i:11082480 original size:22 final size:22
Alignment explanation
Indices: 11082446--11082501 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
11082436 ATGTCTATTT
11082446 TTTA-TTTGT-TTTTATATTCT-
1 TTTATTTTGTCTTTTA-ATTCTA
* *
11082466 TTTATTTTTTCTTTTAATTTTA
1 TTTATTTTGTCTTTTAATTCTA
11082488 TTTATTTTGTCTTT
1 TTTATTTTGTCTTT
11082502 ATTTTTCCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 4 0.13
21 8 0.27
22 18 0.60
ACGTcount: A:0.14, C:0.05, G:0.04, T:0.77
Consensus pattern (22 bp):
TTTATTTTGTCTTTTAATTCTA
Found at i:11082628 original size:16 final size:13
Alignment explanation
Indices: 11082596--11082633 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
11082586 AAATTTTTAA
11082596 AATTATTTTGTAT
1 AATTATTTTGTAT
*
11082609 AATTATTTTGTGT
1 AATTATTTTGTAT
*
11082622 AATAATTTTGTA
1 AATTATTTTGTA
11082634 CAACTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (13 bp):
AATTATTTTGTAT
Found at i:11083835 original size:20 final size:20
Alignment explanation
Indices: 11083812--11083856 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
11083802 ACATACAATG
* *
11083812 ATACATTTTATCTTACAAAC
1 ATACATTTCACCTTACAAAC
11083832 ATACATTTCACCTTACAAAC
1 ATACATTTCACCTTACAAAC
11083852 ATACA
1 ATACA
11083857 CATTCATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.33
Consensus pattern (20 bp):
ATACATTTCACCTTACAAAC
Found at i:11087164 original size:142 final size:141
Alignment explanation
Indices: 11086905--11087352 Score: 400
Period size: 142 Copynumber: 3.1 Consensus size: 141
11086895 ATATTTTTAG
* * ** * * * * *
11086905 AATTTGACCTTCTCAAGTTTGGTTTTTCTTGAAAAACTCAAGATCATGTTTTAGTATTATTTCAT
1 AATTTGACCTTCT-AAGGTTGATTTTTGGTGAAAAGCTCCAGATCAGGATTTGGTATTATTTCAT
* * * * * * *
11086970 GGATTTTAGTTTATTAAAAACCCTTATTTCACTTC-GAAAGGATTGAAATTACCAAATGCCCTTT
65 GAATTTTAGTGTATTAGAAACCC-TATTACACCTCAAAAAGG-TTGAAATTACCAAATGCCTTTT
* *
11087034 AGAGGTATTTTCAT
128 AGAGATATTCTCAT
* * * *
11087048 AATTTGACCTTCATAAGGTTTATTTTTTGTGAAAA-CTCCATATTAGGATTTGGTATTATTTCAT
1 AATTTGACCTTC-TAAGGTTGATTTTTGGTGAAAAGCTCCAGATCAGGATTTGGTATTATTTCAT
*
11087112 GAATTTTAGTGCATTAGAAACCCTGATTACACCTCAAAAAGGTTGAAATTACCAAATGCCTTTTA
65 GAATTTTAGTGTATTAGAAACCCT-ATTACACCTCAAAAAGGTTGAAATTACCAAATGCCTTTTA
* *
11087177 GCGATATTGTCAT
129 GAGATATTCTCAT
* * * * * * * *
11087190 AATTTGACATTTCCAAGGTTGATTTTTGGTGAAAAGTTTCAGATCATGTTTTGATATTACTTCAT
1 AATTTGAC-CTTCTAAGGTTGATTTTTGGTGAAAAGCTCCAGATCAGGATTTGGTATTATTTCAT
* * * * * * **
11087255 -AATTTTTGATGTATTAGAAACCCTATTTGCACCTTGAAACA-GTTAAAATTACTAAAATATCTT
65 GAATTTTAG-TGTATTAGAAACCCTA-TTACACC-TCAAAAAGGTTGAAATTAC-CAAATGCCTT
11087318 TTAGAGATATTCTCAT
126 TTAGAGATATTCTCAT
11087334 AATTTGACCTTCCTAAGGT
1 AATTTGACCTT-CTAAGGT
11087353 CAAATTTTCA
Statistics
Matches: 248, Mismatches: 47, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
141 1 0.00
142 117 0.47
143 89 0.36
144 41 0.17
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (141 bp):
AATTTGACCTTCTAAGGTTGATTTTTGGTGAAAAGCTCCAGATCAGGATTTGGTATTATTTCATG
AATTTTAGTGTATTAGAAACCCTATTACACCTCAAAAAGGTTGAAATTACCAAATGCCTTTTAGA
GATATTCTCAT
Found at i:11088871 original size:6 final size:6
Alignment explanation
Indices: 11088855--11088886 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
11088845 AAACTTCAAC
*
11088855 CCTAAG TCTAAG CCTAAG CCTAAG CCTAAG CC
1 CCTAAG CCTAAG CCTAAG CCTAAG CCTAAG CC
11088887 AAACTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.31, C:0.34, G:0.16, T:0.19
Consensus pattern (6 bp):
CCTAAG
Found at i:11089059 original size:58 final size:58
Alignment explanation
Indices: 11088926--11089068 Score: 178
Period size: 58 Copynumber: 2.4 Consensus size: 58
11088916 AAATCCCAAA
* * * * * *
11088926 CTTAAACCCCAAACCAAAACTAAGCCCTTATACCAACCTAAGCCGAACCAAACACTAG
1 CTTAAACCCCAAACCAAGACTAAACCCCTAAACCAACCCAAACCGAACCAAACACTAG
* * * *
11088984 TTTAAACCCCAAACCAAGACTAAACCCCTAAACCAACCCAAATCGAAGCAAACCCTAG
1 CTTAAACCCCAAACCAAGACTAAACCCCTAAACCAACCCAAACCGAACCAAACACTAG
*
11089042 CTTAAACCCCAAACCAAGCCCTAAACC
1 CTTAAACCCCAAACCAAG-ACTAAACC
11089069 AATTCCTAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
58 65 0.90
59 7 0.10
ACGTcount: A:0.43, C:0.38, G:0.06, T:0.13
Consensus pattern (58 bp):
CTTAAACCCCAAACCAAGACTAAACCCCTAAACCAACCCAAACCGAACCAAACACTAG
Found at i:11089192 original size:20 final size:20
Alignment explanation
Indices: 11089132--11089194 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
11089122 ACCTTAAGTC
*
11089132 AAACCCTTAAATCCTAAACC-
1 AAACCCTTAAACCCT-AACCT
* *
11089152 AAA-CCTCAAACCCTAAACT
1 AAACCCTTAAACCCTAACCT
*
11089171 AAACCCTTAAACCCTAGCCT
1 AAACCCTTAAACCCTAACCT
11089191 AAAC
1 AAAC
11089195 TCTAAACCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 3 0.09
19 12 0.34
20 20 0.57
ACGTcount: A:0.44, C:0.37, G:0.02, T:0.17
Consensus pattern (20 bp):
AAACCCTTAAACCCTAACCT
Found at i:11089254 original size:43 final size:43
Alignment explanation
Indices: 11089207--11089294 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 43
11089197 TAAACCAATT
11089207 CCTAAACCCCAAACCAAACCTTAAA-CCAATCCTAAACCCTAAA
1 CCTAAACCCCAAACCAAACCTTAAATCCAA-CCTAAACCCTAAA
* * **
11089250 CCTAAACCCTAAACCAAATCTTAAATTGAACCTAAACCCTAAA
1 CCTAAACCCCAAACCAAACCTTAAATCCAACCTAAACCCTAAA
11089293 CC
1 CC
11089295 AATCCTTAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 38 0.95
44 2 0.05
ACGTcount: A:0.45, C:0.36, G:0.01, T:0.17
Consensus pattern (43 bp):
CCTAAACCCCAAACCAAACCTTAAATCCAACCTAAACCCTAAA
Found at i:11089303 original size:30 final size:31
Alignment explanation
Indices: 11089141--11089514 Score: 140
Period size: 30 Copynumber: 12.0 Consensus size: 31
11089131 CAAACCCTTA
*
11089141 AATCC-TAAACC-AAACCTCAAACCCTAAACTA
1 AATCCTTAAACCTAAACCT-AAACCCTAAAC-C
* * *
11089172 AACCCTTAAACCCT-AGCCTAAACTCTAAACC
1 AATCCTTAAA-CCTAAACCTAAACCCTAAACC
* *
11089203 AATTCC-TAAACCCCAAACC-AAACCTTAAACC
1 AA-TCCTTAAA-CCTAAACCTAAACCCTAAACC
11089234 AATCC-TAAACCCTAAACCTAAACCCTAAACC
1 AATCCTTAAA-CCTAAACCTAAACCCTAAACC
* *
11089265 AAAT-CTTAAA-TTGAACCTAAACCCTAAACC
1 -AATCCTTAAACCTAAACCTAAACCCTAAACC
* *
11089295 AATCCTTAAGCCTTAAACTAAATCTAAACCCTAAATC
1 AATCCTTAAACC-TAAAC-----CTAAACCCTAAACC
* * * * * *
11089332 AAACCCTAAACCTTAAATC-AAATCATAAATCA
1 AATCCTTAAACC-TAAACCTAAACCCTAAA-CC
* *
11089364 AACCTAAACTTAAACC-AAATCCTAAACCTTAAACC
1 AA--T--CCTTAAACCTAAA-CCTAAACCCTAAACC
* * * *
11089399 AAACCCTAAA-TTAAACCTAAACCCTTTAACTC
1 AATCCTTAAACCTAAACCTAAACCC-TAAAC-C
* * *
11089431 AAACC--GAACC-AAACCTAAACCTTAAACC
1 AATCCTTAAACCTAAACCTAAACCCTAAACC
** *
11089459 -ATCCCCAACCCTAAACCCTAAA-CCTAAACC
1 AATCCTTAAACCTAAA-CCTAAACCCTAAACC
*
11089489 AA-CCCTAAA-C-AAACC-AAACCCTAAAC
1 AATCCTTAAACCTAAACCTAAACCCTAAAC
11089515 TTACACTCAA
Statistics
Matches: 262, Mismatches: 48, Indels: 70
0.69 0.13 0.18
Matches are distributed among these distances:
26 3 0.01
27 12 0.05
28 4 0.02
29 11 0.04
30 74 0.28
31 64 0.24
32 39 0.15
33 6 0.02
34 3 0.01
35 4 0.02
36 15 0.06
37 27 0.10
ACGTcount: A:0.46, C:0.34, G:0.01, T:0.18
Consensus pattern (31 bp):
AATCCTTAAACCTAAACCTAAACCCTAAACC
Found at i:11089337 original size:12 final size:12
Alignment explanation
Indices: 11089312--11089419 Score: 54
Period size: 12 Copynumber: 9.4 Consensus size: 12
11089302 AAGCCTTAAA
11089312 CTAAATCTAAACC
1 CTAAATC-AAACC
11089325 CTAAATCAAACC
1 CTAAATCAAACC
11089337 C----T-AAACC
1 CTAAATCAAACC
* *
11089344 TTAAATCAAATC
1 CTAAATCAAACC
*
11089356 ATAAATCAAA-C
1 CTAAATCAAACC
*
11089367 CTAAACTTAAA-C
1 CTAAA-TCAAACC
11089379 C-AAATCCTAAACC
1 CTAAAT-C-AAACC
* *
11089392 TTAAACCAAACC
1 CTAAATCAAACC
*
11089404 CTAAATTAAA-C
1 CTAAATCAAACC
11089415 CTAAA
1 CTAAA
11089420 CCCTTTAACT
Statistics
Matches: 74, Mismatches: 11, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
7 5 0.07
8 1 0.01
10 1 0.01
11 15 0.20
12 40 0.54
13 9 0.12
14 3 0.04
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (12 bp):
CTAAATCAAACC
Found at i:11089355 original size:24 final size:24
Alignment explanation
Indices: 11089327--11089401 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
11089317 TCTAAACCCT
*
11089327 AAATCAAACCCTAAACCTTAAATC
1 AAATCAAAACCTAAACCTTAAATC
* *
11089351 AAATCATAAATC-AAACC-TAAACTT
1 AAATCA-AAACCTAAACCTTAAA-TC
* * *
11089375 AAACCAAATCCTAAACCTTAAACC
1 AAATCAAAACCTAAACCTTAAATC
11089399 AAA
1 AAA
11089402 CCCTAAATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
23 7 0.18
24 25 0.64
25 7 0.18
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (24 bp):
AAATCAAAACCTAAACCTTAAATC
Found at i:11089355 original size:37 final size:37
Alignment explanation
Indices: 11089215--11089408 Score: 124
Period size: 37 Copynumber: 5.3 Consensus size: 37
11089205 TTCCTAAACC
*
11089215 CCAAA-CC-AAACCTTAAAC-CAATCCTAAACCCTAAA
1 CCAAACCCTAAACCTTAAACTAAAT-CTAAACCCTAAA
* * *
11089250 CCTAAACCCTAAACCAAATCTTAAATTGAACCTAAACCCTAAA
1 CC-AAACCCTAAA-C----CTTAAACTAAATCTAAACCCTAAA
* * *
11089293 CCAATCCTTAAGCCTTAAACTAAATCTAAACCCTAAA
1 CCAAACCCTAAACCTTAAACTAAATCTAAACCCTAAA
*
11089330 TCAAACCCTAAACCTTAAA-TCAAATC---A---TAAA
1 CCAAACCCTAAACCTTAAACT-AAATCTAAACCCTAAA
* * *
11089361 TCAAA-CCTAAA-CTTAAACCAAATCCTAAACCTTAAA
1 CCAAACCCTAAACCTTAAACTAAAT-CTAAACCCTAAA
11089397 CCAAACCCTAAA
1 CCAAACCCTAAA
11089409 TTAAACCTAA
Statistics
Matches: 125, Mismatches: 15, Indels: 36
0.71 0.09 0.20
Matches are distributed among these distances:
29 10 0.08
30 7 0.06
31 9 0.07
33 1 0.01
34 1 0.01
35 2 0.02
36 12 0.10
37 49 0.39
38 3 0.02
39 1 0.01
41 1 0.01
42 7 0.06
43 20 0.16
44 2 0.02
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.20
Consensus pattern (37 bp):
CCAAACCCTAAACCTTAAACTAAATCTAAACCCTAAA
Found at i:11089406 original size:19 final size:19
Alignment explanation
Indices: 11089096--11089540 Score: 105
Period size: 19 Copynumber: 23.8 Consensus size: 19
11089086 TAAAATCGAA
11089096 CCTAAACCTTAAACCAAAATC
1 CCTAAACCTTAAACC-AAA-C
**
11089117 TCC-AAACCTTAAGTCAAAC
1 -CCTAAACCTTAAACCAAAC
11089136 CCTTAAATCC-TAAACCAAA-
1 CC-TAAA-CCTTAAACCAAAC
* *
11089155 CCTCAAACCCTAAACTAAAC
1 CCT-AAACCTTAAACCAAAC
* *
11089175 CCTTAAACCCT-AGCCTAAAC
1 CC-TAAACCTTAAACC-AAAC
*
11089195 TCTAAACCAATTCCTAAACCCCAAA-
1 CCTAAACC---T--TAAA--CCAAAC
*
11089220 CC-AAACCTTAAACC-AAT
1 CCTAAACCTTAAACCAAAC
*
11089237 CCTAAACCCTAAACCTAAAC
1 CCTAAACCTTAAACC-AAAC
***
11089257 CCTAAACCAAATCTTAAATTGAA-
1 CCTAAA-C----CTTAAACCAAAC
* *
11089280 CCTAAACCCTAAACCAATC
1 CCTAAACCTTAAACCAAAC
* * *
11089299 CTTAAGCCTTAAACTAAA-
1 CCTAAACCTTAAACCAAAC
* * *
11089317 TCTAAACCCTAAATCAAAC
1 CCTAAACCTTAAACCAAAC
*
11089336 CCTAAACCTTAAATCAAA-
1 CCTAAACCTTAAACCAAAC
* *
11089354 --T----CATAAATCAAA-
1 CCTAAACCTTAAACCAAAC
*
11089366 CCTAAA-CTTAAACCAAAT
1 CCTAAACCTTAAACCAAAC
11089384 CCTAAACCTTAAACCAAAC
1 CCTAAACCTTAAACCAAAC
11089403 CCTAAA--TTAAACCTAAAC
1 CCTAAACCTTAAACC-AAAC
* * *
11089421 CCTTTAA-CTCAAACCGAA-
1 CC-TAAACCTTAAACCAAAC
11089439 CC-AAACC-TAAACCTTAAA-
1 CCTAAACCTTAAACC--AAAC
* ** *
11089457 CC--ATCCCCAACCCTAAAC
1 CCTAAACCTTAAACC-AAAC
11089475 CCTAAACC-TAAACC-AAC
1 CCTAAACCTTAAACCAAAC
11089492 CCTAAA-C--AAACCAAAC
1 CCTAAACCTTAAACCAAAC
*
11089508 CCTAAA-CTTACACTCAAACC
1 CCTAAACCTTAAAC-CAAA-C
11089528 CCT-AA-CTTAAACC
1 CCTAAACCTTAAACC
11089541 CTAAACTGAA
Statistics
Matches: 321, Mismatches: 53, Indels: 102
0.67 0.11 0.21
Matches are distributed among these distances:
12 10 0.03
14 1 0.00
15 5 0.02
16 21 0.07
17 37 0.12
18 62 0.19
19 93 0.29
20 48 0.15
21 15 0.05
22 3 0.01
23 6 0.02
24 8 0.02
25 7 0.02
26 3 0.01
27 2 0.01
ACGTcount: A:0.45, C:0.34, G:0.01, T:0.19
Consensus pattern (19 bp):
CCTAAACCTTAAACCAAAC
Found at i:11089413 original size:24 final size:22
Alignment explanation
Indices: 11089338--11089421 Score: 62
Period size: 24 Copynumber: 3.5 Consensus size: 22
11089328 AATCAAACCC
* *
11089338 TAAACCTTAAATCAAATCATAAAT
1 TAAACC-TAAACCAAA-CCTAAAT
* *
11089362 CAAACCTAAACTTAAACC-AAAT
1 TAAACCTAAAC-CAAACCTAAAT
11089384 CCTAAACCTTAAACCAAACCCTAAAT
1 --TAAACC-TAAACCAAA-CCTAAAT
11089410 TAAACCTAAACC
1 TAAACCTAAACC
11089422 CTTTAACTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
22 4 0.08
23 11 0.23
24 22 0.46
25 7 0.15
26 4 0.08
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.21
Consensus pattern (22 bp):
TAAACCTAAACCAAACCTAAAT
Found at i:11089458 original size:7 final size:6
Alignment explanation
Indices: 11089139--11089514 Score: 116
Period size: 7 Copynumber: 61.8 Consensus size: 6
11089129 GTCAAACCCT
11089139 TAAATCC TAAACC -AAACC TCAAACCC TAAA-C TAAACCC TTAAACCC
1 TAAA-CC TAAACC TAAACC T-AAA-CC TAAACC TAAA-CC -TAAA-CC
* * *
11089185 T-AGCC TAAACTC TAAACC -AATTCC TAAACCC CAAACC -AAACC TTAAACC
1 TAAACC TAAAC-C TAAACC TAA-ACC TAAA-CC TAAACC TAAACC -TAAACC
* * * *
11089234 -AATCC TAAACCC TAAACC TAAACCC TAAACC -AAATCT TAAA-T TGAACC
1 TAAACC TAAA-CC TAAACC TAAA-CC TAAACC TAAA-CC TAAACC TAAACC
* * * *
11089282 TAAACCC TAAACC -AATCC TTAAGCC TTAAA-C TAAATC TAAACCC TAAATC
1 TAAA-CC TAAACC TAAACC -TAAACC -TAAACC TAAACC TAAA-CC TAAACC
* * * *
11089332 -AAACCC TAAACC TTAAATC -AAATCA TAAATC -AAACC TAAACT TAAACC
1 TAAA-CC TAAACC -TAAACC TAAA-CC TAAACC TAAACC TAAACC TAAACC
* *
11089380 -AAATCC TAAACC TTAAACC -AAACCC TAAA-T TAAACC TAAACCC TTTAA-C
1 TAAA-CC TAAACC -TAAACC TAAA-CC TAAACC TAAACC TAAA-CC -TAAACC
* ** * *
11089429 TCAAACC -GAACC -AAACC TAAACC TTAAACC -ATCCC CAACCC TAAACCC
1 T-AAACC TAAACC TAAACC TAAACC -TAAACC TAAACC TAAACC TAAA-CC
*
11089477 TAAACC TAAACC -AACCC TAAA-C -AAACC -AAACCC TAAAC
1 TAAACC TAAACC TAAACC TAAACC TAAACC TAAA-CC TAAAC
11089515 TTACACTCAA
Statistics
Matches: 283, Mismatches: 38, Indels: 97
0.68 0.09 0.23
Matches are distributed among these distances:
4 3 0.01
5 80 0.28
6 82 0.29
7 105 0.37
8 13 0.05
ACGTcount: A:0.46, C:0.34, G:0.01, T:0.19
Consensus pattern (6 bp):
TAAACC
Found at i:11089490 original size:24 final size:24
Alignment explanation
Indices: 11089437--11089498 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
11089427 ACTCAAACCG
* *
11089437 AACCAAACCTAAACCTTAAACCAT
1 AACCAACCCTAAACCCTAAACCAT
**
11089461 CCCCAACCCTAAACCCTAAACC-T
1 AACCAACCCTAAACCCTAAACCAT
11089484 AAACCAACCCTAAAC
1 -AACCAACCCTAAAC
11089499 AAACCAAACC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
23 1 0.03
24 30 0.97
ACGTcount: A:0.45, C:0.42, G:0.00, T:0.13
Consensus pattern (24 bp):
AACCAACCCTAAACCCTAAACCAT
Found at i:11089510 original size:16 final size:17
Alignment explanation
Indices: 11089357--11089515 Score: 87
Period size: 17 Copynumber: 9.1 Consensus size: 17
11089347 AATCAAATCA
*
11089357 TAAATCAAA-CCTAAAC
1 TAAACCAAACCCTAAAC
*
11089373 TTAAACCAAATCCTAAACC
1 -TAAACCAAACCCTAAA-C
*
11089392 TTAAACCAAACCCTAAAT
1 -TAAACCAAACCCTAAAC
*
11089410 TAAACCTAAACCCTTTAAC
1 TAAACC-AAACCC-TAAAC
*
11089429 TCAAACCGAA-CC-AAACC
1 T-AAACCAAACCCTAAA-C
* **
11089446 TAAACCTTAAACCAT-CCC
1 TAAACC--AAACCCTAAAC
* *
11089464 CAACCCTAAACCCTAAACC
1 TAAACC-AAACCCTAAA-C
11089483 TAAACC-AACCCTAAAC
1 TAAACCAAACCCTAAAC
11089499 -AAACCAAACCCTAAAC
1 TAAACCAAACCCTAAAC
11089515 T
1 T
11089516 TACACTCAAA
Statistics
Matches: 110, Mismatches: 18, Indels: 28
0.71 0.12 0.18
Matches are distributed among these distances:
15 5 0.05
16 18 0.16
17 32 0.29
18 21 0.19
19 29 0.26
20 5 0.05
ACGTcount: A:0.47, C:0.35, G:0.01, T:0.17
Consensus pattern (17 bp):
TAAACCAAACCCTAAAC
Found at i:11090160 original size:20 final size:20
Alignment explanation
Indices: 11090131--11090170 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
11090121 ATTGATCAAG
*
11090131 CAACTCAAACAATAACCAAA
1 CAACTCAAACAACAACCAAA
*
11090151 CAACTTAAACAACAACCAAA
1 CAACTCAAACAACAACCAAA
11090171 GATGATAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.60, C:0.30, G:0.00, T:0.10
Consensus pattern (20 bp):
CAACTCAAACAACAACCAAA
Found at i:11091584 original size:12 final size:12
Alignment explanation
Indices: 11091567--11091612 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
11091557 GAATGTAGCC
11091567 AAAAAAAATGAG
1 AAAAAAAATGAG
11091579 AAAAAAAATGAG
1 AAAAAAAATGAG
* * *
11091591 AATTAACAATAAG
1 AA-AAAAAATGAG
11091604 AAAAAAAAT
1 AAAAAAAAT
11091613 TCAAGTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.74, C:0.02, G:0.11, T:0.13
Consensus pattern (12 bp):
AAAAAAAATGAG
Found at i:11093303 original size:43 final size:43
Alignment explanation
Indices: 11093218--11093362 Score: 116
Period size: 43 Copynumber: 3.3 Consensus size: 43
11093208 TTTTCTTTTT
* * * * * **
11093218 ATTTCCATTTTCAAACTTTGATTTTGTCTAGGTTATCATCATTA
1 ATTT-CATTTTTAGACTTTGATTTTGTCCAAGTCATTTTCATTA
*
11093262 ATTTCATTTTTAGACTTTGATTTTGTCCAAGTCATTTTCATTTTC
1 ATTTCATTTTTAGACTTTGATTTTGTCCAAGTCATTTTCA--TTA
* * *
11093307 ATTAT-ATTTTTAGACTTTGATTTCGT-CTAGTCACTTTT-ATTT
1 ATT-TCATTTTTAGACTTTGATTTTGTCCAAGTCA-TTTTCATTA
*
11093349 ATTTTATTTTTAGA
1 ATTTCATTTTTAGA
11093363 ATTAGGCTAT
Statistics
Matches: 85, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
41 1 0.01
42 14 0.16
43 29 0.34
44 11 0.13
45 29 0.34
46 1 0.01
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.55
Consensus pattern (43 bp):
ATTTCATTTTTAGACTTTGATTTTGTCCAAGTCATTTTCATTA
Found at i:11093978 original size:66 final size:64
Alignment explanation
Indices: 11093893--11094057 Score: 174
Period size: 63 Copynumber: 2.6 Consensus size: 64
11093883 TACATTATTA
* * * *
11093893 AACAAAGCAATGCAGTAATTAGATTGTTTTAAAA-AATTTTAATATCAATCAATTATTGTGTTAT
1 AACAATGCAACGCAGTAATTAGATTGTTTTAAAACAA--TTAATAT-AATCAAATATTGCGTTAT
*
11093957 AT
63 AC
* * * * * *
11093959 ACCAATGCAACGCAATAATT-GAATGTTTCAAAACAATTACTATTATCAAATATTGCGTTATAC
1 AACAATGCAACGCAGTAATTAGATTGTTTTAAAACAATTAATATAATCAAATATTGCGTTATAC
*
11094022 AACTATGCAACGCAGT-ATTAGATTGTTTTAAAACAA
1 AACAATGCAACGCAGTAATTAGATTGTTTTAAAACAA
11094058 ATTTTCATGA
Statistics
Matches: 81, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
62 3 0.04
63 43 0.53
64 6 0.07
65 11 0.14
66 18 0.22
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.35
Consensus pattern (64 bp):
AACAATGCAACGCAGTAATTAGATTGTTTTAAAACAATTAATATAATCAAATATTGCGTTATAC
Found at i:11096119 original size:13 final size:13
Alignment explanation
Indices: 11096084--11096127 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
11096074 TTTAATTTGA
*
11096084 TTTTAGTTTTAGT
1 TTTTAATTTTAGT
* * *
11096097 TTTGATTTTTGGT
1 TTTTAATTTTAGT
11096110 TTTTAATTTTAGT
1 TTTTAATTTTAGT
11096123 TTTTA
1 TTTTA
11096128 TTATTTTCAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.14, T:0.70
Consensus pattern (13 bp):
TTTTAATTTTAGT
Found at i:11096687 original size:14 final size:16
Alignment explanation
Indices: 11096668--11096699 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11096658 TTTTTTTGAG
11096668 AATTTTT-A-TTTCTA
1 AATTTTTAATTTTCTA
11096682 AATTTTTAATTTTCTA
1 AATTTTTAATTTTCTA
11096698 AA
1 AA
11096700 AGATTCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 1 0.06
16 8 0.50
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (16 bp):
AATTTTTAATTTTCTA
Found at i:11097280 original size:7 final size:7
Alignment explanation
Indices: 11097270--11097340 Score: 62
Period size: 6 Copynumber: 10.7 Consensus size: 7
11097260 AGGTTTTCCT
11097270 TTTTTCA
1 TTTTTCA
11097277 -TTTTCA
1 TTTTTCA
11097283 -TTTTCA
1 TTTTTCA
11097289 -TTTTCA
1 TTTTTCA
11097295 -TTTT-A
1 TTTTTCA
*
11097300 TTTTTTA
1 TTTTTCA
*
11097307 TTTTTTA
1 TTTTTCA
*
11097314 TTTTTGA
1 TTTTTCA
11097321 TTTTTCA
1 TTTTTCA
*
11097328 TATTTCCA
1 T-TTTTCA
11097336 TTTTT
1 TTTTT
11097341 TATATTTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
5 1 0.02
6 26 0.46
7 24 0.42
8 6 0.11
ACGTcount: A:0.15, C:0.10, G:0.01, T:0.73
Consensus pattern (7 bp):
TTTTTCA
Found at i:11097286 original size:14 final size:14
Alignment explanation
Indices: 11097263--11097341 Score: 55
Period size: 12 Copynumber: 5.9 Consensus size: 14
11097253 TAGTTACAGG
*
11097263 TTTTCCTTTTTTCA
1 TTTTCATTTTTTCA
11097277 TTTTCA--TTTTCA
1 TTTTCATTTTTTCA
11097289 TTTTCATTTTATT--
1 TTTTCATTTT-TTCA
11097302 TTTT-ATTTTTT-A
1 TTTTCATTTTTTCA
*
11097314 TTTTTGA-TTTTTCA
1 -TTTTCATTTTTTCA
11097328 TATTTCCATTTTTT
1 T-TTT-CATTTTTT
11097342 ATATTTTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 18
0.73 0.03 0.25
Matches are distributed among these distances:
11 2 0.04
12 17 0.32
13 14 0.26
14 12 0.23
15 3 0.06
16 5 0.09
ACGTcount: A:0.14, C:0.11, G:0.01, T:0.73
Consensus pattern (14 bp):
TTTTCATTTTTTCA
Found at i:11097317 original size:31 final size:35
Alignment explanation
Indices: 11097283--11097349 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 35
11097273 TTCATTTTCA
11097283 TTTTCA-TTTTCAT-TTT-ATTTTTTATTTTTTAT
1 TTTTCATTTTTCATATTTCATTTTTTATTTTTTAT
*
11097315 TTTTGATTTTTCATATTTCCATTTTTTATATTTTT
1 TTTTCATTTTTCATATTT-CATTTTTTAT-TTTTT
11097350 TTACTATGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 5 0.17
33 7 0.24
34 3 0.10
36 9 0.31
37 5 0.17
ACGTcount: A:0.16, C:0.07, G:0.01, T:0.75
Consensus pattern (35 bp):
TTTTCATTTTTCATATTTCATTTTTTATTTTTTAT
Found at i:11097325 original size:13 final size:14
Alignment explanation
Indices: 11097295--11097348 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
11097285 TTCATTTTCA
*
11097295 TTTTATTTTTTATT
1 TTTTATTTTTGATT
11097309 TTTTATTTTTGATT
1 TTTTATTTTTGATT
* **
11097323 TTTCATATTTCCATT
1 TTTTAT-TTTTGATT
11097338 TTTTATATTTT
1 TTTTAT-TTTT
11097349 TTTACTATGT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 18 0.55
15 15 0.45
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTTATTTTTGATT
Found at i:11097367 original size:3 final size:3
Alignment explanation
Indices: 11097361--11097386 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11097351 TACTATGTGT
11097361 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
11097387 GCTAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:11097636 original size:18 final size:18
Alignment explanation
Indices: 11097613--11097649 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
11097603 TTTCAAATTT
*
11097613 AAAAAAA-AAAGATTTTC
1 AAAAAAATAAAAATTTTC
11097630 AAAAAAATAAAAATTTTC
1 AAAAAAATAAAAATTTTC
11097648 AA
1 AA
11097650 TCTTATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (18 bp):
AAAAAAATAAAAATTTTC
Found at i:11102038 original size:19 final size:19
Alignment explanation
Indices: 11102014--11102064 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
11102004 TGTAAAAAAA
11102014 AAAAAAAGAAAAAATAG-AG
1 AAAAAAAGAAAAAA-AGAAG
11102033 AAAAAAAGCAAAAAAAGAAG
1 AAAAAAAG-AAAAAAAGAAG
11102053 AAGAAAAAGAAA
1 AA-AAAAAGAAA
11102065 TTGATAGGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.34
20 13 0.45
21 6 0.21
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (19 bp):
AAAAAAAGAAAAAAAGAAG
Found at i:11103557 original size:22 final size:22
Alignment explanation
Indices: 11103532--11103599 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
11103522 AAAGAGAACT
11103532 TTTAAATTTTTGGATGTGAATC
1 TTTAAATTTTTGGATGTGAATC
** *
11103554 TTTAAAATTTTTTTAAAGTGAATC
1 TTT-AAA-TTTTTGGATGTGAATC
* * *
11103578 TCTGAAGTTTTGGATGTGAATC
1 TTTAAATTTTTGGATGTGAATC
11103600 CCTAAGTTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
22 15 0.43
23 5 0.14
24 15 0.43
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (22 bp):
TTTAAATTTTTGGATGTGAATC
Found at i:11103574 original size:24 final size:24
Alignment explanation
Indices: 11103508--11103578 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
11103498 TGCAAAACTC
* *
11103508 TTAAAGTTTTTTTGAAAGAGAA-CT
1 TTAAAATTTTTTT-AAAGTGAATCT
* ** *
11103532 TTTAAA-TTTTTGGATGTGAATCT
1 TTAAAATTTTTTTAAAGTGAATCT
11103555 TTAAAATTTTTTTAAAGTGAATCT
1 TTAAAATTTTTTTAAAGTGAATCT
11103579 CTGAAGTTTT
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
22 5 0.14
23 12 0.34
24 18 0.51
ACGTcount: A:0.34, C:0.04, G:0.14, T:0.48
Consensus pattern (24 bp):
TTAAAATTTTTTTAAAGTGAATCT
Found at i:11103912 original size:19 final size:17
Alignment explanation
Indices: 11103848--11103912 Score: 55
Period size: 17 Copynumber: 3.8 Consensus size: 17
11103838 TGAATCTAAA
11103848 AATT-TTGTGAATATTT-
1 AATTCTTGTGAAT-TTTG
11103864 AATTCTTGTGAA-TTTG
1 AATTCTTGTGAATTTTG
**
11103880 AAATTCTTACGAATTTTTG
1 -AATTCTTGTGAA-TTTTG
11103899 AATTTCTTGTGAAT
1 AA-TTCTTGTGAAT
11103913 CTAAAAATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
15 3 0.08
16 4 0.10
17 17 0.44
18 3 0.08
19 12 0.31
ACGTcount: A:0.29, C:0.06, G:0.14, T:0.51
Consensus pattern (17 bp):
AATTCTTGTGAATTTTG
Found at i:11103915 original size:70 final size:70
Alignment explanation
Indices: 11103827--11103963 Score: 179
Period size: 70 Copynumber: 2.0 Consensus size: 70
11103817 CTTGCAAGCC
* **
11103827 TGAAATTCTTATGAATCTAAAAATT-TTGTGAATA-TTTAATTCTTGTGAATTTGAAATTCTTAC
1 TGAAATTCTTATGAATCTAAAAATTCTTGT-AAAACTAAAATTCTTGTGAATTT-AAATTCTTAC
11103890 GAATTTT
64 GAATTTT
* * * *
11103897 TGAATTTCTTGTGAATCTAAAAATTCTTGTAAAACTAAAATTCTTGTGAATTTAAGTTCTTTCGA
1 TGAAATTCTTATGAATCTAAAAATTCTTGTAAAACTAAAATTCTTGTGAATTTAAATTCTTACGA
11103962 AT
66 AT
11103964 CTAAAAGTTC
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
70 38 0.66
71 20 0.34
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (70 bp):
TGAAATTCTTATGAATCTAAAAATTCTTGTAAAACTAAAATTCTTGTGAATTTAAATTCTTACGA
ATTTT
Found at i:11103938 original size:17 final size:18
Alignment explanation
Indices: 11103902--11103943 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
11103892 ATTTTTGAAT
* *
11103902 TTCTTGTGAATCTAAAAA
1 TTCTTGTAAAACTAAAAA
11103920 TTCTTGTAAAACT-AAAA
1 TTCTTGTAAAACTAAAAA
11103937 TTCTTGT
1 TTCTTGT
11103944 GAATTTAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.43
Consensus pattern (18 bp):
TTCTTGTAAAACTAAAAA
Found at i:11105268 original size:23 final size:23
Alignment explanation
Indices: 11105237--11105292 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
11105227 AGATTCTGGG
*
11105237 TTTTGAATTCTAGGATGATTTTT
1 TTTTTAATTCTAGGATGATTTTT
* *
11105260 TTTTTAATTTTGGGATGATTTTT
1 TTTTTAATTCTAGGATGATTTTT
11105283 TTTTCTAATT
1 TTTT-TAATT
11105293 TGTAGAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 24 0.83
24 5 0.17
ACGTcount: A:0.20, C:0.04, G:0.14, T:0.62
Consensus pattern (23 bp):
TTTTTAATTCTAGGATGATTTTT
Found at i:11105294 original size:23 final size:23
Alignment explanation
Indices: 11105249--11105293 Score: 81
Period size: 23 Copynumber: 1.9 Consensus size: 23
11105239 TTGAATTCTA
11105249 GGATGATTTTTTTTTTAATTTTG
1 GGATGATTTTTTTTTTAATTTTG
11105272 GGATGATTTTTTTTTCTAATTT
1 GGATGATTTTTTTTT-TAATTT
11105294 GTAGAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.18, C:0.02, G:0.16, T:0.64
Consensus pattern (23 bp):
GGATGATTTTTTTTTTAATTTTG
Found at i:11105805 original size:13 final size:13
Alignment explanation
Indices: 11105789--11105838 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
11105779 TCCCATTTTC
11105789 TTTTTTTTTATTA
1 TTTTTTTTTATTA
11105802 -TTTTTTTT-TTA
1 TTTTTTTTTATTA
11105813 --TTTTTTTATTA
1 TTTTTTTTTATTA
* *
11105824 TGTTTTATTATTA
1 TTTTTTTTTATTA
11105837 TT
1 TT
11105839 ATTATTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 7 0.22
11 6 0.19
12 8 0.25
13 11 0.34
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (13 bp):
TTTTTTTTTATTA
Found at i:11105806 original size:14 final size:13
Alignment explanation
Indices: 11105789--11105819 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
11105779 TCCCATTTTC
11105789 TTTTTTTTTATTAT
1 TTTTTTTTTATT-T
11105803 TTTTTTTTTATTT
1 TTTTTTTTTATTT
11105816 TTTT
1 TTTT
11105820 ATTATGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTTTTATTT
Found at i:11105807 original size:11 final size:11
Alignment explanation
Indices: 11105791--11105838 Score: 69
Period size: 11 Copynumber: 4.2 Consensus size: 11
11105781 CCATTTTCTT
11105791 TTTTTTTATTA
1 TTTTTTTATTA
*
11105802 TTTTTTTTTTA
1 TTTTTTTATTA
11105813 TTTTTTTATTA
1 TTTTTTTATTA
11105824 TGTTTTATTATTA
1 T-TTTT-TTATTA
11105837 TT
1 TT
11105839 ATTATTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
11 21 0.64
12 5 0.15
13 7 0.21
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (11 bp):
TTTTTTTATTA
Found at i:11105843 original size:22 final size:20
Alignment explanation
Indices: 11105794--11105845 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
11105784 TTTTCTTTTT
*
11105794 TTTTATTATT-TTTTTTTTA
1 TTTTATTATTATTTTTATTA
*
11105813 TTTTTTTATTATGTTTTATTA
1 TTTTATTATTAT-TTTTATTA
11105834 TTATTATTATTA
1 TT-TTATTATTA
11105846 AATAATGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 9 0.33
20 1 0.04
21 9 0.33
22 8 0.30
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTATTATTATTTTTATTA
Found at i:11106051 original size:18 final size:18
Alignment explanation
Indices: 11106027--11106064 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
11106017 AATTTACAAA
*
11106027 CAAAAAAA-AAAAGTTTT
1 CAAAAAAATAAAAATTTT
11106044 CAAAAAAATAAAAATTTT
1 CAAAAAAATAAAAATTTT
11106062 CAA
1 CAA
11106065 TCCTACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.66, C:0.08, G:0.03, T:0.24
Consensus pattern (18 bp):
CAAAAAAATAAAAATTTT
Found at i:11107039 original size:73 final size:73
Alignment explanation
Indices: 11106930--11107080 Score: 214
Period size: 73 Copynumber: 2.1 Consensus size: 73
11106920 TAATCTATTA
** * * * * *
11106930 TATT-GAAATTCAAAGACTTTAAAAGTAGATTGACAACAAAATATATTCTTCCATTTGTTGACAA
1 TATTGGAAATTCAAAGACTTTAAAAACAAATTAACAACAAAATATACTCTTCCATTTGCTAACAA
*
11106994 TGTTGAAT
66 TGCTGAAT
11107002 TATTGGAAATTCAAAGACTTTAAAAACAAATTAACAACAAAATATACTCTTCCATTTGCTAACAA
1 TATTGGAAATTCAAAGACTTTAAAAACAAATTAACAACAAAATATACTCTTCCATTTGCTAACAA
11107067 TGCTGAAT
66 TGCTGAAT
*
11107075 TGTTGG
1 TATTGG
11107081 CATTATCGGT
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
72 4 0.06
73 65 0.94
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (73 bp):
TATTGGAAATTCAAAGACTTTAAAAACAAATTAACAACAAAATATACTCTTCCATTTGCTAACAA
TGCTGAAT
Found at i:11110308 original size:3 final size:3
Alignment explanation
Indices: 11110302--11110471 Score: 80
Period size: 3 Copynumber: 60.7 Consensus size: 3
11110292 AGTATTGCTG
* * * * * *
11110302 TTA TTA TTT TTG TTA TTA GTA TTA GTA TTA TTTG TTG TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* * * * * *
11110347 TTA TTG TTA TTA TTA CTA GTA -TA GTA -TA GTA -TA GTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
11110391 -TA TCA -TA TTA TTA TCA -TA TTA TTA -TA TTA -TA TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
11110434 TTA TTA TATA TTA -TA ATA TT- TTA TT- TTA TT- TTA TTA TT
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
11110472 CTTCTTTCCT
Statistics
Matches: 131, Mismatches: 20, Indels: 32
0.72 0.11 0.17
Matches are distributed among these distances:
2 26 0.20
3 100 0.76
4 5 0.04
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:11110332 original size:27 final size:27
Alignment explanation
Indices: 11110280--11110361 Score: 80
Period size: 27 Copynumber: 3.0 Consensus size: 27
11110270 ATCAAGATCA
*
11110280 ATTTTTATTATTAGTATTGCTGTTATT
1 ATTTTTATTATTAGTATTGCTATTATT
*
11110307 ATTTTTGTTATTAGTATTAG-TATTATT
1 ATTTTTATTATTAGTATT-GCTATTATT
* *
11110334 -TGTTGTTATT-TTATTATTGTTATTATT
1 AT-TT-TTATTATTAGTATTGCTATTATT
11110361 A
1 A
11110362 CTAGTATAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
26 2 0.04
27 39 0.85
28 5 0.11
ACGTcount: A:0.23, C:0.01, G:0.11, T:0.65
Consensus pattern (27 bp):
ATTTTTATTATTAGTATTGCTATTATT
Found at i:11110358 original size:33 final size:34
Alignment explanation
Indices: 11110287--11110358 Score: 78
Period size: 33 Copynumber: 2.2 Consensus size: 34
11110277 TCAATTTTTA
*
11110287 TTATTAGTATTGCTGTTATTATTTTTGTTATTAG
1 TTATTAGTATTGCTGTTATTATTTTTATTATTAG
** *
11110321 -TATTAGTATTATTTGTTGTTA-TTTTATTATT-G
1 TTATTAGTATT-GCTGTTATTATTTTTATTATTAG
11110353 TTATTA
1 TTATTA
11110359 TTACTAGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
32 1 0.03
33 24 0.75
34 7 0.22
ACGTcount: A:0.22, C:0.01, G:0.12, T:0.64
Consensus pattern (34 bp):
TTATTAGTATTGCTGTTATTATTTTTATTATTAG
Found at i:11110410 original size:24 final size:24
Alignment explanation
Indices: 11110382--11110442 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
11110372 ATAGTATAGT
11110382 ATATTATTATATCATATTATTATC
1 ATATTATTATATCATATTATTATC
*
11110406 ATATTATTATATTATATTATTATC
1 ATATTATTATATCATATTATTATC
11110430 ATTATTATTATAT
1 A-TATTATTATAT
11110443 ATTATAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
24 24 0.69
25 11 0.31
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (24 bp):
ATATTATTATATCATATTATTATC
Found at i:11111309 original size:6 final size:6
Alignment explanation
Indices: 11111300--11111380 Score: 55
Period size: 6 Copynumber: 13.5 Consensus size: 6
11111290 TTCTTTTTCC
*
11111300 TTTTAT TTTTAT TTTT-T GATTTTAT TTTTA- -TTTAT TTTATAT TTTGAGT
1 TTTTAT TTTTAT TTTTAT --TTTTAT TTTTAT TTTTAT TTT-TAT TTTTA-T
* *
11111349 TTTTTT CTTTTAT TTTTA- ATTT-T TTTTAT TTT
1 TTTTAT -TTTTAT TTTTAT TTTTAT TTTTAT TTT
11111381 ACTAACTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
4 4 0.07
5 7 0.12
6 28 0.47
7 19 0.32
8 1 0.02
ACGTcount: A:0.16, C:0.01, G:0.04, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:11116251 original size:13 final size:13
Alignment explanation
Indices: 11116233--11116261 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
11116223 TTTCTTTTAA
11116233 TTTTATTTATTCT
1 TTTTATTTATTCT
11116246 TTTTATTTATTCT
1 TTTTATTTATTCT
11116259 TTT
1 TTT
11116262 GTCAGTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTATTTATTCT
Found at i:11116419 original size:13 final size:13
Alignment explanation
Indices: 11116401--11116425 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11116391 TTTAAGATTA
11116401 ATTTGTAAATAAT
1 ATTTGTAAATAAT
11116414 ATTTGTAAATAA
1 ATTTGTAAATAA
11116426 ATTAAATGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
ATTTGTAAATAAT
Found at i:11117213 original size:3 final size:3
Alignment explanation
Indices: 11117205--11117231 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
11117195 GAGTTATTGG
11117205 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
11117232 ATTATGATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:11118725 original size:14 final size:14
Alignment explanation
Indices: 11118697--11118742 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
11118687 ATTTTTTATT
11118697 AAATATATAAAAGAA
1 AAATAT-TAAAAGAA
* * *
11118712 AATTTTTAATAGAA
1 AAATATTAAAAGAA
11118726 AAATATTAAAAGAA
1 AAATATTAAAAGAA
11118740 AAA
1 AAA
11118743 GAGAAAAAAG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (14 bp):
AAATATTAAAAGAA
Found at i:11119480 original size:13 final size:13
Alignment explanation
Indices: 11119462--11119507 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
11119452 TAACTTTATC
11119462 AATATAATATATA
1 AATATAATATATA
*
11119475 AATATAAAATAT-
1 AATATAATATATA
*
11119487 AAT-TAATATTAAA
1 AATATAATA-TATA
11119500 AATATAAT
1 AATATAAT
11119508 TTTATATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
11 4 0.15
12 5 0.19
13 14 0.52
14 4 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATAATATATA
Found at i:11124954 original size:283 final size:290
Alignment explanation
Indices: 11124414--11124990 Score: 774
Period size: 283 Copynumber: 2.0 Consensus size: 290
11124404 TAATCAATTT
* * *
11124414 AGACAATTATGTAATGAAAGGGCATTGATAGGTAGTTGACCATTTCAAGGACTCTATAACAAAAT
1 AGACAATTATGTAATGAAAGGGCATTAATAGGTAGTTGACCATTCCAAGGACTCCATAACAAAAT
* * * *
11124479 GGTGTTACGGAGAGAAGAAATAAAACTCTTCTAAAAATGGTGAGATCTATGATGGCCCAAGCAAA
66 GGTGTTAC-GAAAAAAAAAATAAAACTCTTCTAAAAATGGTGAGATCTATGATAGCCCAAGCAAA
* * *
11124544 TTTGCTAATCACCTTTTGAGGTGATGCATTGTTAACTGTTGCCTATATATTCAATAGAGTACCTT
130 TTTGCCAATCACCTTTTGAGGTGATGCATTGTTAACTGCTGCCTATATATTCAATAAAGTACCTT
* * *** * * *
11124609 TCAAGTTGGTTACATCCACCCCTTATGAATTATGAACTGAAAGAAAACCTAATCTCAGTAATTTA
195 CCAACTCAATTACATCCACCCCTCATAAATTATGAACTGAAAGAAAACCTAATCTCAGTAATTCA
* *
11124674 AGACCTTAGGGTTGTGCTGCCTATATGTATG
260 AGACCTTAGGGTTATGCTACCTATATGTATG
* * * *
11124705 AGACAATTATGTGATGAAATGGTATTAATAGGTAGTTGACCATTCCAAGGACTCCATAATAAAAT
1 AGACAATTATGTAATGAAAGGGCATTAATAGGTAGTTGACCATTCCAAGGACTCCATAACAAAAT
*
11124770 -GTGTTAC-AAAAAAAAAAT-AAA-TCTTCTAAAAATGGTGAGATCTATGATAGCTCAAGCAAAT
66 GGTGTTACGAAAAAAAAAATAAAACTCTTCTAAAAATGGTGAGATCTATGATAGCCCAAGCAAAT
* *
11124831 TTGCCAATCACCTTTTGA-G-G-TGCATTTTTAATTGCTGCCTATATACTT-AATAAAGTACCTT
131 TTGCCAATCACCTTTTGAGGTGATGCATTGTTAACTGCTGCCTATATA-TTCAATAAAGTACCTT
* ** *
11124892 CCAACTCAATTACATTCACCCCTCATAAATTATGAACTGGGAGAAAACCTAATCTTAGTAATTCA
195 CCAACTCAATTACATCCACCCCTCATAAATTATGAACTGAAAGAAAACCTAATCTCAGTAATTCA
* * *
11124957 ATACCTTGGGGTTATGCTACCTATGTGTATG
260 AGACCTTAGGGTTATGCTACCTATATGTATG
11124988 AGA
1 AGA
11124991 TCGCTTATCC
Statistics
Matches: 251, Mismatches: 34, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
283 116 0.46
284 3 0.01
285 1 0.00
286 55 0.22
287 3 0.01
288 8 0.03
290 7 0.03
291 58 0.23
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (290 bp):
AGACAATTATGTAATGAAAGGGCATTAATAGGTAGTTGACCATTCCAAGGACTCCATAACAAAAT
GGTGTTACGAAAAAAAAAATAAAACTCTTCTAAAAATGGTGAGATCTATGATAGCCCAAGCAAAT
TTGCCAATCACCTTTTGAGGTGATGCATTGTTAACTGCTGCCTATATATTCAATAAAGTACCTTC
CAACTCAATTACATCCACCCCTCATAAATTATGAACTGAAAGAAAACCTAATCTCAGTAATTCAA
GACCTTAGGGTTATGCTACCTATATGTATG
Found at i:11141633 original size:11 final size:11
Alignment explanation
Indices: 11141598--11141639 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
11141588 CATGTTAAAC
*
11141598 TCTTTTTTCTT
1 TCTTTTTCCTT
* *
11141609 T-TTTCTCTTT
1 TCTTTTTCCTT
11141619 TCTTTTTCCTT
1 TCTTTTTCCTT
11141630 TCTTTTTCCT
1 TCTTTTTCCT
11141640 CTCCCCATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
10 7 0.28
11 18 0.72
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TCTTTTTCCTT
Found at i:11142768 original size:20 final size:19
Alignment explanation
Indices: 11142742--11142789 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
11142732 TTCAAAACTT
* *
11142742 TTTAAAAGATTTTTAAA-A
1 TTTAAAAAAATTTTAAACA
11142760 TTTCAAAAAAATTTTAAACA
1 TTT-AAAAAAATTTTAAACA
11142780 TTTAAAAAAA
1 TTTAAAAAAA
11142790 AGTTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 3 0.12
19 19 0.73
20 4 0.15
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (19 bp):
TTTAAAAAAATTTTAAACA
Found at i:11142782 original size:29 final size:29
Alignment explanation
Indices: 11142727--11142782 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
11142717 GCATCAAAAA
** *
11142727 AAAATTTCAAAACTTTTTAAAAGATTTTT
1 AAAATTTCAAAAAATTTTAAAACATTTTT
11142756 AAAATTTCAAAAAAATTTT-AAACATTT
1 AAAATTTC-AAAAAATTTTAAAACATTT
11142783 AAAAAAAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 15 0.65
30 8 0.35
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (29 bp):
AAAATTTCAAAAAATTTTAAAACATTTTT
Found at i:11142788 original size:29 final size:29
Alignment explanation
Indices: 11142725--11142788 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
11142715 TAGCATCAAA
** *
11142725 AAAAAATTTCAAAACTTTTTAAAAGATTT
1 AAAAAATTTCAAAAAATTTTAAAACATTT
**
11142754 TTAAAATTTCAAAAAAATTTT-AAACATTT
1 AAAAAATTTC-AAAAAATTTTAAAACATTT
11142783 AAAAAA
1 AAAAAA
11142789 AAGTTTAAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAAAATTTCAAAAAATTTTAAAACATTT
Found at i:11142790 original size:20 final size:20
Alignment explanation
Indices: 11142723--11142797 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
11142713 ATTAGCATCA
* *
11142723 AAAAAAAATTTCAAAACTTTT
1 AAAAAAAATTT-TAAACATTT
* * *
11142744 TAAAAGATTTTTAAA-ATTT
1 AAAAAAAATTTTAAACATTT
*
11142763 CAAAAAAATTTTAAACATTT
1 AAAAAAAATTTTAAACATTT
*
11142783 AAAAAAAAGTTTAAA
1 AAAAAAAATTTTAAA
11142798 AATATGAAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
19 15 0.35
20 20 0.47
21 8 0.19
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (20 bp):
AAAAAAAATTTTAAACATTT
Found at i:11142863 original size:22 final size:20
Alignment explanation
Indices: 11142834--11142881 Score: 78
Period size: 22 Copynumber: 2.3 Consensus size: 20
11142824 ACATAAAATT
11142834 AAATTTTTGAAATGTTTTGAA
1 AAATTTTTGAAATGTTTT-AA
11142855 AAATATTTTGAAATGTTTTAA
1 AAAT-TTTTGAAATGTTTTAA
11142876 AAATTT
1 AAATTT
11142882 ATAACAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.08
21 10 0.38
22 14 0.54
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (20 bp):
AAATTTTTGAAATGTTTTAA
Found at i:11142915 original size:19 final size:19
Alignment explanation
Indices: 11142871--11142917 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
11142861 TTTGAAATGT
*
11142871 TTTAAAAATTTATAACAAA
1 TTTAAAATTTTATAACAAA
* *
11142890 TTAAAAATTTTATGAA-AAC
1 TTTAAAATTTTAT-AACAAA
11142909 TTTAAAATT
1 TTTAAAATT
11142918 CATAAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 21 0.91
20 2 0.09
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (19 bp):
TTTAAAATTTTATAACAAA
Found at i:11142934 original size:19 final size:17
Alignment explanation
Indices: 11142911--11142953 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
11142901 ATGAAAACTT
11142911 TAAAATTCATAAAAAAAA
1 TAAAATT-ATAAAAAAAA
* *
11142929 TGAAAATTTTAATAAAAA
1 T-AAAATTATAAAAAAAA
11142947 TAAAATT
1 TAAAATT
11142954 TTTGTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 6 0.27
18 10 0.45
19 6 0.27
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
TAAAATTATAAAAAAAA
Found at i:11142989 original size:15 final size:16
Alignment explanation
Indices: 11142969--11143002 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11142959 AAAATTCAAA
*
11142969 AAAAATT-AATAATCT
1 AAAAATTAAAAAATCT
11142984 AAAAATTAAAAAATCT
1 AAAAATTAAAAAATCT
11143000 AAA
1 AAA
11143003 TTTTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATTAAAAAATCT
Found at i:11143169 original size:21 final size:20
Alignment explanation
Indices: 11143134--11143179 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
11143124 TCATTTATCA
* * *
11143134 TTTTTTAGAATTTTTTATAT
1 TTTTTTAGAAGTTTTAAGAT
11143154 TTTTTTAGGAAGTTTTAAGAT
1 TTTTTTA-GAAGTTTTAAGAT
11143175 TTTTT
1 TTTTT
11143180 GATTTAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.65
Consensus pattern (20 bp):
TTTTTTAGAAGTTTTAAGAT
Found at i:11145051 original size:24 final size:24
Alignment explanation
Indices: 11144998--11145052 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
11144988 TTATCTTAAC
* *
11144998 TATATATATTAAAATTTATCTTTA
1 TATATTTATTAAAATTTATATTTA
* *
11145022 -ATTATTTATTTAATTTTATATTTA
1 TA-TATTTATTAAAATTTATATTTA
11145046 TATATTT
1 TATATTT
11145053 GTATTATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 1 0.04
24 23 0.92
25 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
TATATTTATTAAAATTTATATTTA
Found at i:11147233 original size:2 final size:2
Alignment explanation
Indices: 11147226--11147266 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
11147216 TAAACTTATT
*
11147226 TA TA TA TA T- TG T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11147266 T
1 T
11147267 TAGATTACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:11148376 original size:17 final size:17
Alignment explanation
Indices: 11148337--11148376 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
11148327 TAATTTGAAA
11148337 ATTTTATAATTTAATAG
1 ATTTTATAATTTAATAG
* * *
11148354 AATTTATAATTTTATAT
1 ATTTTATAATTTAATAG
11148371 ATTTTA
1 ATTTTA
11148377 ATGTGTATAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
ATTTTATAATTTAATAG
Found at i:11148807 original size:13 final size:14
Alignment explanation
Indices: 11148769--11148804 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
11148759 TTTGTTTCAC
11148769 AAAAAATAATTTTT
1 AAAAAATAATTTTT
11148783 AAAAAATAATTTTT
1 AAAAAATAATTTTT
*
11148797 GAAAAATA
1 AAAAAATA
11148805 TTTATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (14 bp):
AAAAAATAATTTTT
Found at i:11148916 original size:26 final size:25
Alignment explanation
Indices: 11148861--11148929 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 25
11148851 GAAAAATATT
* *
11148861 TTTATTGTTAAAA-TATTAAAAATTA
1 TTTATTATTAAAATTATT-GAAATTA
11148886 TTTATTATTAAAATGTATTGAAATTA
1 TTTATTATTAAAAT-TATTGAAATTA
11148912 TTTATTATTAAAATTATT
1 TTTATTATTAAAATTATT
11148930 AATATTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
25 16 0.40
26 20 0.50
27 4 0.10
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (25 bp):
TTTATTATTAAAATTATTGAAATTA
Found at i:11148936 original size:25 final size:26
Alignment explanation
Indices: 11148854--11148936 Score: 102
Period size: 25 Copynumber: 3.3 Consensus size: 26
11148844 AGTTGATGAA
*
11148854 AAATATT-TTTATTGTTAAAA-TATT
1 AAATATTATTTATTATTAAAATTATT
*
11148878 AAAAATTATTTATTATTAAAATGTATT
1 AAATATTATTTATTATTAAAAT-TATT
*
11148905 GAA-ATTATTTATTATTAAAATTATT
1 AAATATTATTTATTATTAAAATTATT
11148930 -AATATTA
1 AAATATTA
11148937 AAATATAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
24 8 0.15
25 20 0.38
26 18 0.35
27 6 0.12
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (26 bp):
AAATATTATTTATTATTAAAATTATT
Found at i:11149050 original size:23 final size:24
Alignment explanation
Indices: 11149023--11149160 Score: 111
Period size: 23 Copynumber: 5.3 Consensus size: 24
11149013 TATTATTCTT
11149023 TATATTATTTATTAATATATTATA
1 TATATTATTTATTAATATATTATA
11149047 -ATATTATTTATTAATAATATTTATTA
1 TATATTATTTATTAAT-ATA-TTA-TA
11149073 TTATATTATTTATTAATATACTATATTAA
1 -TATATTATTTATTAATATA-T-TA-T-A
*
11149102 TAGTATACTATTTATTATTATATTATA
1 TA-TAT--TATTTATTAATATATTATA
* *
11149129 -ACATTATTTATTATTAGTTATTA-A
1 TATATTATTTATTAATA--TATTATA
11149153 TATATTAT
1 TATATTAT
11149161 ATCAATAATA
Statistics
Matches: 97, Mismatches: 4, Indels: 25
0.77 0.03 0.20
Matches are distributed among these distances:
23 27 0.28
24 4 0.04
25 16 0.16
26 3 0.03
27 5 0.05
28 22 0.23
29 6 0.06
30 1 0.01
31 13 0.13
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (24 bp):
TATATTATTTATTAATATATTATA
Found at i:11149141 original size:41 final size:41
Alignment explanation
Indices: 11149023--11149198 Score: 145
Period size: 41 Copynumber: 4.3 Consensus size: 41
11149013 TATTATTCTT
* * *
11149023 TATATTATTTATTAATATATTATAATATTATTTATTAATAA
1 TATATTATTTATTATTATATTATAACATTATTTATTAATAG
11149064 TATTTATTATTATATTATT-TATTAATATAC--TA--TATTAATAG
1 TA--TATTATT-TATTATTATATT-ATA-ACATTATTTATTAATAG
* *
11149105 TATACTATTTATTATTATATTATAACATTATTTATTATTAG
1 TATATTATTTATTATTATATTATAACATTATTTATTAATAG
* *
11149146 T-TATTAATATATTA-TATCAATAATAA-ATTATTTATTAATA-
1 TATATT-ATTTATTATTAT--ATTATAACATTATTTATTAATAG
11149186 TAATATTATTTAT
1 T-ATATTATTTAT
11149199 AAATAAAATT
Statistics
Matches: 110, Mismatches: 10, Indels: 30
0.73 0.07 0.20
Matches are distributed among these distances:
37 2 0.02
38 10 0.09
39 12 0.11
40 7 0.06
41 46 0.42
42 10 0.09
43 13 0.12
44 9 0.08
45 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (41 bp):
TATATTATTTATTATTATATTATAACATTATTTATTAATAG
Found at i:11149182 original size:82 final size:80
Alignment explanation
Indices: 11149023--11149203 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 80
11149013 TATTATTCTT
* * * * *
11149023 TATATTATTTATTAATATATTATAATATTATTTATTAATAATATTTATTATTATATTATTTATTA
1 TATATTATTTATTAATATATTATAACATTATTTATTAAT-ATAGTTATTAATATATTATTCAATA
*
11149088 ATATACTATATTAATA
65 ATAAACTATATTAATA
* *
11149104 GTATACTATTTATTATTATATTATAACATTATTTATT-AT-TAGTTATTAATATATTATATCAAT
1 -TATATTATTTATTAATATATTATAACATTATTTATTAATATAGTTATTAATATATTAT-TCAAT
*
11149167 AATAAATTATTTATTAATA
64 AATAAACTA--TATTAATA
*
11149186 TAATATTATTTATAAATA
1 T-ATATTATTTATTAATA
11149204 AAATTATACT
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
79 16 0.19
80 10 0.12
81 3 0.04
82 54 0.65
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (80 bp):
TATATTATTTATTAATATATTATAACATTATTTATTAATATAGTTATTAATATATTATTCAATAA
TAAACTATATTAATA
Found at i:11149210 original size:34 final size:31
Alignment explanation
Indices: 11149044--11149191 Score: 95
Period size: 31 Copynumber: 4.8 Consensus size: 31
11149034 TTAATATATT
* *
11149044 ATAATATTATTTATT-A-ATAATAT-TTATTA
1 ATAA-ATTATTTATTAATATAATATATCAATA
* * * *
11149073 TTATATTATTTATTAATATACTATATTAATA
1 ATAAATTATTTATTAATATAATATATCAATA
* * * * * * *
11149104 GTATACTATTTATTATTATATTATAACATTA
1 ATAAATTATTTATTAATATAATATATCAATA
* * * *
11149135 TTTATTATTAGTTATTAATATATTATATCAATA
1 -ATA-AATTATTTATTAATATAATATATCAATA
11149168 ATAAATTATTTATTAATATAATAT
1 ATAAATTATTTATTAATATAATAT
11149192 TATTTATAAA
Statistics
Matches: 93, Mismatches: 21, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
28 10 0.11
29 3 0.03
30 6 0.06
31 47 0.51
32 4 0.04
33 23 0.25
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (31 bp):
ATAAATTATTTATTAATATAATATATCAATA
Found at i:11149324 original size:18 final size:19
Alignment explanation
Indices: 11149278--11149339 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 19
11149268 AAATACCTAA
*
11149278 AATAATTTTATTTTTTATTGAT
1 AATAAATTTATTTTTTA-T--T
*
11149300 CAATAAA-TTATTTTTTGTT
1 -AATAAATTTATTTTTTATT
11149319 AATAAATTTATTTTTTATT
1 AATAAATTTATTTTTTATT
11149338 AA
1 AA
11149340 AATATCTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
18 6 0.17
19 14 0.40
21 1 0.03
22 9 0.26
23 5 0.14
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (19 bp):
AATAAATTTATTTTTTATT
Found at i:11149557 original size:14 final size:14
Alignment explanation
Indices: 11149512--11149559 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 14
11149502 ATTTTTTTAA
11149512 TTATTTAAAATATCT
1 TTATTTAAAATAT-T
11149527 TTCA-TTAAAA-A-T
1 TT-ATTTAAAATATT
11149539 TTATTTAAAATATT
1 TTATTTAAAATATT
11149553 TTATTTA
1 TTATTTA
11149560 TATATGCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
11 1 0.03
12 9 0.31
13 1 0.03
14 9 0.31
15 8 0.28
16 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (14 bp):
TTATTTAAAATATT
Found at i:11153834 original size:368 final size:367
Alignment explanation
Indices: 11153158--11153891 Score: 1423
Period size: 368 Copynumber: 2.0 Consensus size: 367
11153148 ATTTTCCTCT
11153158 ATATGTTCATAACCATTTGCTGGAACAACAGATTTACATGTATAGCCTTCTTGTAAAGCATTATA
1 ATATGTTCATAACCATTTGCTGGAACAACAGATTTACATGTATAGCCTTCTTGTAAAGCATTATA
11153223 GTTAATAAATAATTAGTCAGTAGTTTCTTCTGGACCTCTATTCAACAGGTTTATTGACCATTTTT
66 GTTAATAAATAATTAGTCAGTAGTTTCTTCTGGACCTCTATTCAACAGGTTTATTGACCATTTTT
*
11153288 AGTTATTTGTTTTATGAGCGTTACCTATTTTATTTGACTTCCAGTTTGTACCAGGTCAAAAATTG
131 AGTTATTTGTTTTATGAGCATTACCTATTTTATTTGACTTCCAGTTTGTACCAGGTCAAAAATTG
11153353 GGAATTCATTTTTGTTATGGATAAATATGTAAAGTGGATGCAACCATGTTTTAGGGACTAGAAAA
196 GGAATTCATTTTTGTTATGGATAAATATGTAAAGTGGATGCAACCATGTTTTAGGGACTAGAAAA
* *
11153418 GTTATGTTCTTGAATGCTTGTTGGTTCCATATCTCTTGCTTTTATGTCTTTTTTCTTCAATATAG
261 GTTATGTTCTTGAATGCTTATTGGTTCCATATATCTTGCTTTTATGTCTTTTTTCTTCAATATAG
11153483 ATTGAACTCAATAGTGATTTTTAAATTAAACTTTATGAAGAC
326 ATTGAACTCAATAGTGATTTTTAAATTAAACTTTATGAAGAC
11153525 ATATGTTCATAACCATTTGCTGGAACAACAGATTTACATGTATAGCCTTCTTGTAAAGCATTATA
1 ATATGTTCATAACCATTTGCTGGAACAACAGATTTACATGTATAGCCTTCTTGTAAAGCATTATA
11153590 GTTAATAAATAATTAGTCAGTAGTTTCTTCTGGACCTCTATTCAACAGGTTTATTGACCATTTTT
66 GTTAATAAATAATTAGTCAGTAGTTTCTTCTGGACCTCTATTCAACAGGTTTATTGACCA-TTTT
11153655 TAGTTATTTGTTTTATGAGCATTACCTATTTTATTTGACTTCCAGTTTGTACCAGGTCAAAAATT
130 TAGTTATTTGTTTTATGAGCATTACCTATTTTATTTGACTTCCAGTTTGTACCAGGTCAAAAATT
11153720 GGGAATTCATTTTTGTTATGGATAAATATGTAAAGTGGATGCAACCATGTTTTAGGGACTAGAAA
195 GGGAATTCATTTTTGTTATGGATAAATATGTAAAGTGGATGCAACCATGTTTTAGGGACTAGAAA
*
11153785 AGTTATGTTCTTGAATGCTTATTGGTTCCATATATCTTGTTTTTATGTCTTTTTTCTTCAATATA
260 AGTTATGTTCTTGAATGCTTATTGGTTCCATATATCTTGCTTTTATGTCTTTTTTCTTCAATATA
11153850 GATTGAACTCAATAGTGATTTTTAAATTAAACTTTATGAAGA
325 GATTGAACTCAATAGTGATTTTTAAATTAAACTTTATGAAGA
11153892 GGATAGCTGG
Statistics
Matches: 362, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
367 125 0.35
368 237 0.65
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (367 bp):
ATATGTTCATAACCATTTGCTGGAACAACAGATTTACATGTATAGCCTTCTTGTAAAGCATTATA
GTTAATAAATAATTAGTCAGTAGTTTCTTCTGGACCTCTATTCAACAGGTTTATTGACCATTTTT
AGTTATTTGTTTTATGAGCATTACCTATTTTATTTGACTTCCAGTTTGTACCAGGTCAAAAATTG
GGAATTCATTTTTGTTATGGATAAATATGTAAAGTGGATGCAACCATGTTTTAGGGACTAGAAAA
GTTATGTTCTTGAATGCTTATTGGTTCCATATATCTTGCTTTTATGTCTTTTTTCTTCAATATAG
ATTGAACTCAATAGTGATTTTTAAATTAAACTTTATGAAGAC
Found at i:11157771 original size:2 final size:2
Alignment explanation
Indices: 11157764--11157794 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11157754 CCTCAAATAC
11157764 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11157795 CATTGCTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11160350 original size:22 final size:22
Alignment explanation
Indices: 11160306--11160353 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
11160296 AAGTCATTTG
*
11160306 TTTTTTTTCTCTCTTTTTCTCT
1 TTTTTTTTCTCTCATTTTCTCT
*
11160328 TTTTTTTTCTATTCATTTT-TCT
1 TTTTTTTTCT-CTCATTTTCTCT
11160350 TTTT
1 TTTT
11160354 GCCATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTTTTTCTCTCATTTTCTCT
Found at i:11160399 original size:18 final size:19
Alignment explanation
Indices: 11160357--11160404 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
11160347 TCTTTTTGCC
11160357 ATTTTTAAATATTTAATAA
1 ATTTTTAAATATTTAATAA
*
11160376 ATTTTTATATATTATAA-AA
1 ATTTTTAAATATT-TAATAA
*
11160395 ATTTTAAAAT
1 ATTTTTAAAT
11160405 GTCAGTCCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 22 0.88
20 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTTTAAATATTTAATAA
Found at i:11161971 original size:2 final size:2
Alignment explanation
Indices: 11161959--11161990 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
11161949 GCGAGCACCC
11161959 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11161991 AAAGTTAGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11167687 original size:43 final size:43
Alignment explanation
Indices: 11167639--11167720 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
11167629 TCTGATGTCA
* * * *
11167639 TTTCTTTCAGTGTCATTGACAGTCTCCTAGTCTTTTATCTCAC
1 TTTCTTTCACTCTCATTCACAGTCTCCTAGTCTGTTATCTCAC
11167682 TTTCTTTCACTCTCATTCACAGTCTCCTAGTCTGTTATC
1 TTTCTTTCACTCTCATTCACAGTCTCCTAGTCTGTTATC
11167721 CTTTTAGCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.16, C:0.28, G:0.10, T:0.46
Consensus pattern (43 bp):
TTTCTTTCACTCTCATTCACAGTCTCCTAGTCTGTTATCTCAC
Found at i:11179861 original size:44 final size:44
Alignment explanation
Indices: 11179798--11179885 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
11179788 TAGATAAACA
*
11179798 GAATGCTTCTTTCTTGTCTTGAGCTAGGAAACAACTGGAAGCTT
1 GAATGCTTCTTTCTTGTCTTGAGATAGGAAACAACTGGAAGCTT
11179842 GAATGCTTCTTTCTTGTCTTGAGATAGGAAACAACTGGAAGCTT
1 GAATGCTTCTTTCTTGTCTTGAGATAGGAAACAACTGGAAGCTT
11179886 TCTCCCTCTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (44 bp):
GAATGCTTCTTTCTTGTCTTGAGATAGGAAACAACTGGAAGCTT
Found at i:11181304 original size:25 final size:25
Alignment explanation
Indices: 11181276--11181325 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
11181266 CACACTAAGA
11181276 AATAATGTGCAATATAAGTTTTCTG
1 AATAATGTGCAATATAAGTTTTCTG
11181301 AATAATGTGCAATATAAGTTTTCTG
1 AATAATGTGCAATATAAGTTTTCTG
11181326 CCCTTGACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (25 bp):
AATAATGTGCAATATAAGTTTTCTG
Found at i:11184685 original size:3 final size:3
Alignment explanation
Indices: 11184677--11184711 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
11184667 CGGTGCTTAC
11184677 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11184712 ATCAGATTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11184949 original size:3 final size:3
Alignment explanation
Indices: 11184943--11184976 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
11184933 TTATTCATTT
11184943 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
11184977 ATTATATCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:11185087 original size:15 final size:14
Alignment explanation
Indices: 11185045--11185091 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
11185035 AATTCGTTTA
11185045 TATTT-ATTAAGATT
1 TATTTAATTAA-ATT
*
11185059 TATTTATTTAAATT
1 TATTTAATTAAATT
*
11185073 TGTTTAATTATAATT
1 TATTTAATTA-AATT
11185088 TATT
1 TATT
11185092 CATTATTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (14 bp):
TATTTAATTAAATT
Found at i:11187614 original size:14 final size:13
Alignment explanation
Indices: 11187579--11187661 Score: 59
Period size: 13 Copynumber: 6.4 Consensus size: 13
11187569 AAAAAGTCAG
**
11187579 TAAAATTAAAATTT
1 TAAAA-TAAAATAA
11187593 TAAAATAAAATAA
1 TAAAATAAAATAA
11187606 TAAATATAAAATTCAA
1 TAAA-ATAAAA-T-AA
*
11187622 -AATATAAAATCAA
1 TAAAATAAAAT-AA
11187635 -AAAAT-AAA-AA
1 TAAAATAAAATAA
11187645 TAAAATAAAATAA
1 TAAAATAAAATAA
11187658 -AAAA
1 TAAAA
11187662 CCTGTAATCA
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
10 2 0.03
11 5 0.08
12 10 0.17
13 20 0.34
14 17 0.29
15 3 0.05
16 2 0.03
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.25
Consensus pattern (13 bp):
TAAAATAAAATAA
Found at i:11187630 original size:33 final size:33
Alignment explanation
Indices: 11187579--11187655 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
11187569 AAAAAGTCAG
* *
11187579 TAAAATTAAAATTTTAAAAT-AAAATAATAAATA
1 TAAAATTAAAATTATAAAATCAAAA-AATAAAAA
11187612 TAAAATTCAAAA-TATAAAATCAAAAAATAAAAA
1 TAAAATT-AAAATTATAAAATCAAAAAATAAAAA
11187645 TAAAA-TAAAAT
1 TAAAATTAAAAT
11187656 AAAAAACCTG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
31 4 0.10
32 1 0.03
33 26 0.67
34 8 0.21
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (33 bp):
TAAAATTAAAATTATAAAATCAAAAAATAAAAA
Found at i:11187631 original size:21 final size:19
Alignment explanation
Indices: 11187594--11187654 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 19
11187584 TTAAAATTTT
11187594 AAAATAAAATA-ATAAATATA
1 AAAATAAAATATA-AAATA-A
*
11187614 AAATTCAAAATATAAAATCAA
1 AAAAT-AAAATATAAAAT-AA
11187635 AAAATAAAA-ATAAAATAA
1 AAAATAAAATATAAAATAA
11187653 AA
1 AA
11187655 TAAAAAACCT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
18 4 0.11
19 7 0.19
20 8 0.22
21 15 0.42
22 2 0.06
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAATAAAATATAAAATAA
Found at i:11187636 original size:13 final size:13
Alignment explanation
Indices: 11187597--11187643 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
11187587 AAATTTTAAA
*
11187597 ATAAAATAATAAAT
1 ATAAAATCA-AAAT
11187611 ATAAAATTCAAAAT
1 ATAAAA-TCAAAAT
*
11187625 ATAAAATCAAAAA
1 ATAAAATCAAAAT
11187638 ATAAAA
1 ATAAAA
11187644 ATAAAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 12 0.40
14 16 0.53
15 2 0.07
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.23
Consensus pattern (13 bp):
ATAAAATCAAAAT
Found at i:11188457 original size:3 final size:3
Alignment explanation
Indices: 11188447--11188539 Score: 108
Period size: 3 Copynumber: 32.7 Consensus size: 3
11188437 AATAATGTAG
* *
11188447 TAA T-A TAA TAA TAA GAA TAA TAA T-A TAA TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
11188493 TAA TAA TAA TAA TAA -CA TACA TAA T-A TAA T-A TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
11188535 TAA TA
1 TAA TA
11188540 TAAACAATGA
Statistics
Matches: 77, Mismatches: 6, Indels: 14
0.79 0.06 0.14
Matches are distributed among these distances:
2 11 0.14
3 63 0.82
4 3 0.04
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:11189023 original size:55 final size:55
Alignment explanation
Indices: 11188964--11189170 Score: 181
Period size: 55 Copynumber: 3.8 Consensus size: 55
11188954 ACCGAAACTG
* * *
11188964 AGCCACAAGTCAAGAAAATGATTTAGATTGAGCCAAGATCGAATGACTAAGATTA
1 AGCCACAAGTCAAAAAAATGATCTAGATTGAGCCAAGATCGAACGACTAAGATTA
* * * *
11189019 AGCCATAAGTCAAAAAAATGATCTAGATTGAACCAAG-TCGAACGGCTGAA-ATTG
1 AGCCACAAGTCAAAAAAATGATCTAGATTGAGCCAAGATCGAACGACT-AAGATTA
* * * **
11189073 AGCCATAAGTCAGAAAAAATGATCT-GAATTGAGTCAAGATC-AAGCGATTGGGATTGA
1 AGCCACAAGTCA-AAAAAATGATCTAG-ATTGAGCCAAGATCGAA-CGACTAAGATT-A
* * * * *
11189130 A-CTACAAGTCTAGAAAATGATCTGGACTGAGCCAAGATCGA
1 AGCCACAAGTCAAAAAAATGATCTAGATTGAGCCAAGATCGA
11189171 GTGACTGTGA
Statistics
Matches: 123, Mismatches: 20, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
54 24 0.20
55 81 0.66
56 17 0.14
57 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (55 bp):
AGCCACAAGTCAAAAAAATGATCTAGATTGAGCCAAGATCGAACGACTAAGATTA
Found at i:11189183 original size:55 final size:54
Alignment explanation
Indices: 11189086--11189221 Score: 148
Period size: 55 Copynumber: 2.5 Consensus size: 54
11189076 CATAAGTCAG
* * *
11189086 AAAAAATGATCTGAATTGAGTCAAGATCAAGCGATTGGGATTGAA-CTACAAGTC
1 AAAAAATGATCTGGACTGAGTCAAGATCAAGCGACTGGGATTGAATC-ACAAGTC
* * * * * * *
11189140 TAGAAAATGATCTGGACTGAGCCAAGATCGAGTGACTGTGATTGAATCGCGAGTC
1 -AAAAAATGATCTGGACTGAGTCAAGATCAAGCGACTGGGATTGAATCACAAGTC
*
11189195 AAAAAATGATCTAGACTGAGTCAAGAT
1 AAAAAATGATCTGGACTGAGTCAAGAT
11189222 AAAAAACGAG
Statistics
Matches: 67, Mismatches: 13, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
54 24 0.36
55 42 0.63
56 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (54 bp):
AAAAAATGATCTGGACTGAGTCAAGATCAAGCGACTGGGATTGAATCACAAGTC
Found at i:11194708 original size:19 final size:19
Alignment explanation
Indices: 11194684--11194777 Score: 84
Period size: 19 Copynumber: 4.7 Consensus size: 19
11194674 TAATAAAGTC
*
11194684 AATAAAATAAAAAACTGAA
1 AATAAAATAAAAAACTAAA
*
11194703 AATAAAATAATAAA-TAAA
1 AATAAAATAAAAAACTAAA
*
11194721 AATTTAAAATATAAAATAAATAAAA
1 AA--T-AAA-ATAAAA-AACT-AAA
11194746 AATAAAAT-AAAAACTAAA
1 AATAAAATAAAAAACTAAA
*
11194764 AATAAAAGAAAAAA
1 AATAAAATAAAAAA
11194778 AAACCTGCAA
Statistics
Matches: 62, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
18 15 0.24
19 21 0.34
20 4 0.06
21 5 0.08
22 8 0.13
23 3 0.05
24 1 0.02
25 5 0.08
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (19 bp):
AATAAAATAAAAAACTAAA
Found at i:11194717 original size:12 final size:11
Alignment explanation
Indices: 11194688--11194780 Score: 64
Period size: 11 Copynumber: 7.9 Consensus size: 11
11194678 AAAGTCAATA
11194688 AAATAAAAAACT
1 AAATAAAAAA-T
11194700 GAAAATAAAATAAT
1 --AAATAAAA-AAT
*
11194714 AAATAAAAATTT
1 AAATAAAAA-AT
*
11194726 AAAATATAAAAT
1 -AAATAAAAAAT
11194738 AAATAAAAAAT
1 AAATAAAAAAT
*
11194749 AAAATAAAAACT
1 -AAATAAAAAAT
*
11194761 AAA-AATAAAAG
1 AAATAA-AAAAT
11194772 AAA-AAAAAA
1 AAATAAAAAA
11194781 CCTGCAATTA
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
10 6 0.09
11 22 0.33
12 20 0.30
13 8 0.12
14 9 0.13
15 2 0.03
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.18
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:11194742 original size:36 final size:34
Alignment explanation
Indices: 11194702--11194780 Score: 99
Period size: 36 Copynumber: 2.3 Consensus size: 34
11194692 AAAAAACTGA
* *
11194702 AAATAAAATAAT-AAATAAAAATTTAAAATATAAAAT
1 AAATAAAA-AATAAAATAAAAA-CTAAAA-ATAAAAG
11194738 AAATAAAAAATAAAATAAAAACTAAAAATAAAAG
1 AAATAAAAAATAAAATAAAAACTAAAAATAAAAG
11194772 AAA-AAAAAA
1 AAATAAAAAA
11194781 CCTGCAATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
33 6 0.15
34 9 0.22
35 8 0.20
36 17 0.43
ACGTcount: A:0.78, C:0.01, G:0.01, T:0.19
Consensus pattern (34 bp):
AAATAAAAAATAAAATAAAAACTAAAAATAAAAG
Found at i:11195616 original size:5 final size:5
Alignment explanation
Indices: 11195606--11195641 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
11195596 ACAAACTATA
*
11195606 ATAAT ATAAT ATAAT ATAAT ATACT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A
11195642 CTAGTAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:11195654 original size:20 final size:20
Alignment explanation
Indices: 11195611--11195656 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
11195601 CTATAATAAT
*
11195611 ATAATATAATATAATATACT
1 ATAATATAATATAATATACA
*
11195631 ATAATATAATACTAGTA-ACA
1 ATAATATAATA-TAATATACA
11195651 ATAATA
1 ATAATA
11195657 ACAAATAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.35
Consensus pattern (20 bp):
ATAATATAATATAATATACA
Found at i:11195689 original size:12 final size:12
Alignment explanation
Indices: 11195674--11195700 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
11195664 ATCATAATAC
11195674 TAATAACAAAAA
1 TAATAACAAAAA
11195686 TAATAACAAAAA
1 TAATAACAAAAA
11195698 TAA
1 TAA
11195701 AATTGATCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (12 bp):
TAATAACAAAAA
Found at i:11195695 original size:34 final size:30
Alignment explanation
Indices: 11195631--11195688 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
11195621 ATAATATACT
*
11195631 ATAATATAATACTAGTAACAATAATAACAA
1 ATAATATAATACTAATAACAATAATAACAA
*
11195661 ATAATCATAATACTAATAACAAAAATAA
1 ATAAT-ATAATACTAATAACAATAATAA
11195689 TAACAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.26
Consensus pattern (30 bp):
ATAATATAATACTAATAACAATAATAACAA
Found at i:11198008 original size:30 final size:30
Alignment explanation
Indices: 11197974--11198030 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
11197964 ACCCAGATAA
11197974 AATTTTAA-TCAACAATCAAAATCCAAATAT
1 AATTTTAAGT-AACAATCAAAATCCAAATAT
*
11198004 AATTTTAAGTGACAATCAAAATCCAAA
1 AATTTTAAGTAACAATCAAAATCCAAA
11198031 ATTAGTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.28
Consensus pattern (30 bp):
AATTTTAAGTAACAATCAAAATCCAAATAT
Found at i:11206511 original size:78 final size:77
Alignment explanation
Indices: 11206403--11206558 Score: 258
Period size: 78 Copynumber: 2.0 Consensus size: 77
11206393 TACTTAATCT
* *
11206403 ACACCCTCTCTGCCTACACTCCCAGGCAATCTGGTGGTTTAGATCAACCATTGGGACATAAGAAA
1 ACACCCTCTCTGCCTACACTCCCAGGCAATCTGGTGGTCTAGATCAACCATTGGGACACAA-AAA
11206468 AAGAGAATAAGCC
65 AAGAGAATAAGCC
* * *
11206481 ACACCCTCTCTGCCTGCCCTCCCGGGCAATCTGGTGGTCTAGATCAACCATTGGGACACAAAAAA
1 ACACCCTCTCTGCCTACACTCCCAGGCAATCTGGTGGTCTAGATCAACCATTGGGACACAAAAAA
11206546 AGAGAATAAGCC
66 AGAGAATAAGCC
11206558 A
1 A
11206559 ATCAATTACT
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
77 17 0.23
78 56 0.77
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.19
Consensus pattern (77 bp):
ACACCCTCTCTGCCTACACTCCCAGGCAATCTGGTGGTCTAGATCAACCATTGGGACACAAAAAA
AGAGAATAAGCC
Found at i:11208642 original size:11 final size:11
Alignment explanation
Indices: 11208626--11208652 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
11208616 TTATTTATAC
11208626 TTATTAAATAA
1 TTATTAAATAA
11208637 TTATTAAATAA
1 TTATTAAATAA
11208648 TTATT
1 TTATT
11208653 TTATATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTATTAAATAA
Found at i:11217099 original size:7 final size:7
Alignment explanation
Indices: 11217084--11217465 Score: 163
Period size: 7 Copynumber: 58.4 Consensus size: 7
11217074 GGGTTTTGAT
*
11217084 TTTAAGG
1 TTTAGGG
11217091 TTTAGGG
1 TTTAGGG
11217098 -TTAGGG
1 TTTAGGG
11217104 TTT--GG
1 TTTAGGG
*
11217109 TTCAGGG
1 TTTAGGG
11217116 TTT-GGG
1 TTTAGGG
* *
11217122 TTTATGT
1 TTTAGGG
11217129 TTTA-GG
1 TTTAGGG
*
11217135 TTTAGAG
1 TTTAGGG
* *
11217142 CTTGGGG
1 TTTAGGG
* *
11217149 TTTATGA
1 TTTAGGG
*
11217156 TTT-GGA
1 TTTAGGG
* *
11217162 TTTAAGA
1 TTTAGGG
*
11217169 TTTAAGG
1 TTTAGGG
*
11217176 TTTGGGG
1 TTTAGGG
*
11217183 TTTA-AG
1 TTTAGGG
**
11217189 TTTAAAG
1 TTTAGGG
*
11217196 TTT-GAG
1 TTTAGGG
11217202 TTTAGGG
1 TTTAGGG
11217209 TTTA-GG
1 TTTAGGG
*
11217215 TTT-TGG
1 TTTAGGG
11217221 TTTAGGG
1 TTTAGGG
11217228 TTTA-GG
1 TTTAGGG
11217234 TTTA-GG
1 TTTAGGG
11217240 TTTA-GG
1 TTTAGGG
11217246 TTTAGGG
1 TTTAGGG
**
11217253 TTTAGAA
1 TTTAGGG
*
11217260 TTT-GGA
1 TTTAGGG
*
11217266 TTTAGAG
1 TTTAGGG
*
11217273 TTTAGCG
1 TTTAGGG
*
11217280 TTTAAGG
1 TTTAGGG
*
11217287 TTTA-AG
1 TTTAGGG
11217293 TTTAGGG
1 TTTAGGG
11217300 TTT-GGG
1 TTTAGGG
11217306 -TTAGGG
1 TTTAGGG
*
11217312 TGTA-GG
1 TTTAGGG
*
11217318 TTT-TGG
1 TTTAGGG
* *
11217324 TTAAAGG
1 TTTAGGG
11217331 TTTA-GG
1 TTTAGGG
*
11217337 TTTTGGG
1 TTTAGGG
11217344 TTTAGGG
1 TTTAGGG
*
11217351 TTT-GAG
1 TTTAGGG
* *
11217357 TTTACGA
1 TTTAGGG
*
11217364 TTT-GAG
1 TTTAGGG
*
11217370 TTTAAGG
1 TTTAGGG
*
11217377 TTTA-AG
1 TTTAGGG
11217383 TTT-GGAG
1 TTTAGG-G
11217390 TTTAGGG
1 TTTAGGG
11217397 TTTAGGG
1 TTTAGGG
11217404 TTTA-GG
1 TTTAGGG
* *
11217410 TTTATGA
1 TTTAGGG
11217417 TTTAGGG
1 TTTAGGG
*
11217424 -TTA-AG
1 TTTAGGG
11217429 TTTAGGG
1 TTTAGGG
*
11217436 TTT-TGG
1 TTTAGGG
*
11217442 TTTAGGA
1 TTTAGGG
* *
11217449 CTTAAGG
1 TTTAGGG
11217456 TTTAGGG
1 TTTAGGG
11217463 TTT
1 TTT
11217466 CATGAAAATG
Statistics
Matches: 283, Mismatches: 65, Indels: 54
0.70 0.16 0.13
Matches are distributed among these distances:
5 7 0.02
6 118 0.42
7 156 0.55
8 2 0.01
ACGTcount: A:0.19, C:0.01, G:0.34, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:11217115 original size:18 final size:18
Alignment explanation
Indices: 11217089--11217124 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11217079 TTGATTTTAA
*
11217089 GGTTTAGGGTTAGGGTTT
1 GGTTCAGGGTTAGGGTTT
*
11217107 GGTTCAGGGTTTGGGTTT
1 GGTTCAGGGTTAGGGTTT
11217125 ATGTTTTAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.08, C:0.03, G:0.44, T:0.44
Consensus pattern (18 bp):
GGTTCAGGGTTAGGGTTT
Found at i:11217179 original size:20 final size:19
Alignment explanation
Indices: 11217156--11217199 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
11217146 GGGTTTATGA
*
11217156 TTTGGATTTAAGATTTAAGG
1 TTTGGATTTAAG-TTTAAAG
*
11217176 TTTGGGGTTTAAGTTTAAAG
1 TTT-GGATTTAAGTTTAAAG
11217196 TTTG
1 TTTG
11217200 AGTTTAGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 1 0.05
20 12 0.57
21 8 0.38
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (19 bp):
TTTGGATTTAAGTTTAAAG
Found at i:11217216 original size:6 final size:6
Alignment explanation
Indices: 11217201--11217461 Score: 134
Period size: 6 Copynumber: 40.2 Consensus size: 6
11217191 TAAAGTTTGA
*
11217201 GTTTAGG GTTTAG GTTTTG GTTTAGG GTTTAG GTTTAG GTTTAG GTTTAGG
1 GTTTA-G GTTTAG GTTTAG GTTTA-G GTTTAG GTTTAG GTTTAG GTTTA-G
* *
11217252 GTTTAG AATTT-G GATTTAG AGTTTAG CGTTTAAG GTTTAA GTTTAGG
1 GTTTAG -GTTTAG G-TTTAG -GTTTAG -GTTT-AG GTTTAG GTTTA-G
* * * * *
11217299 GTTT-G GGTTAGG GTGTAG GTTTTG GTTAAAG GTTTAG GTTTTGG GTTTAGG
1 GTTTAG GTTTA-G GTTTAG GTTTAG GTT-TAG GTTTAG G-TTTAG GTTTA-G
* * *
11217350 GTTT-G AGTTTACG ATTT-G AGTTTAAG GTTTAA GTTTGG AGTTTAGG
1 GTTTAG -GTTTA-G GTTTAG -GTTT-AG GTTTAG GTTTAG -GTTTA-G
* * * *
11217396 GTTTAGG GTTTAG GTTTATG ATTTAG GGTTAA GTTTAGG GTTTTG GTTTAG
1 GTTTA-G GTTTAG GTTTA-G GTTTAG GTTTAG GTTTA-G GTTTAG GTTTAG
*
11217447 GACTTAAG GTTTAG G
1 G--TTTAG GTTTAG G
11217462 GTTTCATGAA
Statistics
Matches: 196, Mismatches: 33, Indels: 51
0.70 0.12 0.18
Matches are distributed among these distances:
5 6 0.03
6 91 0.46
7 88 0.45
8 11 0.06
ACGTcount: A:0.19, C:0.01, G:0.34, T:0.46
Consensus pattern (6 bp):
GTTTAG
Found at i:11217411 original size:13 final size:13
Alignment explanation
Indices: 11217084--11217461 Score: 163
Period size: 13 Copynumber: 29.0 Consensus size: 13
11217074 GGGTTTTGAT
*
11217084 TTTAAGGTTTAGG
1 TTTAGGGTTTAGG
*
11217097 GTTAGGGTTT-GG
1 TTTAGGGTTTAGG
* *
11217109 TTCAGGGTTTGGG
1 TTTAGGGTTTAGG
* *
11217122 TTTATGTTTTAGG
1 TTTAGGGTTTAGG
* **
11217135 TTTAGAGCTTGGGG
1 TTTAG-GGTTTAGG
* *
11217149 TTTATGATTT-GG
1 TTTAGGGTTTAGG
* *
11217161 ATTTAAGATTTAAGG
1 -TTTAGGGTTT-AGG
* *
11217176 TTTGGGGTTTAAG
1 TTTAGGGTTTAGG
**
11217189 TTTAAAGTTT-GAG
1 TTTAGGGTTTAG-G
11217202 TTTAGGGTTTAGG
1 TTTAGGGTTTAGG
*
11217215 TTT-TGGTTTAGGG
1 TTTAGGGTTTA-GG
11217228 TTTA-GGTTTAGG
1 TTTAGGGTTTAGG
11217240 TTTA-GGTTTAGGG
1 TTTAGGGTTTA-GG
**
11217253 TTTAGAATTT-GG
1 TTTAGGGTTTAGG
*
11217265 ATTTAGAGTTTAGCG
1 -TTTAGGGTTTAG-G
* *
11217280 TTTAAGGTTTAAG
1 TTTAGGGTTTAGG
11217293 TTTAGGGTTT-GG
1 TTTAGGGTTTAGG
* *
11217305 GTTAGGGTGTAGG
1 TTTAGGGTTTAGG
* *
11217318 TTT-TGGTTAAAGG
1 TTTAGGGTT-TAGG
* *
11217331 TTTAGGTTTTGGG
1 TTTAGGGTTTAGG
11217344 TTTAGGGTTT-GAG
1 TTTAGGGTTTAG-G
* *
11217357 TTTACGATTT-GAG
1 TTTAGGGTTTAG-G
* *
11217370 TTTAAGGTTTAAG
1 TTTAGGGTTTAGG
11217383 TTT-GGAGTTTAGGG
1 TTTAGG-GTTTA-GG
11217397 TTTAGGGTTTAGG
1 TTTAGGGTTTAGG
* *
11217410 TTTATGATTTAGG
1 TTTAGGGTTTAGG
* *
11217423 GTTA-AGTTTAGGG
1 TTTAGGGTTTA-GG
*
11217436 TTT-TGGTTTAGG
1 TTTAGGGTTTAGG
* *
11217448 ACTTAAGGTTTAGG
1 -TTTAGGGTTTAGG
11217462 GTTTCATGAA
Statistics
Matches: 277, Mismatches: 62, Indels: 51
0.71 0.16 0.13
Matches are distributed among these distances:
12 52 0.19
13 170 0.61
14 50 0.18
15 5 0.02
ACGTcount: A:0.19, C:0.01, G:0.34, T:0.46
Consensus pattern (13 bp):
TTTAGGGTTTAGG
Found at i:11217465 original size:27 final size:25
Alignment explanation
Indices: 11217371--11217461 Score: 76
Period size: 27 Copynumber: 3.5 Consensus size: 25
11217361 CGATTTGAGT
* * *
11217371 TTAAGGTTTAAGTTTGGAGTTTAGGGT
1 TTAAGGTTTAGGTTTTG-GTTTA-GGC
* * *
11217398 TTAGGGTTTAGGTTTATGATTTAGGG
1 TTAAGGTTTAGGTTT-TGGTTTAGGC
11217424 TTAA-GTTTAGGGTTTTGGTTTAGGAC
1 TTAAGGTTTA-GGTTTTGGTTTAGG-C
11217450 TTAAGGTTTAGG
1 TTAAGGTTTAGG
11217462 GTTTCATGAA
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
25 13 0.25
26 16 0.31
27 22 0.42
28 1 0.02
ACGTcount: A:0.21, C:0.01, G:0.33, T:0.45
Consensus pattern (25 bp):
TTAAGGTTTAGGTTTTGGTTTAGGC
Found at i:11231076 original size:26 final size:26
Alignment explanation
Indices: 11231046--11231100 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
11231036 GTTTAATGCA
* *
11231046 ATATGACTTTTATTTGTTTATATTTT
1 ATATGACTTTTACTTGTTTATACTTT
11231072 ATATGACTTTTACTTGTTTATACTTT
1 ATATGACTTTTACTTGTTTATACTTT
11231098 ATA
1 ATA
11231101 CTAGTATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.25, C:0.07, G:0.07, T:0.60
Consensus pattern (26 bp):
ATATGACTTTTACTTGTTTATACTTT
Found at i:11235760 original size:32 final size:32
Alignment explanation
Indices: 11235724--11235806 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 32
11235714 TTTATGCACT
* *
11235724 TTTAATTCCCATATTATTTAGTCCACTTCTAA
1 TTTAATTCCCAAATCATTTAGTCCACTTCTAA
** *
11235756 TTTAATTTTCAAATCATTTAGTCCGCTTCTAA
1 TTTAATTCCCAAATCATTTAGTCCACTTCTAA
**
11235788 TTTAATTTTCAAATCATTT
1 TTTAATTCCCAAATCATTT
11235807 GTTTTTGGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (32 bp):
TTTAATTCCCAAATCATTTAGTCCACTTCTAA
Found at i:11237858 original size:3 final size:3
Alignment explanation
Indices: 11237850--11237894 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
11237840 TAATTCTTTC
11237850 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
11237895 AAGGAAAACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Done.