Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 61 of 322
Found at i:19428914 original size:20 final size:20
Alignment explanation
Indices: 19428891--19428965 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 20
19428881 ATTAAAACAT
19428891 ATTAAATAAACTTAAGACAA
1 ATTAAATAAACTTAAGACAA
* *
19428911 ATTAAATTGCTAAACTAATTAGAACAT
1 ATTAAA----TAAACT--TAAG-ACAA
19428938 ATTAAATAAACTTAAGACAA
1 ATTAAATAAACTTAAGACAA
19428958 ATTAAATA
1 ATTAAATA
19428966 CTTAAACTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
20 17 0.39
21 3 0.07
23 6 0.14
24 6 0.14
26 3 0.07
27 9 0.20
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.29
Consensus pattern (20 bp):
ATTAAATAAACTTAAGACAA
Found at i:19431021 original size:299 final size:299
Alignment explanation
Indices: 19430483--19431080 Score: 1178
Period size: 299 Copynumber: 2.0 Consensus size: 299
19430473 GGCAAACCCA
19430483 AGCAGTTTAGCATATAGATGATTATTGAGGGCATACCTTCATGACAATGCATCCGCAACTATGTT
1 AGCAGTTTAGCATATAGATGATTATTGAGGGCATACCTTCATGACAATGCATCCGCAACTATGTT
19430548 CTACTTACCTTTCTTGTATTTGATCACGTAGGGAAATGACTCAAGGAACTCTACCCATTTAGCAT
66 CTACTTACCTTTCTTGTATTTGATCACGTAGGGAAATGACTCAAGGAACTCTACCCATTTAGCAT
19430613 GGCACTTGTTTAGCTTGTTTTGTCCCTTAAGGTGCTTCAATGCTTCGTGATCCGTATGTATAACA
131 GGCACTTGTTTAGCTTGTTTTGTCCCTTAAGGTGCTTCAATGCTTCGTGATCCGTATGTATAACA
19430678 AATTCCTTAGGCCAAAGATAGTGCTGCTATGTCTCCAACGCCTGAATTATGGCATACATCTCCTT
196 AATTCCTTAGGCCAAAGATAGTGCTGCTATGTCTCCAACGCCTGAATTATGGCATACATCTCCTT
19430743 GTCAAATGTGGGATAATTAAGACCGGCCTCGTTGAGTTT
261 GTCAAATGTGGGATAATTAAGACCGGCCTCGTTGAGTTT
*
19430782 AGCAGTTTAGCATATAGATGATTATTGAGGGCATACCTTCGTGACAATGCATCCGCAACTATGTT
1 AGCAGTTTAGCATATAGATGATTATTGAGGGCATACCTTCATGACAATGCATCCGCAACTATGTT
19430847 CTACTTACCTTTCTTGTATTTGATCACGTAGGGAAATGACTCAAGGAACTCTACCCATTTAGCAT
66 CTACTTACCTTTCTTGTATTTGATCACGTAGGGAAATGACTCAAGGAACTCTACCCATTTAGCAT
19430912 GGCACTTGTTTAGCTTGTTTTGTCCCTTAAGGTGCTTCAATGCTTCGTGATCCGTATGTATAACA
131 GGCACTTGTTTAGCTTGTTTTGTCCCTTAAGGTGCTTCAATGCTTCGTGATCCGTATGTATAACA
19430977 AATTCCTTAGGCCAAAGATAGTGCTGCTATGTCTCCAACGCCTGAATTATGGCATACATCTCCTT
196 AATTCCTTAGGCCAAAGATAGTGCTGCTATGTCTCCAACGCCTGAATTATGGCATACATCTCCTT
*
19431042 GTCAAATGTGGGATAATTAAGAGCGGCCTCGTTGAGTTT
261 GTCAAATGTGGGATAATTAAGACCGGCCTCGTTGAGTTT
19431081 CTCACTGAAA
Statistics
Matches: 297, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
299 297 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (299 bp):
AGCAGTTTAGCATATAGATGATTATTGAGGGCATACCTTCATGACAATGCATCCGCAACTATGTT
CTACTTACCTTTCTTGTATTTGATCACGTAGGGAAATGACTCAAGGAACTCTACCCATTTAGCAT
GGCACTTGTTTAGCTTGTTTTGTCCCTTAAGGTGCTTCAATGCTTCGTGATCCGTATGTATAACA
AATTCCTTAGGCCAAAGATAGTGCTGCTATGTCTCCAACGCCTGAATTATGGCATACATCTCCTT
GTCAAATGTGGGATAATTAAGACCGGCCTCGTTGAGTTT
Found at i:19432374 original size:8 final size:8
Alignment explanation
Indices: 19432363--19432412 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
19432353 ATTTTTCCTC
19432363 TCTTTTTT
1 TCTTTTTT
19432371 TC-TTTTT
1 TCTTTTTT
19432378 TCTTTTTTT
1 TC-TTTTTT
*
19432387 TCTTTCTT
1 TCTTTTTT
*
19432395 TC--TATT
1 TCTTTTTT
19432401 TCTTTTTT
1 TCTTTTTT
19432409 TCTT
1 TCTT
19432413 GTTCTTTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
6 5 0.14
7 7 0.20
8 16 0.46
9 7 0.20
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (8 bp):
TCTTTTTT
Found at i:19432383 original size:6 final size:6
Alignment explanation
Indices: 19432367--19432426 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
19432357 TTCCTCTCTT
* * * *
19432367 TTTTTC TTTTTTC TTTTTT TTCTTTC TTTCTA TTTCTT- TTTTTC TTGTTC
1 TTTTTC -TTTTTC TTTTTC TT-TTTC TTTTTC TTT-TTC TTTTTC TTTTTC
19432417 TTTTTC TTTT
1 TTTTTC TTTT
19432427 GATTTTTCTA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
5 2 0.05
6 29 0.67
7 12 0.28
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:19432405 original size:30 final size:30
Alignment explanation
Indices: 19432369--19432425 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
19432359 CCTCTCTTTT
* *
19432369 TTTC-TTTTTTCTTTTTTTTCTTTCTTTCTA
1 TTTCTTTTTTTCTTGTTCTT-TTTCTTTCTA
19432399 TTTCTTTTTTTCTTGTTCTTTTTCTTT
1 TTTCTTTTTTTCTTGTTCTTTTTCTTT
19432426 TGATTTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (30 bp):
TTTCTTTTTTTCTTGTTCTTTTTCTTTCTA
Found at i:19435135 original size:42 final size:43
Alignment explanation
Indices: 19435073--19435170 Score: 126
Period size: 42 Copynumber: 2.3 Consensus size: 43
19435063 TACTTACGAT
* ** *
19435073 TTACGCGTAAGACCATGTCTGGGTTATTGGCATTG-TATTTGA
1 TTACACGTAAGACCATGTCTGGGACAGTGGCATTGATATTTGA
* * *
19435115 TTTCATGTAAGACCCTGTCTGGGACAGTGGCATTGATATTTGA
1 TTACACGTAAGACCATGTCTGGGACAGTGGCATTGATATTTGA
19435158 TTACACGTAAGAC
1 TTACACGTAAGAC
19435171 TACATCTGGG
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 28 0.61
43 18 0.39
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (43 bp):
TTACACGTAAGACCATGTCTGGGACAGTGGCATTGATATTTGA
Found at i:19435179 original size:43 final size:42
Alignment explanation
Indices: 19435100--19435182 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 42
19435090 TCTGGGTTAT
* * * *
19435100 TGGCATTGTATTTGATTTCATGTAAGACCCTGTCTGGGACAG
1 TGGCATTGTATTTGATTACACGTAAGACACTATCTGGGACAG
19435142 TGGCATTGATATTTGATTACACGTAAGACTAC-ATCTGGGAC
1 TGGCATTG-TATTTGATTACACGTAAGAC-ACTATCTGGGAC
19435183 GCTGGTATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 8 0.23
43 26 0.74
44 1 0.03
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (42 bp):
TGGCATTGTATTTGATTACACGTAAGACACTATCTGGGACAG
Found at i:19448107 original size:20 final size:20
Alignment explanation
Indices: 19448082--19448131 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
19448072 ATGAGCTGAA
**
19448082 ATTGAGCTGGATGTGAACTT
1 ATTGAGCTGGAACTGAACTT
* *
19448102 ATTGAGTTGGAACTGAGCTT
1 ATTGAGCTGGAACTGAACTT
*
19448122 GTTGAGCTGG
1 ATTGAGCTGG
19448132 TTGTAAGCTG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.10, G:0.34, T:0.34
Consensus pattern (20 bp):
ATTGAGCTGGAACTGAACTT
Found at i:19455000 original size:20 final size:20
Alignment explanation
Indices: 19454971--19455028 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
19454961 TGAGCTAAAA
19454971 TTGAGCTGGATGTGAACTTG
1 TTGAGCTGGATGTGAACTTG
* ** *
19454991 TTGAGTTGGAACTGAGCTTG
1 TTGAGCTGGATGTGAACTTG
* *
19455011 CTGAGCTGGTTGTGAACT
1 TTGAGCTGGATGTGAACT
19455029 GGACGAGCTA
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.19, C:0.12, G:0.34, T:0.34
Consensus pattern (20 bp):
TTGAGCTGGATGTGAACTTG
Found at i:19459333 original size:43 final size:43
Alignment explanation
Indices: 19459197--19459368 Score: 172
Period size: 43 Copynumber: 4.0 Consensus size: 43
19459187 ACATAGGATC
* * *
19459197 CGATATGTGTTTTCGTGTACA-ACCACGTCTGGGA-AGCTGGCAT
1 CGATATTTGATTTCGTGTA-AGACCATGTCTGGGACAG-TGGCAT
* * * *
19459240 CGAGT-TATGATTTACATGTAAGACCATTTCTGGGACATTGGCAT
1 CGA-TATTTGATTT-CGTGTAAGACCATGTCTGGGACAGTGGCAT
* *
19459284 CG-TATTTGATTTCGTGTAAGACCCTGTCTGGGATAGTGGCAT
1 CGATATTTGATTTCGTGTAAGACCATGTCTGGGACAGTGGCAT
* * *
19459326 CGATATTTGATTACGTGTATGACCATGTCTGGGACATTGGCAT
1 CGATATTTGATTTCGTGTAAGACCATGTCTGGGACAGTGGCAT
19459369 TGTACGAGCT
Statistics
Matches: 106, Mismatches: 17, Indels: 12
0.79 0.13 0.09
Matches are distributed among these distances:
42 28 0.26
43 52 0.49
44 25 0.24
45 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (43 bp):
CGATATTTGATTTCGTGTAAGACCATGTCTGGGACAGTGGCAT
Found at i:19459383 original size:86 final size:86
Alignment explanation
Indices: 19459205--19459383 Score: 197
Period size: 86 Copynumber: 2.1 Consensus size: 86
19459195 TCCGATATGT
*
19459205 GTTTTCGTGTACAACCACGTCTGGGAAGCTGGCATCGAGTTATGATTTACATGTAAGACCATTTC
1 GTTTTCGTGTACAACCACGTCTGGGAAGCTGGCATCGAGTTATGATTTACATGTAAGACCATGTC
***
19459270 TGGGACATTGGCATCGTATTT
66 TGGGACATTGGCATCGTACGA
* * * *
19459291 GATTTCGTGTA-AGACC-CTGTCTGGGATAG-TGGCATCGA-TATTTGA-TTACGTGTATGACCA
1 GTTTTCGTGTACA-ACCAC-GTCTGGGA-AGCTGGCATCGAGT-TATGATTTACATGTAAGACCA
*
19459351 TGTCTGGGACATTGGCATTGTACGA
62 TGTCTGGGACATTGGCATCGTACGA
19459376 GCTTTTCG
1 G-TTTTCG
19459384 AGCTATCCAC
Statistics
Matches: 78, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
85 37 0.47
86 39 0.50
87 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (86 bp):
GTTTTCGTGTACAACCACGTCTGGGAAGCTGGCATCGAGTTATGATTTACATGTAAGACCATGTC
TGGGACATTGGCATCGTACGA
Found at i:19460127 original size:23 final size:23
Alignment explanation
Indices: 19460097--19460140 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
19460087 TTATGTAACA
19460097 TATGTTTTGGTATGACTTTGACT
1 TATGTTTTGGTATGACTTTGACT
* *
19460120 TATGTTTTGTTATGATTTTGA
1 TATGTTTTGGTATGACTTTGA
19460141 TATGATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.05, G:0.20, T:0.57
Consensus pattern (23 bp):
TATGTTTTGGTATGACTTTGACT
Found at i:19462735 original size:19 final size:19
Alignment explanation
Indices: 19462698--19462740 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
19462688 CTAAAAACAC
19462698 AATT-AATTCAGCTAGGAA
1 AATTAAATTCAGCTAGGAA
19462716 AACTTAAATTCAGCTA-GAA
1 AA-TTAAATTCAGCTAGGAA
19462735 AATTAA
1 AATTAA
19462741 CTCAACCAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.26
19 7 0.30
20 10 0.43
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.28
Consensus pattern (19 bp):
AATTAAATTCAGCTAGGAA
Found at i:19462781 original size:25 final size:25
Alignment explanation
Indices: 19462747--19462795 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
19462737 TTAACTCAAC
*
19462747 CAGCTAATTAAGTTGTAATGAGCTT
1 CAGCTAATTAAGTTGTAATAAGCTT
19462772 CAGCTAATTAAGTTGTAATAAGCT
1 CAGCTAATTAAGTTGTAATAAGCT
19462796 AAGACAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (25 bp):
CAGCTAATTAAGTTGTAATAAGCTT
Found at i:19462805 original size:25 final size:25
Alignment explanation
Indices: 19462752--19462807 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
19462742 TCAACCAGCT
* * *
19462752 AATTAAGTTGTAATGAGCTTCAGCT
1 AATTAAGTTGTAATAAGCTTAAGCA
19462777 AATTAAGTTGTAATAAGC-TAAGACA
1 AATTAAGTTGTAATAAGCTTAAG-CA
19462802 AATTAA
1 AATTAA
19462808 ATAGCTGTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 3 0.11
25 24 0.89
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (25 bp):
AATTAAGTTGTAATAAGCTTAAGCA
Found at i:19462855 original size:47 final size:47
Alignment explanation
Indices: 19462798--19462961 Score: 145
Period size: 47 Copynumber: 3.5 Consensus size: 47
19462788 AATAAGCTAA
* * *
19462798 GACAAATTAAATAGCTGTACTAGCTAAAACATATTAAATTAACTTAG
1 GACAAATTAAATAGCTGAACTAACTAAAACATATTAAATGAACTTAG
* * * *
19462845 GACATATTAAATAGCTGAACTAATTAGAACATATTAGATGAACTTTA-
1 GACAAATTAAATAGCTGAACTAACTAAAACATATTAAATGAAC-TTAG
* ** * * * * *
19462892 GATAAATTAAATTTCTGAACCAATTAGAACATATTAAAT-AAATTGAA
1 GACAAATTAAATAGCTGAACTAACTAAAACATATTAAATGAACTT-AG
19462939 GACAAATTAAATA-CTTGAACTAA
1 GACAAATTAAATAGC-TGAACTAA
19462962 AATAACTAAA
Statistics
Matches: 96, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
45 2 0.02
46 4 0.04
47 87 0.91
48 3 0.03
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.30
Consensus pattern (47 bp):
GACAAATTAAATAGCTGAACTAACTAAAACATATTAAATGAACTTAG
Found at i:19462876 original size:27 final size:27
Alignment explanation
Indices: 19462841--19462931 Score: 72
Period size: 27 Copynumber: 3.6 Consensus size: 27
19462831 TTAAATTAAC
*
19462841 TTAGGACATATTAAATAGCTGAACTAA
1 TTAGAACATATTAAATAGCTGAACTAA
*
19462868 TTAGAACATA-T---TAGATGAACT--
1 TTAGAACATATTAAATAGCTGAACTAA
** *
19462889 TTAGATA-A-ATTAAATTTCTGAACCAA
1 TTAGA-ACATATTAAATAGCTGAACTAA
19462915 TTAGAACATATTAAATA
1 TTAGAACATATTAAATA
19462932 AATTGAAGAC
Statistics
Matches: 48, Mismatches: 7, Indels: 18
0.66 0.10 0.25
Matches are distributed among these distances:
20 1 0.02
21 7 0.15
22 1 0.02
23 9 0.19
24 6 0.12
25 1 0.02
26 7 0.15
27 16 0.33
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (27 bp):
TTAGAACATATTAAATAGCTGAACTAA
Found at i:19463515 original size:24 final size:24
Alignment explanation
Indices: 19463483--19463531 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
19463473 GGCTAAATTG
19463483 CCTAAACACATGCATCCAATCAAA
1 CCTAAACACATGCATCCAATCAAA
19463507 CCTAAACACATGCATCCAATCAAA
1 CCTAAACACATGCATCCAATCAAA
19463531 C
1 C
19463532 ATGTTAGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.35, G:0.04, T:0.16
Consensus pattern (24 bp):
CCTAAACACATGCATCCAATCAAA
Found at i:19466350 original size:40 final size:40
Alignment explanation
Indices: 19466306--19466528 Score: 385
Period size: 40 Copynumber: 5.6 Consensus size: 40
19466296 TACTTACTCG
* *
19466306 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACC
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
19466346 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
19466386 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
19466426 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
* * *
19466466 AATGCCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCA
1 AATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACA
19466506 AATGCCTTCGGGACTTAGCCCGG
1 AATGCCTTCGGGACTTAGCCCGG
19466529 TTATCATCCA
Statistics
Matches: 177, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
39 1 0.01
40 176 0.99
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.22
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
Found at i:19471541 original size:46 final size:46
Alignment explanation
Indices: 19471491--19471666 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
19471481 TGGTTGAGCA
19471491 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
19471537 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
19471582 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
19471630 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
19471667 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 64 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:19471647 original size:93 final size:93
Alignment explanation
Indices: 19471488--19471658 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
19471478 GGATGGTTGA
* *
19471488 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
19471553 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
19471581 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
19471646 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
19471659 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:19474888 original size:30 final size:30
Alignment explanation
Indices: 19474854--19474910 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
19474844 TCTGAATCTT
*
19474854 GGGGT-AAAAGTGCAAATATACAAAAATTTA
1 GGGGTCAAAA-TGAAAATATACAAAAATTTA
* *
19474884 GGGGTCAAAATGAAAATTTATAAAAAT
1 GGGGTCAAAATGAAAATATACAAAAAT
19474911 ATGATTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.25
Consensus pattern (30 bp):
GGGGTCAAAATGAAAATATACAAAAATTTA
Found at i:19475337 original size:49 final size:49
Alignment explanation
Indices: 19475265--19475438 Score: 240
Period size: 49 Copynumber: 3.5 Consensus size: 49
19475255 TGAGGTCACG
*
19475265 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGTA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
* * *** *
19475314 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGACGGTTAGGTCACA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT-GGTCGCA
* * *
19475364 TGCGTAGTACTAAGTGCAAGCTACTACGTGGACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
*
19475413 TTTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
19475439 TGCGTACTAG
Statistics
Matches: 105, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
49 66 0.63
50 39 0.37
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
Found at i:19475428 original size:99 final size:99
Alignment explanation
Indices: 19475257--19475438 Score: 310
Period size: 99 Copynumber: 1.8 Consensus size: 99
19475247 ATCTATTGTG
* * * * *
19475257 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGTATGTGTAGT
1 AGGTCACATGCGTAGTACTAAGTGCAAGCTACTACGTGGACCGGATAATTGGTCGCATGTGTAGT
19475322 ACTAAGTGCAGGCTACTACGTGTATCAGACGGTT
66 ACTAAGTGCAGGCTACTACGTGTATCAGACGGTT
*
19475356 AGGTCACATGCGTAGTACTAAGTGCAAGCTACTACGTGGACCGGATAATTGGTCGCATTTGTAGT
1 AGGTCACATGCGTAGTACTAAGTGCAAGCTACTACGTGGACCGGATAATTGGTCGCATGTGTAGT
19475421 ACTAAGTGCAGGCTACTA
66 ACTAAGTGCAGGCTACTA
19475439 TGCGTACTAG
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 77 1.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (99 bp):
AGGTCACATGCGTAGTACTAAGTGCAAGCTACTACGTGGACCGGATAATTGGTCGCATGTGTAGT
ACTAAGTGCAGGCTACTACGTGTATCAGACGGTT
Found at i:19486459 original size:28 final size:28
Alignment explanation
Indices: 19486361--19486459 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
19486351 CATGAGATTT
* * **
19486361 GCACTAAGTGTGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
19486390 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
19486418 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
19486446 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
19486460 GACTTACTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 46 0.73
29 17 0.27
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:19491390 original size:37 final size:37
Alignment explanation
Indices: 19491290--19491392 Score: 161
Period size: 37 Copynumber: 2.8 Consensus size: 37
19491280 CGAATAGTCC
* *
19491290 CCACACGTAGTTATCGGGTCTTACCCAGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
* * *
19491327 CCACACATAGTCATCAGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
19491364 CCACACGTAGTCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
19491393 ATATATTTCC
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.23
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:19491581 original size:48 final size:48
Alignment explanation
Indices: 19491525--19492174 Score: 971
Period size: 48 Copynumber: 13.2 Consensus size: 48
19491515 CAGCCACAAT
19491525 ATTAGCCATTCGGCTTTACCACATGTACATATCTCATACATATTTCAC
1 ATTAGCCATTCGGCTTTACCACATGTACATATCTCATACATATTTCAC
19491573 ATTAGCCATTCGGCTTTACCACATGTACATATCTCATACATATTTCAC
1 ATTAGCCATTCGGCTTTACCACATGTACATATCTCATACATATTTCAC
19491621 ATTAGCCATTCGGCTTTACCACATGTACATATCTCATACATATTTCAC
1 ATTAGCCATTCGGCTTTACCACATGTACATATCTCATACATATTTCAC
19491669 ATTAGCCATTCGGCTTTACCACATGTACATATCTCATACATATTTCAC
1 ATTAGCCATTCGGCTTTACCACATGTACATATCTCATACATATTTCAC
* *
19491717 ATTAGCCATTCGGCTTTACCACATATACCTATCTCATACATATTTCAC
1 ATTAGCCATTCGGCTTTACCACATGTACATATCTCATACATATTTCAC
*
19491765 ATTAGCCATTTGGCTTTACCACATGTACATATCTCATACATATTTCAC
1 ATTAGCCATTCGGCTTTACCACATGTACATATCTCATACATATTTCAC
19491813 ATTAGCCATTCGGCTTTACCACATGTACATATCTCATACATATTTCAC
1 ATTAGCCATTCGGCTTTACCACATGTACATATCTCATACATATTTCAC
19491861 ATTAGCCATTCGGCTTTACCACAT-TACCACATATGCCTATCTCATACATATTTCAC
1 ATTAGCCATTCGGCTTTACCACATGT---AC--A----TATCTCATACATATTTCAC
* ** *
19491917 ATTAGCCATTCGCCTTTACCACATAAACATATCTCATACGTATTTCAC
1 ATTAGCCATTCGGCTTTACCACATGTACATATCTCATACATATTTCAC
* *
19491965 ATTAGCCATTCGACTTTACCACATATACATATCTCATACATATTTCAC
1 ATTAGCCATTCGGCTTTACCACATGTACATATCTCATACATATTTCAC
* * * * *
19492013 ATTAGCTATTTGGCTTTACCACATATGCCTATCTCATACATATTTCAC
1 ATTAGCCATTCGGCTTTACCACATGTACATATCTCATACATATTTCAC
19492061 ATTAGCCATTCGGCTTTACCACAT-TACCACATATGCCTATCTCATACATATTTCAC
1 ATTAGCCATTCGGCTTTACCACATGT---AC--A----TATCTCATACATATTTCAC
* * *
19492117 ATTAGCCATTCGGCTTTACCACATATACATATCTTATACGTATTTCAC
1 ATTAGCCATTCGGCTTTACCACATGTACATATCTCATACATATTTCAC
19492165 ATTAGCCATT
1 ATTAGCCATT
19492175 TCTTCCCACT
Statistics
Matches: 559, Mismatches: 23, Indels: 40
0.90 0.04 0.06
Matches are distributed among these distances:
47 2 0.00
48 461 0.82
50 3 0.01
52 3 0.01
54 4 0.01
56 85 0.15
57 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.08, T:0.36
Consensus pattern (48 bp):
ATTAGCCATTCGGCTTTACCACATGTACATATCTCATACATATTTCAC
Found at i:19491902 original size:56 final size:56
Alignment explanation
Indices: 19491828--19492140 Score: 368
Period size: 56 Copynumber: 6.0 Consensus size: 56
19491818 CCATTCGGCT
* *
19491828 TTACCACATGTACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACA
1 TTACCACATATGCATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACA
* *
19491884 TTACCACATATGCCTATCTCATACATATTTCACATTAGCCATTCGCCTTTACCACA
1 TTACCACATATGCATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACA
* *
19491940 -T---A-A-A--CATATCTCATACGTATTTCACATTAGCCATTCGACTTTACCACA
1 TTACCACATATGCATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACA
* *
19491988 -T-----ATA--CATATCTCATACATATTTCACATTAGCTATTTGGC--T------
1 TTACCACATATGCATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACA
*
19492028 TTACCACATATGCCTATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACA
1 TTACCACATATGCATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACA
*
19492084 TTACCACATATGCCTATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACA
1 TTACCACATATGCATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACA
19492140 T
1 T
19492141 ATACATATCT
Statistics
Matches: 226, Mismatches: 14, Indels: 34
0.82 0.05 0.12
Matches are distributed among these distances:
41 1 0.00
46 4 0.02
47 1 0.00
48 106 0.47
50 2 0.01
51 1 0.00
52 1 0.00
55 1 0.00
56 109 0.48
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (56 bp):
TTACCACATATGCATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACA
Found at i:19492061 original size:26 final size:26
Alignment explanation
Indices: 19492032--19492118 Score: 70
Period size: 26 Copynumber: 3.2 Consensus size: 26
19492022 TTGGCTTTAC
19492032 CACATATGCCTATCTCATACATATTT
1 CACATATGCCTATCTCATACATATTT
* * * *
19492058 CACAT-TAGCC-ATTCGGCTTTACCACATTAC
1 CACATAT-GCCTA-TC-TC-ATA-CATATT-T
19492088 CACATATGCCTATCTCATACATATTT
1 CACATATGCCTATCTCATACATATTT
19492114 CACAT
1 CACAT
19492119 TAGCCATTCG
Statistics
Matches: 45, Mismatches: 8, Indels: 16
0.65 0.12 0.23
Matches are distributed among these distances:
25 2 0.04
26 15 0.33
27 6 0.13
28 4 0.09
29 6 0.13
30 10 0.22
31 2 0.04
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.34
Consensus pattern (26 bp):
CACATATGCCTATCTCATACATATTT
Found at i:19493740 original size:40 final size:40
Alignment explanation
Indices: 19493685--19493850 Score: 296
Period size: 40 Copynumber: 4.2 Consensus size: 40
19493675 NNNNNNNNNN
19493685 TAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGACT
1 TAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGACT
19493725 TAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGACT
1 TAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGACT
*
19493765 TAGCCCGGACATAACACCAGCACGAATGCTCTTCGGGACT
1 TAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGACT
* * *
19493805 TAGCCCGGATATAGCATCAGCACAAATGCTCTTCGGGACT
1 TAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGACT
19493845 TAGCCC
1 TAGCCC
19493851 AGCTATATAA
Statistics
Matches: 121, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 121 1.00
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.20
Consensus pattern (40 bp):
TAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGACT
Found at i:19496050 original size:56 final size:56
Alignment explanation
Indices: 19495988--19496137 Score: 171
Period size: 56 Copynumber: 2.7 Consensus size: 56
19495978 GAGATTGGTG
* *
19495988 CTAAGTGTGTGGGTTTAAAT-TGTGCAGCACTAAGTGTGCGAAT-TGAATATGTAGCA
1 CTAAGTGTGCGAGTTTAAATATGT--AGCACTAAGTGTGCGAATATGAATATGTAGCA
* * * *
19496044 CTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTATGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATATGTAGCACTAAGTGTGCGAATATGAATATGTAGCA
* * * *
19496100 CTAAGTGTGCGAG-TTGATTATATAGCACTGAGTGTGCG
1 CTAAGTGTGCGAGTTTAAATATGTAGCACTAAGTGTGCG
19496138 GACTTAATAT
Statistics
Matches: 83, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
55 39 0.47
56 41 0.49
57 3 0.04
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.32
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTAAATATGTAGCACTAAGTGTGCGAATATGAATATGTAGCA
Found at i:19496070 original size:28 final size:28
Alignment explanation
Indices: 19496013--19496137 Score: 182
Period size: 28 Copynumber: 4.5 Consensus size: 28
19496003 TAAATTGTGC
* *
19496013 AGCACTAAGTGTGCGA-ATTGAATATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
19496040 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
19496068 AGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
19496096 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
19496123 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
19496138 GACTTAATAT
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 38 0.42
28 52 0.58
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:19496076 original size:55 final size:55
Alignment explanation
Indices: 19496013--19496137 Score: 189
Period size: 55 Copynumber: 2.3 Consensus size: 55
19496003 TAAATTGTGC
*
19496013 AGCACTAAGTGTGCGAAT-TGAATATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAATATGAATATGTAGCACTAAGTGTGCGAG-TTGACTATAT
* * *
19496068 AGCACTAAGTGTGCGAGTATGATTATGTAGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATATGAATATGTAGCACTAAGTGTGCGAGTTGACTATAT
*
19496123 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
19496138 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
55 39 0.61
56 25 0.39
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAATATGAATATGTAGCACTAAGTGTGCGAGTTGACTATAT
Found at i:19496970 original size:43 final size:43
Alignment explanation
Indices: 19496922--19497011 Score: 180
Period size: 43 Copynumber: 2.1 Consensus size: 43
19496912 TAGGGGGAAG
19496922 TTTGACAATGATTAGCCTTTGGCATGGTTAGTCATGATCATAA
1 TTTGACAATGATTAGCCTTTGGCATGGTTAGTCATGATCATAA
19496965 TTTGACAATGATTAGCCTTTGGCATGGTTAGTCATGATCATAA
1 TTTGACAATGATTAGCCTTTGGCATGGTTAGTCATGATCATAA
19497008 TTTG
1 TTTG
19497012 TGATATGCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (43 bp):
TTTGACAATGATTAGCCTTTGGCATGGTTAGTCATGATCATAA
Found at i:19498632 original size:6 final size:6
Alignment explanation
Indices: 19498621--19498647 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
19498611 AGCCGGAGAT
19498621 AGAGCC AGAGCC AGAGCC AGAGCC AGA
1 AGAGCC AGAGCC AGAGCC AGAGCC AGA
19498648 ACTACACTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.30, G:0.33, T:0.00
Consensus pattern (6 bp):
AGAGCC
Found at i:19498632 original size:18 final size:18
Alignment explanation
Indices: 19498609--19498647 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
19498599 CACCAAAGCT
* *
19498609 AGAGCCGGAGATAGAGCC
1 AGAGCCAGAGACAGAGCC
*
19498627 AGAGCCAGAGCCAGAGCC
1 AGAGCCAGAGACAGAGCC
19498645 AGA
1 AGA
19498648 ACTACACTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.26, G:0.36, T:0.03
Consensus pattern (18 bp):
AGAGCCAGAGACAGAGCC
Found at i:19504145 original size:28 final size:28
Alignment explanation
Indices: 19504088--19504240 Score: 229
Period size: 28 Copynumber: 5.5 Consensus size: 28
19504078 TAAATTGTGC
* *
19504088 AGCACTAAGTGTGCGA-ATTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
19504115 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
19504143 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
19504171 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
* * *
19504199 AGCACTAGGTGTGCGAG-CTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
19504226 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
19504241 GACTTAATAT
Statistics
Matches: 116, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 37 0.32
28 79 0.68
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:19504231 original size:83 final size:83
Alignment explanation
Indices: 19504088--19504240 Score: 236
Period size: 83 Copynumber: 1.8 Consensus size: 83
19504078 TAAATTGTGC
* *
19504088 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTCTGATTATATAGCACTAAGT
19504153 GTGCGAGTTTGACTATGT
66 GTGCGAGTTTGACTATGT
* * * *
19504171 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAGGTGTGCGAG-CTGATTATATAGCACTGAG
1 AGCACTAAGTGTGCGA-ATTGACTATGTAGCACTAAGTGTGCGAGTCTGATTATATAGCACTAAG
19504235 TGTGCG
65 TGTGCG
19504241 GACTTAATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
83 38 0.60
84 25 0.40
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.31
Consensus pattern (83 bp):
AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTCTGATTATATAGCACTAAGT
GTGCGAGTTTGACTATGT
Found at i:19505227 original size:39 final size:39
Alignment explanation
Indices: 19505184--19505263 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
19505174 AAATCACTAA
*
19505184 AAATAATAGGAGTGGAATTTATTGATGAATAAATTATGT
1 AAATAATAGGAGTGGAATTAATTGATGAATAAATTATGT
*
19505223 AAATAGTAGGAGTGGAATTAATTGATGAATAAATTATGT
1 AAATAATAGGAGTGGAATTAATTGATGAATAAATTATGT
19505262 AA
1 AA
19505264 TCGAAGTTCG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (39 bp):
AAATAATAGGAGTGGAATTAATTGATGAATAAATTATGT
Found at i:19506405 original size:16 final size:16
Alignment explanation
Indices: 19506384--19506416 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
19506374 ATGCACACCC
19506384 GATGAATGTCTAAAGT
1 GATGAATGTCTAAAGT
19506400 GATGAATGTCTAAAGT
1 GATGAATGTCTAAAGT
19506416 G
1 G
19506417 TGCTGTATCT
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:0.06, G:0.27, T:0.30
Consensus pattern (16 bp):
GATGAATGTCTAAAGT
Found at i:19511676 original size:28 final size:28
Alignment explanation
Indices: 19511594--19511771 Score: 234
Period size: 28 Copynumber: 6.4 Consensus size: 28
19511584 GAGATTGGCG
* * * *
19511594 CTAAGTGTGCGGGTTTAAATTGTGCAGCA
1 CTAAGTGTGCGAGTTT-GATTATGTAGCA
* *
19511623 CTAAGTGTGCGA-ATTGACTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
*
19511650 CTAAGTGTGCGAGTTTGACTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
*
19511678 CTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
*
19511706 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
*
19511734 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
*
19511761 CTGAGTGTGCG
1 CTAAGTGTGCG
19511772 GACTTATTAT
Statistics
Matches: 136, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
27 44 0.32
28 81 0.60
29 11 0.08
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATGTAGCA
Found at i:19515933 original size:40 final size:40
Alignment explanation
Indices: 19515874--19516018 Score: 175
Period size: 40 Copynumber: 3.6 Consensus size: 40
19515864 CTCGTACAAG
* * * * * *
19515874 GCCTTCAGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
19515914 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* ** *
19515954 GCCTTC-GGATCTTAGTCCGGATGCAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
19515995 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
19516019 CATTCGAGTA
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
39 3 0.03
40 57 0.64
41 26 0.29
42 3 0.03
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:19516416 original size:45 final size:38
Alignment explanation
Indices: 19516371--19516446 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
19516361 CAAGAACTCC
*
19516371 TTCCTCCCTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
19516409 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
19516447 AAAGGATGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Found at i:19517334 original size:45 final size:45
Alignment explanation
Indices: 19517261--19517522 Score: 370
Period size: 45 Copynumber: 5.9 Consensus size: 45
19517251 CGCACAGTAT
*
19517261 TATTCGGGCCTTTGAGCCTAGCAGGCTGTAATGCCGGTGAGATAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
** * *
19517306 TATTTAGGCCTTTGAGCCTAGCAAGCTGTAATGCCGGTGAGATAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
* * *
19517351 TATTCGGGTCTTTGGGCCTAGCAGGCTATAATGCCGGTGAGAAAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
*
19517396 TATTCGGGCCTTTGAGCCTAGTAGGCTATAATGCCGGTGAGATAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
* *
19517441 TATTCGGGCTTTTGAGCCTAGCAGGCTATAATGCCGGTGAAATGA-
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT-AC
* *
19517486 TA-TCGGG-CTTCGAGCCTAGCAGGCGA-AATGCCGGTGA
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
19517523 ATGAATTTAG
Statistics
Matches: 196, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
42 11 0.06
43 16 0.08
44 5 0.03
45 163 0.83
46 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.27
Consensus pattern (45 bp):
TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
Found at i:19522963 original size:34 final size:34
Alignment explanation
Indices: 19522920--19522998 Score: 122
Period size: 34 Copynumber: 2.3 Consensus size: 34
19522910 AGGACCTCGT
19522920 TACTGATACTGTGATGGGCTAAGGCCCTAATGCA
1 TACTGATACTGTGATGGGCTAAGGCCCTAATGCA
* *
19522954 TACTGATACTGTGATGGGCTAAGGCCTTACTGCA
1 TACTGATACTGTGATGGGCTAAGGCCCTAATGCA
*
19522988 TATTTGATACT
1 TA-CTGATACT
19522999 ATACTGAGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 34 0.83
35 7 0.17
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (34 bp):
TACTGATACTGTGATGGGCTAAGGCCCTAATGCA
Found at i:19526356 original size:40 final size:40
Alignment explanation
Indices: 19526300--19526465 Score: 223
Period size: 40 Copynumber: 4.2 Consensus size: 40
19526290 ATTGATACCA
* * *
19526300 GGGCTAAGTCCTGAAGGCATTTGTGCTAGTGACTA-AATTC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAA-CC
19526340 GGGCTAAGTCCCGAAGGCATTTGTG-TGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCT-AGTTACTATAACC
*
19526380 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAACC
* *
19526420 GGGCTAAGTCCCGAAGGCATTTGAGCTAG-TAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTTA-CTATAACC
19526460 -GGCTAA
1 GGGCTAA
19526466 ACTCCGAAGG
Statistics
Matches: 115, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
39 9 0.08
40 104 0.90
41 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAACC
Found at i:19527776 original size:6 final size:7
Alignment explanation
Indices: 19527759--19527788 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
19527749 TGGACTGTAA
19527759 AAAAAAT
1 AAAAAAT
19527766 AAAAAAT
1 AAAAAAT
19527773 AAAAAAT
1 AAAAAAT
19527780 AAAAAAT
1 AAAAAAT
19527787 AA
1 AA
19527789 GGGAATTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:19535192 original size:50 final size:50
Alignment explanation
Indices: 19535057--19535272 Score: 222
Period size: 50 Copynumber: 4.3 Consensus size: 50
19535047 GCTAAATGAC
* * * * * *
19535057 CTTGTATATTCGGCCACATAGGTATGTACATATGTGATGTTGTATTGGAT
1 CTTGTATATTCGGCCATATAAGTAAGTACATATGTGATATTATATTTGAT
* * * * * *
19535107 TTTGAATATTCGG-C-TATGAAGGTATGGAAAAATGTGATATTATATTTGAAT
1 CTTGTATATTCGGCCATAT-AA-GTAAGTACATATGTGATATTATATTTG-AT
* *
19535158 -TTGTATATTCGGCCATATAAGTAAGTACATATGTGATGTTAAATTTGAT
1 CTTGTATATTCGGCCATATAAGTAAGTACATATGTGATATTATATTTGAT
* * *
19535207 CTTGCATATTCGACCATATAGGTAAGTACATATGTGATATTATATTTGAT
1 CTTGTATATTCGGCCATATAAGTAAGTACATATGTGATATTATATTTGAT
*
19535257 CTTGTATATTTGGCCA
1 CTTGTATATTCGGCCA
19535273 AATGAGTTGT
Statistics
Matches: 135, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
48 2 0.01
49 4 0.03
50 121 0.90
51 5 0.04
52 3 0.02
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (50 bp):
CTTGTATATTCGGCCATATAAGTAAGTACATATGTGATATTATATTTGAT
Found at i:19535195 original size:100 final size:100
Alignment explanation
Indices: 19535057--19535272 Score: 265
Period size: 100 Copynumber: 2.2 Consensus size: 100
19535047 GCTAAATGAC
* * ** * * *
19535057 CTTGTATATTCGGCCACATAGGTATGTACATATGTGATGTTGTATTGGATTTTGAATATTCGGCT
1 CTTGTATATTCGGCCACATAAGTAAGTACATATGTGATGTTAAATTGGATCTTGAATATTCGACC
*
19535122 ATGA-AGGTATGGAAAAATGTGATATTATATTTGAAT
66 AT-ATAGGTAAGGAAAAATGTGATATTATATTTG-AT
* * *
19535158 -TTGTATATTCGGCCATATAAGTAAGTACATATGTGATGTTAAATTTGATCTTGCATATTCGACC
1 CTTGTATATTCGGCCACATAAGTAAGTACATATGTGATGTTAAATTGGATCTTGAATATTCGACC
* * *
19535222 ATATAGGTAAGTACATATGTGATATTATATTTGAT
66 ATATAGGTAAGGAAAAATGTGATATTATATTTGAT
*
19535257 CTTGTATATTTGGCCA
1 CTTGTATATTCGGCCA
19535273 AATGAGTTGT
Statistics
Matches: 98, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
99 3 0.03
100 95 0.97
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (100 bp):
CTTGTATATTCGGCCACATAAGTAAGTACATATGTGATGTTAAATTGGATCTTGAATATTCGACC
ATATAGGTAAGGAAAAATGTGATATTATATTTGAT
Found at i:19554576 original size:93 final size:93
Alignment explanation
Indices: 19554466--19554636 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
19554456 GCCCCTAAGT
* *
19554466 GAACTCGGACTCAACTCAACGAGCTCAGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGAACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAAATCGGACTCAACTCA
19554530 ACGAGTTCGGATGCCTAGTTACATCTCAC
65 ACGAGTTCGGATGCCTAGTTACATCTCAC
*
19554559 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAAATCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAAATCGGACTCAACTCAA
19554624 CGAGTTCGGATGC
66 CGAGTTCGGATGC
19554637 TCAACCATCC
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAAATCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:19554633 original size:46 final size:46
Alignment explanation
Indices: 19554461--19554633 Score: 203
Period size: 46 Copynumber: 3.7 Consensus size: 46
19554451 AACCCGCCCC
*
19554461 TAAGTGAACTCGGACTCAACTCAACGAGCTCAGG-CATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCA
*
19554507 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* * *
19554555 TCA-CGAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
19554600 TAAGTGAAATCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
19554634 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 10, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 57 0.53
47 28 0.26
48 2 0.02
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:19555089 original size:30 final size:30
Alignment explanation
Indices: 19555055--19555114 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
19555045 CATTTAATAC
19555055 AAAC-TTTGAAAAAATTACACTTTTGCCCCT
1 AAACTTTTG-AAAAATTACACTTTTGCCCCT
* *
19555085 AAACTTTTGCATAATTACACTTTTGCCCCT
1 AAACTTTTGAAAAATTACACTTTTGCCCCT
19555115 TGGCTCGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.37
Consensus pattern (30 bp):
AAACTTTTGAAAAATTACACTTTTGCCCCT
Found at i:19555242 original size:50 final size:50
Alignment explanation
Indices: 19555187--19555285 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 50
19555177 CTTCTATGGC
*
19555187 AACATCAAATTCTCTCTCTAACATATACTTGTGACTATTAGGTATTTTTG
1 AACATCAAATTCTCACTCTAACATATACTTGTGACTATTAGGTATTTTTG
*
19555237 AACATCAAATTCTCACTCTAACATGTACTTGTGACTATTAGGTATTTTT
1 AACATCAAATTCTCACTCTAACATATACTTGTGACTATTAGGTATTTTT
19555286 ACCTATTAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.41
Consensus pattern (50 bp):
AACATCAAATTCTCACTCTAACATATACTTGTGACTATTAGGTATTTTTG
Found at i:19568416 original size:50 final size:51
Alignment explanation
Indices: 19568269--19568484 Score: 185
Period size: 50 Copynumber: 4.3 Consensus size: 51
19568259 GCTAAATGAC
* * * * * *
19568269 CTTG-TATATTCGGCCACATAGGTATGTACATATGTGATGTTGTATTGGAT
1 CTTGATATATTCGGCCATATAAGTAAGTACATATGTGATATTATATTTGAT
* * * * * *
19568319 TTTGA-ATATTTGGCCATA-AAGGTATGGACAAACGTGATATTATATTTGAAT
1 CTTGATATATTCGGCCATATAA-GTAAGTACATATGTGATATTATATTTG-AT
* * *
19568370 -TT-ATATATTCGGCCATATAAGTAAGTACATATGTAATGTTAAATTTGAT
1 CTTGATATATTCGGCCATATAAGTAAGTACATATGTGATATTATATTTGAT
* * * *
19568419 CTTGCT-TAATCGGCCATATAGGTAAGCACATATGTGATATTATATTTGAT
1 CTTGATATATTCGGCCATATAAGTAAGTACATATGTGATATTATATTTGAT
*
19568469 CTTG-TATATTTGGCCA
1 CTTGATATATTCGGCCA
19568485 AATGAGTGAT
Statistics
Matches: 131, Mismatches: 27, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
49 5 0.04
50 121 0.92
51 5 0.04
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (51 bp):
CTTGATATATTCGGCCATATAAGTAAGTACATATGTGATATTATATTTGAT
Found at i:19568456 original size:100 final size:100
Alignment explanation
Indices: 19568273--19568484 Score: 237
Period size: 100 Copynumber: 2.1 Consensus size: 100
19568263 AATGACCTTG
* * * ** * * *
19568273 TATATTCGGCCACATAGGTATGTACATATGTGATGTTGTATTGGATTTTGAATATTTGGCCATAA
1 TATATTCGGCCACATAAGTAAGTACATATGTAATGTTAAATTGGATCTTGAATAATCGGCCATAA
* *
19568338 AGGTATGGACAAACGTGATATTATATTTGAAT-TTA
66 AGGTAAGCACAAACGTGATATTATATTTG-ATCTTA
* * ** *
19568373 TATATTCGGCCATATAAGTAAGTACATATGTAATGTTAAATTTGATCTTGCTTAATCGGCCATAT
1 TATATTCGGCCACATAAGTAAGTACATATGTAATGTTAAATTGGATCTTGAATAATCGGCCATAA
* * *
19568438 AGGTAAGCACATATGTGATATTATATTTGATCTTG
66 AGGTAAGCACAAACGTGATATTATATTTGATCTTA
*
19568473 TATATTTGGCCA
1 TATATTCGGCCA
19568485 AATGAGTGAT
Statistics
Matches: 92, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
99 2 0.02
100 90 0.98
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (100 bp):
TATATTCGGCCACATAAGTAAGTACATATGTAATGTTAAATTGGATCTTGAATAATCGGCCATAA
AGGTAAGCACAAACGTGATATTATATTTGATCTTA
Found at i:19569503 original size:17 final size:17
Alignment explanation
Indices: 19569477--19569510 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19569467 ATTGAATAGG
* *
19569477 TATTAGATATGTTTTGT
1 TATTAAATATGATTTGT
19569494 TATTAAATATGATTTGT
1 TATTAAATATGATTTGT
19569511 GCTATAAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (17 bp):
TATTAAATATGATTTGT
Found at i:19570430 original size:22 final size:22
Alignment explanation
Indices: 19570405--19570452 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
19570395 TTTTTTCAGG
19570405 ATTTATTTCCTCTTCTAAACAT
1 ATTTATTTCCTCTTCTAAACAT
19570427 ATTTATTTCCTCTTCTAAACAT
1 ATTTATTTCCTCTTCTAAACAT
19570449 ATTT
1 ATTT
19570453 CTAAATCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.21, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTATTTCCTCTTCTAAACAT
Found at i:19572696 original size:41 final size:41
Alignment explanation
Indices: 19572651--19572733 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
19572641 ATTCCATTTG
19572651 AGCATACATCCAATAGACCTAAACACCTTTCAAACACATAT
1 AGCATACATCCAATAGACCTAAACACCTTTCAAACACATAT
* *
19572692 AGCATACATTCAATAGACTTAAACACCTTTCAAACACATAT
1 AGCATACATCCAATAGACCTAAACACCTTTCAAACACATAT
19572733 A
1 A
19572734 AACATACCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.45, C:0.27, G:0.05, T:0.24
Consensus pattern (41 bp):
AGCATACATCCAATAGACCTAAACACCTTTCAAACACATAT
Found at i:19572736 original size:21 final size:21
Alignment explanation
Indices: 19572670--19572737 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
19572660 CCAATAGACC
19572670 TAAACACCTTTCAAACACATA
1 TAAACACCTTTCAAACACATA
* * * *
19572691 T-AGCATACATTCAATAGAC-T-
1 TAAACA-CCTTTCAA-ACACATA
19572711 TAAACACCTTTCAAACACATA
1 TAAACACCTTTCAAACACATA
19572732 TAAACA
1 TAAACA
19572738 TACCAATTCA
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
19 3 0.09
20 11 0.32
21 17 0.50
22 3 0.09
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (21 bp):
TAAACACCTTTCAAACACATA
Found at i:19574037 original size:25 final size:24
Alignment explanation
Indices: 19574009--19574075 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 24
19573999 TGTGAATCGG
19574009 GAAGAGCATACGAGCTGCAAATTAA
1 GAAG-GCATACGAGCTGCAAATTAA
* * * *
19574034 GAAGCTCATACGAGTTGTAAATTAG
1 GAAG-GCATACGAGCTGCAAATTAA
19574059 GAAGGTCATACGAGCTG
1 GAAGG-CATACGAGCTG
19574076 TGGTGTGTCT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.21
Consensus pattern (24 bp):
GAAGGCATACGAGCTGCAAATTAA
Found at i:19581800 original size:28 final size:28
Alignment explanation
Indices: 19581707--19581811 Score: 110
Period size: 27 Copynumber: 3.9 Consensus size: 28
19581697 AGGAAGCGTC
* *
19581707 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACGATTATCTGTAT
* *
19581734 CTGGTGGCTCTACCA-GATATTTCTGT-T
1 CTGGTGGCTCTGCCACGAT-TATCTGTAT
19581761 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACGATTATCTGTAT
* * *
19581789 CTAGTGACTCTGTCAC-ATTATCT
1 CTGGTGGCTCTGCCACGATTATCT
19581812 ATCCTGGCAG
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
26 2 0.03
27 46 0.71
28 17 0.26
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (28 bp):
CTGGTGGCTCTGCCACGATTATCTGTAT
Found at i:19601281 original size:13 final size:13
Alignment explanation
Indices: 19601263--19601291 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
19601253 TTTAGTTTAA
19601263 TTAGTTAATTAGT
1 TTAGTTAATTAGT
19601276 TTAGTTAATTAGT
1 TTAGTTAATTAGT
19601289 TTA
1 TTA
19601292 ATAAACAACC
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:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:19611923 original size:42 final size:42
Alignment explanation
Indices: 19611860--19611950 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
19611850 TCGTTTACTT
** * *
19611860 GATGCCATAGTCCAACTATGGTCTTATGCGAAGTCTCATATC
1 GATGCCATAGTCCAACTATGGTCTTACACGAAATCACATATC
*
19611902 GATGCCAT-GTCCCAGAC-ATGGTCTTACACGAAATCACATATT
1 GATGCCATAGT-CCA-ACTATGGTCTTACACGAAATCACATATC
19611944 GATGCCA
1 GATGCCA
19611951 ACGCTATATC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 2 0.05
42 38 0.90
43 2 0.05
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (42 bp):
GATGCCATAGTCCAACTATGGTCTTACACGAAATCACATATC
Found at i:19611990 original size:48 final size:48
Alignment explanation
Indices: 19611903--19612275 Score: 548
Period size: 48 Copynumber: 7.6 Consensus size: 48
19611893 TCTCATATCG
* ** *
19611903 ATGCCATGTCCCAGACATGGTCTTACACGAAATCACATATTGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
* * * * *
19611951 ACGCTATATCCTAGATATGGTCTTACATGGGATCACATATCGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
*
19611999 ATGCCATGTCCCGGACATGGTCTTACATGGGATCACATATCGATGCCAATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC---G---ATGCCA
19612053 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
* *
19612101 ATGCCATGACCCAGACATGGTCTTACATGGGATTACATATCGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
* * *
19612149 ATTCCATGTCCCAGACATGATCTTACATGGGATCACATATCGATGCAA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
*
19612197 ATGCCATGTTCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
19612245 ATGCCATGTCCCAGACATGGTCTTACATGGG
1 ATGCCATGTCCCAGACATGGTCTTACATGGG
19612276 GTTACAATGC
Statistics
Matches: 291, Mismatches: 28, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
48 243 0.84
51 2 0.01
54 46 0.16
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
Found at i:19612174 original size:150 final size:144
Alignment explanation
Indices: 19611903--19612281 Score: 553
Period size: 150 Copynumber: 2.6 Consensus size: 144
19611893 TCTCATATCG
* ** * * * * *
19611903 ATGCCATGTCCCAGACATGGTCTTACACGAAATCACATATTGATGCCAACGCTAT-ATCCTAGAT
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCAATGCCATGA-CCCAGAC
* * *
19611967 ATGGTCTTACATGGGATCACATATCGATGCCAATGCCATGTCCCGGACATGGTCTTACATGGGAT
65 ATGGTCTTACATGGGATTACATATCGATGCCAATGCCATGTCCCAGACATGATCTTACATGGGAT
19612032 CACATATCGATGCCAATGCCA
130 CACATATCGATG-C-A----A
19612053 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCAATGCCATGACCCAGACA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCAATGCCATGACCCAGACA
*
19612118 TGGTCTTACATGGGATTACATATCGATGCCAATTCCATGTCCCAGACATGATCTTACATGGGATC
66 TGGTCTTACATGGGATTACATATCGATGCCAATGCCATGTCCCAGACATGATCTTACATGGGATC
19612183 ACATATCGATGCAA
131 ACATATCGATGCAA
* *
19612197 ATGCCATGTTCCAGACATGGTCTTACATGGGATCACATATCGATGCCAATGCCATGTCCCAGACA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCAATGCCATGACCCAGACA
*
19612262 TGGTCTTACATGGGGTTACA
66 TGGTCTTACATGGGATTACA
19612282 ATGCCATAGC
Statistics
Matches: 213, Mismatches: 15, Indels: 8
0.90 0.06 0.03
Matches are distributed among these distances:
144 83 0.39
148 1 0.00
149 1 0.00
150 127 0.60
151 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (144 bp):
ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCAATGCCATGACCCAGACA
TGGTCTTACATGGGATTACATATCGATGCCAATGCCATGTCCCAGACATGATCTTACATGGGATC
ACATATCGATGCAA
Found at i:19616521 original size:33 final size:33
Alignment explanation
Indices: 19616475--19616569 Score: 109
Period size: 33 Copynumber: 2.9 Consensus size: 33
19616465 AGCATGCAGT
* * * * *
19616475 AACAGTCTCGGCCTAAGCCCTATCCAGTATCAT
1 AACAGTCTGGGCCTTAGCCCTATACAGTAACAG
* *
19616508 TACAGTCTGGGCCTTAGCCCTATAGAGTAACAG
1 AACAGTCTGGGCCTTAGCCCTATACAGTAACAG
* *
19616541 AACAGTCTGGGCTTTAGCCCTATATAGTA
1 AACAGTCTGGGCCTTAGCCCTATACAGTA
19616570 GCAGTGTGGG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26
Consensus pattern (33 bp):
AACAGTCTGGGCCTTAGCCCTATACAGTAACAG
Found at i:19616816 original size:27 final size:28
Alignment explanation
Indices: 19616758--19616838 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 28
19616748 AGCTGCCAAA
*
19616758 AACAGTAAATT-TGGCA-AGCCACCAGC
1 AACAGTAAATTGTGGCATAGCCACCAGT
*
19616784 ATCAGT-AATTGTGGCATAGCCACCAGT
1 AACAGTAAATTGTGGCATAGCCACCAGT
* * *
19616811 AACAGTGAA-TGTGACATAGTCACCAGT
1 AACAGTAAATTGTGGCATAGCCACCAGT
19616838 A
1 A
19616839 CAATACTTCC
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
25 4 0.09
26 10 0.21
27 31 0.66
28 2 0.04
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (28 bp):
AACAGTAAATTGTGGCATAGCCACCAGT
Found at i:19617009 original size:27 final size:27
Alignment explanation
Indices: 19616979--19617095 Score: 137
Period size: 27 Copynumber: 4.3 Consensus size: 27
19616969 GGGCATAATC
* * *
19616979 GTCACTTTACCATACAGGGGTATTGCT-
1 GTCATTTTACCCTACAGGGGTATT-ATG
*
19617006 GTCATTTTACCCTACAGGGGAATTATG
1 GTCATTTTACCCTACAGGGGTATTATG
* *
19617033 GTCATTTTACCTTATAGGGGTATTATG
1 GTCATTTTACCCTACAGGGGTATTATG
* *
19617060 GTCATTTTACCCTATAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTATG
*
19617087 ATCATTTTA
1 GTCATTTTA
19617096 AAAATTAGGG
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
26 1 0.01
27 78 0.99
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGTATTATG
Found at i:19617104 original size:27 final size:27
Alignment explanation
Indices: 19617074--19617214 Score: 106
Period size: 27 Copynumber: 5.3 Consensus size: 27
19617064 TTTTACCCTA
*
19617074 TAGGGGTATTACGATCATTTTAAAAAT
1 TAGGGGTATTACGATAATTTTAAAAAT
* *
19617101 TAGGGGTATTTCGATAATTTTACAAAT
1 TAGGGGTATTACGATAATTTTAAAAAT
* * ** * *
19617128 CAAGAATACTT-CGATAATTTCACAAAT
1 TAGGGGTA-TTACGATAATTTTAAAAAT
* * * * **
19617155 CAGGGGTATTTCGGTAATTTTACAACC
1 TAGGGGTATTACGATAATTTTAAAAAT
* *
19617182 TAGGGGTATTTCGATAATTTTACAAAT
1 TAGGGGTATTACGATAATTTTAAAAAT
19617209 T-GGGGT
1 TAGGGGT
19617215 CTTAACGACC
Statistics
Matches: 93, Mismatches: 19, Indels: 5
0.79 0.16 0.04
Matches are distributed among these distances:
26 7 0.08
27 84 0.90
28 2 0.02
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.36
Consensus pattern (27 bp):
TAGGGGTATTACGATAATTTTAAAAAT
Found at i:19617105 original size:54 final size:54
Alignment explanation
Indices: 19617006--19617110 Score: 131
Period size: 54 Copynumber: 1.9 Consensus size: 54
19616996 GGGTATTGCT
* * ***
19617006 GTCATTTTACCCTACAGGGGAATTATGGTCATTTTACCTTATAGGGGTATTATG
1 GTCATTTTACCCTACAGGGGAATTACGATCATTTTAAAATATAGGGGTATTATG
* *
19617060 GTCATTTTACCCTATAGGGGTATTACGATCATTTTAAAA-ATTAGGGGTATT
1 GTCATTTTACCCTACAGGGGAATTACGATCATTTTAAAATA-TAGGGGTATT
19617111 TCGATAATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
53 1 0.02
54 42 0.98
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (54 bp):
GTCATTTTACCCTACAGGGGAATTACGATCATTTTAAAATATAGGGGTATTATG
Found at i:19617195 original size:54 final size:53
Alignment explanation
Indices: 19617073--19617208 Score: 155
Period size: 54 Copynumber: 2.5 Consensus size: 53
19617063 ATTTTACCCT
* * * *
19617073 ATAGGGGTATTACGATCATTTTAAAAATTAGGGGTATTTCGATAATTTTACAA
1 ATAGGGGTATTTCGATAATTTTACAAATCAGGGGTATTTCGATAATTTTACAA
* ** * * *
19617126 ATCAAGAATACTTCGATAATTTCACAAATCAGGGGTATTTCGGTAATTTTACAA
1 AT-AGGGGTATTTCGATAATTTTACAAATCAGGGGTATTTCGATAATTTTACAA
*
19617180 CCTAGGGGTATTTCGATAATTTTACAAAT
1 -ATAGGGGTATTTCGATAATTTTACAAAT
19617209 TGGGGTCTTA
Statistics
Matches: 65, Mismatches: 16, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
53 2 0.03
54 62 0.95
55 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (53 bp):
ATAGGGGTATTTCGATAATTTTACAAATCAGGGGTATTTCGATAATTTTACAA
Found at i:19617441 original size:17 final size:18
Alignment explanation
Indices: 19617419--19617454 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
19617409 ATTAAATGTG
*
19617419 TGGGCCCAC-GAGCCCAT
1 TGGGCCCACACAGCCCAT
19617436 TGGGCCCACACAGCCCAT
1 TGGGCCCACACAGCCCAT
19617454 T
1 T
19617455 TTAGACTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.19, C:0.42, G:0.25, T:0.14
Consensus pattern (18 bp):
TGGGCCCACACAGCCCAT
Found at i:19620617 original size:43 final size:43
Alignment explanation
Indices: 19620556--19620641 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
19620546 ATCATATGTA
* *
19620556 TCGCATCCATTATGAACTC-GAGCCACTCAACGAGCTCGGATGC
1 TCGCATCCATAATGAACTCGGA-CCACTCAACGAACTCGGATGC
* *
19620599 TCGCATCCATAATGAACTCGGACTACTCAACGAACTTGGATGC
1 TCGCATCCATAATGAACTCGGACCACTCAACGAACTCGGATGC
19620642 CACATATATC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 36 0.95
44 2 0.05
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (43 bp):
TCGCATCCATAATGAACTCGGACCACTCAACGAACTCGGATGC
Found at i:19638183 original size:27 final size:26
Alignment explanation
Indices: 19638152--19638246 Score: 93
Period size: 27 Copynumber: 3.5 Consensus size: 26
19638142 TTAGTTTACC
* *
19638152 AAATTACTGAAATACCTTCGACTTGTA
1 AAATTACTCAAATACC-TCGATTTGTA
*
19638179 AAATTAC-CAAAGTACCCTCGATTTATA
1 AAATTACTCAAA-TA-CCTCGATTTGTA
*
19638206 AAATTACCCAAATATCCTCGATTTGTA
1 AAATTACTCAAATA-CCTCGATTTGTA
* *
19638233 AAATCACTGAAATA
1 AAATTACTCAAATA
19638247 AGATAGAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
26 3 0.05
27 48 0.84
28 6 0.11
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (26 bp):
AAATTACTCAAATACCTCGATTTGTA
Found at i:19638629 original size:27 final size:27
Alignment explanation
Indices: 19638249--19638627 Score: 560
Period size: 27 Copynumber: 14.0 Consensus size: 27
19638239 CTGAAATAAG
19638249 ATAGAATTACCATTTTACCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
* * **
19638276 ACAGAATTATCGCTTTACCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
*
19638303 ATAGAATTACTATTTTACCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
* * *
19638330 ATAGAATTATCGTTTTACCCTCAATTT
1 ATAGAATTACCATTTTACCCTCGATTT
*
19638357 ATAGAATTACCATTTTAACCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
* **
19638384 ACAGAATTACTGTTTTACCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
*
19638411 ATAGAATTACCGTTTTACCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
*
19638438 ATAGAATTACTATTTTACCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
*
19638465 ATAGAATTACCGTTTTACCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
*
19638492 ATAGAATTACTATTTTACCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
* *
19638519 ATAGAATTACCGTTTTACCCTCAATTT
1 ATAGAATTACCATTTTACCCTCGATTT
19638546 ATAGAATTACCATTTTACCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
19638573 ATAGAATTACCATTTTACCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
* ** *
19638600 ACAGAATTACTGTTTTATCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
19638627 A
1 A
19638628 CAAAATTATT
Statistics
Matches: 314, Mismatches: 38, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 314 1.00
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.42
Consensus pattern (27 bp):
ATAGAATTACCATTTTACCCTCGATTT
Found at i:19638669 original size:27 final size:26
Alignment explanation
Indices: 19638624--19638832 Score: 161
Period size: 27 Copynumber: 7.8 Consensus size: 26
19638614 TTATCCTCGA
* * *
19638624 TTTACAAAATTATTGAAATACCCTTAG
1 TTTATAAAATTACTAAAATACCC-TAG
* * *
19638651 TTTACAAAATTACCAAAATACCCTCG
1 TTTATAAAATTACTAAAATACCCTAG
* * *
19638677 ATAAGTAAAATTACCAAAATACCCCTAG
1 TTTA-TAAAATTACTAAAATA-CCCTAG
* *
19638705 TTTGTAAAATTACTAAAATACCCTGG
1 TTTATAAAATTACTAAAATACCCTAG
* *
19638731 TTTGTAAAATTACTAAAATACCCTTGG
1 TTTATAAAATTACTAAAATACCC-TAG
*
19638758 TTTGTAAAATTACTAAAATACCCCT-G
1 TTTATAAAATTACTAAAATA-CCCTAG
* * *
19638784 ACTTGTAAAATTACTAAAATACCTCTAA
1 -TTTATAAAATTACTAAAATACC-CTAG
* *
19638812 TTTGTGAAATTA-TCAAAATAC
1 TTTATAAAATTACT-AAAATAC
19638833 TCTCGATTTG
Statistics
Matches: 157, Mismatches: 17, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
26 36 0.23
27 112 0.71
28 9 0.06
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.33
Consensus pattern (26 bp):
TTTATAAAATTACTAAAATACCCTAG
Found at i:19638776 original size:107 final size:107
Alignment explanation
Indices: 19638629--19638832 Score: 261
Period size: 107 Copynumber: 1.9 Consensus size: 107
19638619 CTCGATTTAC
* *
19638629 AAAATTATTGAAATACCCTTAGTTTACAAAATTACCAAAATA-CCCTCGA-TAAGTAAAATTACC
1 AAAATTACTAAAATACCCTTAGTTTACAAAATTACCAAAATACCCCT-GACT-AGTAAAATTACC
*
19638692 AAAATACCCCTAGTTTGTAAAATTA-CTAAAATACCCTGGTTTGT
64 AAAATACCCCTAATTTGTAAAATTATC-AAAATACCCTGGTTTGT
* ** * * *
19638736 AAAATTACTAAAATACCCTTGGTTTGTAAAATTACTAAAATACCCCTGACTTGTAAAATTACTAA
1 AAAATTACTAAAATACCCTTAGTTTACAAAATTACCAAAATACCCCTGACTAGTAAAATTACCAA
* *
19638801 AATACCTCTAATTTGTGAAATTATCAAAATAC
66 AATACCCCTAATTTGTAAAATTATCAAAATAC
19638833 TCTCGATTTG
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
107 77 0.93
108 6 0.07
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.32
Consensus pattern (107 bp):
AAAATTACTAAAATACCCTTAGTTTACAAAATTACCAAAATACCCCTGACTAGTAAAATTACCAA
AATACCCCTAATTTGTAAAATTATCAAAATACCCTGGTTTGT
Found at i:19638841 original size:27 final size:26
Alignment explanation
Indices: 19638656--19638844 Score: 175
Period size: 27 Copynumber: 7.0 Consensus size: 26
19638646 CTTAGTTTAC
* **
19638656 AAAATTACCAAAATACCCTCGATAAGT
1 AAAATTACTAAAATA-CCTCGATTTGT
* * *
19638683 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACTAAAATACCTCGA-TTTGT
*
19638710 AAAATTACTAAAATACC-CTGGTTTGT
1 AAAATTACTAAAATACCTC-GATTTGT
* *
19638736 AAAATTACTAAAATACCCTTGGTTTGT
1 AAAATTACTAAAATA-CCTCGATTTGT
* *
19638763 AAAATTACTAAAATACCCCTGACTTGT
1 AAAATTACTAAAATACCTC-GATTTGT
*
19638790 AAAATTACTAAAATACCTCTAATTTGT
1 AAAATTACTAAAATACCTC-GATTTGT
*
19638817 GAAATTA-TCAAAATACTCTCGATTTGT
1 AAAATTACT-AAAATAC-CTCGATTTGT
19638844 A
1 A
19638845 TAATATCGAA
Statistics
Matches: 137, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
26 28 0.20
27 106 0.77
28 3 0.02
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.32
Consensus pattern (26 bp):
AAAATTACTAAAATACCTCGATTTGT
Found at i:19638844 original size:54 final size:53
Alignment explanation
Indices: 19638618--19638844 Score: 235
Period size: 54 Copynumber: 4.2 Consensus size: 53
19638608 ACTGTTTTAT
** * * ** *
19638618 CCTCGATTTACAAAATTATTGAAATACCCTTAGTTTACAAAATTACCAAAATAC
1 CCTCGATTTGTAAAATTACTAAAATACCC-TAGTTTGTAAAATTACTAAAATAC
** *
19638672 CCTCGATAAGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACTAAAATAC
1 CCTCGATTTGTAAAATTACTAAAATA-CCCTAGTTTGTAAAATTACTAAAATAC
* *
19638726 CCT-GGTTTGTAAAATTACTAAAATACCCTTGGTTTGTAAAATTACTAAAATAC
1 CCTCGATTTGTAAAATTACTAAAATACCC-TAGTTTGTAAAATTACTAAAATAC
* * *
19638779 CC-CTGACTTGTAAAATTACTAAAATACCTCTAATTTGTGAAATTA-TCAAAATAC
1 CCTC-GATTTGTAAAATTACTAAAATACC-CTAGTTTGTAAAATTACT-AAAATAC
*
19638833 TCTCGATTTGTA
1 CCTCGATTTGTA
19638845 TAATATCGAA
Statistics
Matches: 144, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
52 3 0.02
53 44 0.31
54 92 0.64
55 5 0.03
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (53 bp):
CCTCGATTTGTAAAATTACTAAAATACCCTAGTTTGTAAAATTACTAAAATAC
Found at i:19638857 original size:80 final size:79
Alignment explanation
Indices: 19638629--19638863 Score: 224
Period size: 80 Copynumber: 2.9 Consensus size: 79
19638619 CTCGATTTAC
* * * ** ** *
19638629 AAAATTATTGAAATACCCTTAGTTTACAAAATTACCAAAATACCCTCGATAAGTAAAATTACCAA
1 AAAATTACTAAAATACCC-TAATTTGTAAAATTA-CAAAATACCCTCGATTTGTAAAA-TATCAA
*
19638694 AATACCCCT-AGTTTGT
63 AATACCCCTGAGCTTGT
** * *
19638710 AAAATTACTAAAATACCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTGTAAAAT-TACTAA
1 AAAATTACTAAAATACCCTAATTTGTAAAATTAC-AAAATACCCTCGATTTGTAAAATAT-C-AA
19638774 AATACCCCTGA-CTTGT
63 AATACCCCTGAGCTTGT
* * * *
19638790 AAAATTACTAAAATACCTCTAATTTGTGAAATTATCAAAATACTCTCGATTTGTATAATATCGAA
1 AAAATTACTAAAATACC-CTAATTTGTAAAATTA-CAAAATACCCTCGATTTGTAAAATATCAAA
19638855 ATACCCCTG
64 ATACCCCTG
19638864 TAGGGTAGAA
Statistics
Matches: 128, Mismatches: 19, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
79 3 0.02
80 73 0.57
81 50 0.39
82 2 0.02
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (79 bp):
AAAATTACTAAAATACCCTAATTTGTAAAATTACAAAATACCCTCGATTTGTAAAATATCAAAAT
ACCCCTGAGCTTGT
Found at i:19638857 original size:107 final size:107
Alignment explanation
Indices: 19638629--19638860 Score: 258
Period size: 107 Copynumber: 2.2 Consensus size: 107
19638619 CTCGATTTAC
*
19638629 AAAATTATTGAAATACCCTTAGTTTACAAAATTACCAAAATACCCTCGATAAGTAAAATTACCAA
1 AAAATTACTGAAATACCCTTAGTTTACAAAATTACCAAAATACCCTCGATAAGTAAAATTACCAA
* *
19638694 AATACCCCTAGTTTGTAAAATTACTAAAATACCCTGGTTTGT
66 AATACCCCTAATTTGTAAAATTACTAAAATACCCTGATTTGT
* * ** * * *
19638736 AAAATTACTAAAATACCCTTGGTTTGTAAAATTACTAAAATACCC-CTGACT-TGTAAAATTACT
1 AAAATTACTGAAATACCCTTAGTTTACAAAATTACCAAAATACCCTC-GA-TAAGTAAAATTACC
* * *
19638799 AAAATACCTCTAATTTGTGAAATTA-TCAAAATACTCTCGATTTGT
64 AAAATACCCCTAATTTGTAAAATTACT-AAAATACCCT-GATTTGT
*
19638844 ATAA-TA-TCGAAATACCC
1 AAAATTACT-GAAATACCC
19638861 CTGTAGGGTA
Statistics
Matches: 105, Mismatches: 15, Indels: 10
0.81 0.12 0.08
Matches are distributed among these distances:
106 3 0.03
107 92 0.88
108 10 0.10
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.32
Consensus pattern (107 bp):
AAAATTACTGAAATACCCTTAGTTTACAAAATTACCAAAATACCCTCGATAAGTAAAATTACCAA
AATACCCCTAATTTGTAAAATTACTAAAATACCCTGATTTGT
Found at i:19638923 original size:27 final size:27
Alignment explanation
Indices: 19638851--19639227 Score: 623
Period size: 27 Copynumber: 14.0 Consensus size: 27
19638841 TGTATAATAT
19638851 CGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
*
19638878 CGGAATA-CCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* *
19638904 TGAAATACCCCTATAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
*
19638931 TGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
19638958 CGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
19638985 CGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
*
19639012 CGGAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
19639039 CGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
*
19639066 CGGAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
19639093 CGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* *
19639120 CTAAATACCCCTGTAAGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
19639147 CGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
*
19639174 TGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* * * *
19639201 CGAGATA-CCTTGTAAGGTAAAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
19639227 C
1 C
19639228 ATTTTGCCCC
Statistics
Matches: 329, Mismatches: 20, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
26 41 0.12
27 288 0.88
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (27 bp):
CGAAATACCCCTGTAGGGTAGAATTAC
Found at i:19639669 original size:6 final size:6
Alignment explanation
Indices: 19639629--19639716 Score: 56
Period size: 6 Copynumber: 14.3 Consensus size: 6
19639619 TTGCATTCAC
* * *
19639629 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTT ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
19639678 -TCACCTA ATTCTA ATTCTG ATTCTG ATTCT- AGTTCTG AT
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
19639717 AATGTTTCTT
Statistics
Matches: 64, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
5 4 0.06
6 52 0.81
7 6 0.09
8 2 0.03
ACGTcount: A:0.20, C:0.18, G:0.12, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:19639674 original size:31 final size:31
Alignment explanation
Indices: 19639629--19639732 Score: 104
Period size: 31 Copynumber: 3.4 Consensus size: 31
19639619 TTGCATTCAC
*
19639629 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTG
* * * * *
19639660 ATTCTTATTCTGATTCTGTCACCTAATTCTA
1 ATTCTGATTCTGATTCTGTTACCTGATACTG
*
19639691 ATTCTGATTCTGATTCTAGTT--CTGATAATG
1 ATTCTGATTCTGATTCT-GTTACCTGATACTG
* *
19639721 TTTCTTATTCTG
1 ATTCTGATTCTG
19639733 TAATGGGTTA
Statistics
Matches: 58, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
30 15 0.26
31 41 0.71
32 2 0.03
ACGTcount: A:0.20, C:0.17, G:0.12, T:0.50
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTTACCTGATACTG
Found at i:19651860 original size:46 final size:46
Alignment explanation
Indices: 19651810--19651985 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
19651800 TGGTTGAGCA
19651810 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
19651856 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
19651901 CATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
19651949 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
19651986 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.57
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:19651966 original size:93 final size:93
Alignment explanation
Indices: 19651807--19651978 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
19651797 GGATGGTTGA
* *
19651807 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
19651872 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
19651900 GCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
19651965 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
19651979 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:19654637 original size:63 final size:63
Alignment explanation
Indices: 19654569--19654819 Score: 493
Period size: 63 Copynumber: 4.0 Consensus size: 63
19654559 ATGTGTAATT
*
19654569 ATGCAAGAGGGTAAAATTGTGGCTTATACCTCGAGACAATTGAAACCTCACGAGAAAAACTAG
1 ATGCAAGAGGGTACAATTGTGGCTTATACCTCGAGACAATTGAAACCTCACGAGAAAAACTAG
19654632 ATGCAAGAGGGTACAATTGTGGCTTATACCTCGAGACAATTGAAACCTCACGAGAAAAACTAG
1 ATGCAAGAGGGTACAATTGTGGCTTATACCTCGAGACAATTGAAACCTCACGAGAAAAACTAG
19654695 ATGCAAGAGGGTACAATTGTGGCTTATACCTCGAGACAATTGAAACCTCACGAGAAAAACTAG
1 ATGCAAGAGGGTACAATTGTGGCTTATACCTCGAGACAATTGAAACCTCACGAGAAAAACTAG
19654758 ATGCAAGAGGGTACAATTGTGGCTTATACCTCGAGACAATTGAAACCTCACGAGAAAAACTA
1 ATGCAAGAGGGTACAATTGTGGCTTATACCTCGAGACAATTGAAACCTCACGAGAAAAACTA
19654820 TCTAACATAC
Statistics
Matches: 187, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 187 1.00
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.21
Consensus pattern (63 bp):
ATGCAAGAGGGTACAATTGTGGCTTATACCTCGAGACAATTGAAACCTCACGAGAAAAACTAG
Found at i:19665948 original size:24 final size:23
Alignment explanation
Indices: 19665921--19665971 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 23
19665911 TTTTCTCCTA
*
19665921 AATTTT-AATTTTATTTAATTAATT
1 AATTTTCAA-TTTATTGAATT-ATT
19665945 AATTTTTCAATTTATTGAATTATT
1 AA-TTTTCAATTTATTGAATTATT
19665969 AAT
1 AAT
19665972 ATTTTATACT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
23 1 0.04
24 7 0.29
25 14 0.58
26 2 0.08
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
AATTTTCAATTTATTGAATTATT
Found at i:19666879 original size:21 final size:21
Alignment explanation
Indices: 19666854--19666893 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19666844 GCAATAAGCT
19666854 GAAGAA-AGCAAGGATCCCAAA
1 GAAGAAGAGCAA-GATCCCAAA
*
19666875 GAAGAAGAGGAAGATCCCA
1 GAAGAAGAGCAAGATCCCA
19666894 CAGAGATCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.50, C:0.17, G:0.28, T:0.05
Consensus pattern (21 bp):
GAAGAAGAGCAAGATCCCAAA
Found at i:19670831 original size:83 final size:83
Alignment explanation
Indices: 19670692--19670857 Score: 282
Period size: 83 Copynumber: 2.0 Consensus size: 83
19670682 CTATAAAAAA
*
19670692 GAGAGAAACAAAAGGGAGTGAGCATAAAGCTTAGTAAGTTCGCATGTAAATAAATAACAACA-TC
1 GAGAGAAACAAAAGGGAGTAAGCATAAAGCTTAGTAAGTTCGCATGTAAATAAATAACAACAGT-
19670756 CTAAATGAATTATCAAGAT
65 CTAAATGAATTATCAAGAT
*
19670775 GAGAGAAA-AGAAAGGGAGTAAGCATAAAGCTTAGTAAGTTTGCATGTAAATAAATAACAACAGT
1 GAGAGAAACA-AAAGGGAGTAAGCATAAAGCTTAGTAAGTTCGCATGTAAATAAATAACAACAGT
19670839 CTAAATGAATTATCAAGAT
65 CTAAATGAATTATCAAGAT
19670858 AACCTAAACC
Statistics
Matches: 79, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
82 1 0.01
83 77 0.97
84 1 0.01
ACGTcount: A:0.48, C:0.10, G:0.20, T:0.22
Consensus pattern (83 bp):
GAGAGAAACAAAAGGGAGTAAGCATAAAGCTTAGTAAGTTCGCATGTAAATAAATAACAACAGTC
TAAATGAATTATCAAGAT
Found at i:19671032 original size:53 final size:54
Alignment explanation
Indices: 19670968--19671175 Score: 184
Period size: 55 Copynumber: 3.8 Consensus size: 54
19670958 TTCCTTTTTA
* *
19670968 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * * * * * *
19671021 AACTCACCATTGCCATGCCTTGGCATGGTTTTACATGGGATCTTTTCCTTATCG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
** * * * * * * *
19671075 TAGTTTATCAATGCCATGTCTTAACATGGTCTTACATGATTTCCTTGCCTTCTAA
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * *
19671130 AACTTACCAAATGTCATGCCTTGGCATGGTTTTACTTGGTATCCTT
1 AACTTACC-AATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
19671176 AAGCCCTAAT
Statistics
Matches: 117, Mismatches: 35, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
53 45 0.38
54 6 0.05
55 66 0.56
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:19681107 original size:40 final size:39
Alignment explanation
Indices: 19680951--19681112 Score: 141
Period size: 40 Copynumber: 4.1 Consensus size: 39
19680941 AATGATGTCT
* * *
19680951 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGT-ACTATAACC
* *
19680991 GGACTAAGAT-CAGAAGGCATTTGTGCGAGTTACTA-AATCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TACTATAA-CC
* *
19681031 GGGTTAAGTCCCGAAGGCATTTGTGCGATTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGA-GTACTATAACC
* ** *
19681071 GGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTA-CTATAACC
19681111 GG
1 GG
19681113 TTAAATTCCG
Statistics
Matches: 99, Mismatches: 15, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
39 4 0.04
40 84 0.85
41 11 0.11
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (39 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAACC
Found at i:19681387 original size:47 final size:47
Alignment explanation
Indices: 19681318--19681698 Score: 368
Period size: 47 Copynumber: 7.6 Consensus size: 47
19681308 AAGGGTTGGT
19681318 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
19681365 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGA--TG-TG-ATG
* ** *** * *
19681416 AATGTGAAAGTGGATGTGATGAATGTGA-AAGTGTATATATGTGATAAGGCCTAATGG
1 AATGTGAAAGT-G-TAT-AT--ATGTGATAAG-GCCTA-ATG-GCCGATG--TGAT-G
*
19681473 CCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 --AATGTG---------AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
19681531 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
19681578 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
19681625 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
19681672 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
19681699 TCTCGAAGGG
Statistics
Matches: 279, Mismatches: 29, Indels: 52
0.77 0.08 0.14
Matches are distributed among these distances:
47 192 0.69
49 2 0.01
50 2 0.01
51 14 0.05
52 1 0.00
53 2 0.01
54 2 0.01
55 3 0.01
56 17 0.06
57 5 0.02
58 3 0.01
59 8 0.03
61 3 0.01
62 3 0.01
63 9 0.03
64 3 0.01
65 2 0.01
66 2 0.01
67 1 0.00
68 5 0.02
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:19681529 original size:119 final size:119
Alignment explanation
Indices: 19681318--19681534 Score: 434
Period size: 119 Copynumber: 1.8 Consensus size: 119
19681308 AAGGGTTGGT
19681318 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
19681383 TGTGATAAGGCCTAATGGCCGATGTGATGAATGAATGTGAAAGTGGATGTGATG
66 TGTGATAAGGCCTAATGGCCGATGTGATGAATGAATGTGAAAGTGGATGTGATG
19681437 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
19681502 TGTGATAAGGCCTAATGGCCGATGTGATGAATG
66 TGTGATAAGGCCTAATGGCCGATGTGATGAATG
19681535 TGAAAGTGTA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 98 1.00
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.29
Consensus pattern (119 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
TGTGATAAGGCCTAATGGCCGATGTGATGAATGAATGTGAAAGTGGATGTGATG
Found at i:19681536 original size:94 final size:94
Alignment explanation
Indices: 19681428--19681698 Score: 470
Period size: 94 Copynumber: 2.9 Consensus size: 94
19681418 TGTGAAAGTG
19681428 GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
19681493 GTGTATATATGTGATAAGGCCTAATGGCC
66 GTGTATATATGTGATAAGGCCTAATGGCC
19681522 GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
19681587 GTGTATATATGTGATAAGGCCTAATGGCC
66 GTGTATATATGTGATAAGGCCTAATGGCC
* * * * * * *
19681616 GATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAA
1 GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
*
19681681 GTGTATAAATGTGATAAG
66 GTGTATATATGTGATAAG
19681699 TCTCGAAGGG
Statistics
Matches: 169, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 169 1.00
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (94 bp):
GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
GTGTATATATGTGATAAGGCCTAATGGCC
Found at i:19681594 original size:141 final size:141
Alignment explanation
Indices: 19681428--19681698 Score: 470
Period size: 141 Copynumber: 1.9 Consensus size: 141
19681418 TGTGAAAGTG
19681428 GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
* * * * *
19681493 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
66 GTGTATATATGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAAATGTGATAAG
19681558 GCCTAATGGCC
131 GCCTAATGGCC
19681569 GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
* * *
19681634 GTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
66 GTGTATATATGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAAATGTGATAAG
19681699 TCTCGAAGGG
Statistics
Matches: 122, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
141 122 1.00
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (141 bp):
GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
GTGTATATATGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAAATGTGATAAG
GCCTAATGGCC
Found at i:19685199 original size:43 final size:44
Alignment explanation
Indices: 19685146--19685234 Score: 153
Period size: 43 Copynumber: 2.0 Consensus size: 44
19685136 GAATCACTTA
*
19685146 CTACGAAGCTTGGAAGCTTGACAAAACCCT-GCTATGAAGAACC
1 CTACAAAGCTTGGAAGCTTGACAAAACCCTAGCTATGAAGAACC
*
19685189 CTACAAAGCTTGGAAGCTTGACAAAACCCTAGCTCTGAAGAACC
1 CTACAAAGCTTGGAAGCTTGACAAAACCCTAGCTATGAAGAACC
19685233 CT
1 CT
19685235 TGAAATTTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
43 29 0.67
44 14 0.33
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (44 bp):
CTACAAAGCTTGGAAGCTTGACAAAACCCTAGCTATGAAGAACC
Found at i:19686766 original size:46 final size:46
Alignment explanation
Indices: 19686664--19686828 Score: 176
Period size: 46 Copynumber: 3.6 Consensus size: 46
19686654 TTATTTGTGT
* * * *
19686664 GCCAGTGTAAGACATGTCTGGGACATGGCATCGGCATTGAGACG-AGA
1 GCCAATGTAAGACATGTCTAGGACAT-GCATCGGCCTTGAGATGTA-A
* *
19686711 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTTGAGATGTAA
1 GCCAATGTAAGACATGTCTAGGACATGCATCGGCCTTGAGATGTAA
* **
19686757 GCCAATGTAAGACATGTCTAGGACATGCATCAG-CTACAAGATGT--
1 GCCAATGTAAGACATGTCTAGGACATGCATCGGCCT-TGAGATGTAA
*
19686801 GTCAATGTAAGACCATGTCTAGGACATG
1 GCCAATGTAAGA-CATGTCTAGGACATG
19686829 GCATTGGCAC
Statistics
Matches: 105, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
44 11 0.10
45 17 0.16
46 52 0.50
47 25 0.24
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (46 bp):
GCCAATGTAAGACATGTCTAGGACATGCATCGGCCTTGAGATGTAA
Found at i:19686862 original size:48 final size:49
Alignment explanation
Indices: 19686762--19686924 Score: 164
Period size: 48 Copynumber: 3.4 Consensus size: 49
19686752 TGTAAGCCAA
* *
19686762 TGTAAGA-CATGTCTAGGACAT-GCATCAGCTACAAGA--T--GTGTCAA
1 TGTAAGACCATGTCTAGGACATGGCATCAGC-ACAATATGTGAGTGTCAG
** *
19686806 TGTAAGACCATGTCTAGGACATGGCATTGGCAC-GTATG-GAGGTGTCAG
1 TGTAAGACCATGTCTAGGACATGGCATCAGCACAATATGTGA-GTGTCAG
* *
19686854 TGTAAGACCATGTCTGGGACATGGCATCAGCACAAATATGTGAGAG-CTAG
1 TGTAAGACCATGTCTAGGACATGGCATCAGCAC-AATATGTGAGTGTC-AG
19686904 TGTAAGACCATGTCTAGGACA
1 TGTAAGACCATGTCTAGGACA
19686925 GGGTGTCAGC
Statistics
Matches: 97, Mismatches: 11, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
44 8 0.08
45 16 0.16
46 6 0.06
48 36 0.37
49 1 0.01
50 28 0.29
51 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.24
Consensus pattern (49 bp):
TGTAAGACCATGTCTAGGACATGGCATCAGCACAATATGTGAGTGTCAG
Found at i:19689630 original size:80 final size:80
Alignment explanation
Indices: 19689541--19689711 Score: 315
Period size: 80 Copynumber: 2.1 Consensus size: 80
19689531 GAAATGATTA
19689541 GAGCCGAATGTGGCTAAATTATTAATCCGAAATAGACATAGAAATATAATATGCTGCATGTGTGT
1 GAGCCGAATGTGGCTAAATTATTAATCCGAAATAGACATAGAAATATAATATGCTGCATGTGTGT
19689606 TTGAATAAATAAATT
66 TTGAATAAATAAATT
* *
19689621 GAGCTGAATGTGGCTAAATTATTAATCCGAAATAGACATAGAAATATAATATGTTGCATGTGTGT
1 GAGCCGAATGTGGCTAAATTATTAATCCGAAATAGACATAGAAATATAATATGCTGCATGTGTGT
19689686 TTGAATAAATAAATT
66 TTGAATAAATAAATT
*
19689701 AAGCCGAATGT
1 GAGCCGAATGT
19689712 AGTTATACTT
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 87 1.00
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (80 bp):
GAGCCGAATGTGGCTAAATTATTAATCCGAAATAGACATAGAAATATAATATGCTGCATGTGTGT
TTGAATAAATAAATT
Found at i:19694461 original size:40 final size:40
Alignment explanation
Indices: 19694416--19694792 Score: 609
Period size: 40 Copynumber: 9.4 Consensus size: 40
19694406 CAAGCTCAAT
* * * * *
19694416 TGCCTTCGGGTCTTAACCTGGGTATAGCAACTCGCACGA-A
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCAC-ATA
19694456 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACA-A
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACATA
*
19694495 TTGCCTTCGGGTCTTAGCCCGGATATATCAA-TTCGCACAAA
1 -TGCCTTCGGGTCTTAGCCCGGATATATCAACTT-GCACATA
* *
19694536 TGCCTTCAGGTCTTAGCCCGGATATATCAA-TTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTT-GCACATA
*
19694576 TGCCTTCGGGTCTTATCCCGGATATATCAACTTGCACATA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACATA
19694616 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACATA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACATA
19694656 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACATA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACATA
19694696 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACATA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACATA
19694736 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACATA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACATA
19694776 TGCCTTCGGGTCTTAGC
1 TGCCTTCGGGTCTTAGC
19694793 TTTCCAGACA
Statistics
Matches: 323, Mismatches: 10, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
39 4 0.01
40 316 0.98
41 3 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (40 bp):
TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACATA
Found at i:19695045 original size:52 final size:52
Alignment explanation
Indices: 19694970--19695069 Score: 164
Period size: 52 Copynumber: 1.9 Consensus size: 52
19694960 CAAAGTCCCA
*
19694970 CATGTTACAGGGATCGACTACACTGACCTTTGCACATTACGACTTGGACTCC
1 CATGTTACAGGGATCGACTACACTGACCTTTGCACATTACGACCTGGACTCC
* * *
19695022 CATGTTGCAGGGGTCGACTACACTGACCTTTGCCCATTACGACCTGGA
1 CATGTTACAGGGATCGACTACACTGACCTTTGCACATTACGACCTGGA
19695070 TATCTCCCTG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (52 bp):
CATGTTACAGGGATCGACTACACTGACCTTTGCACATTACGACCTGGACTCC
Found at i:19696148 original size:27 final size:27
Alignment explanation
Indices: 19696118--19696295 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
19696108 ATATTGAGTC
* * * *
19696118 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
19696145 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
19696172 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
19696200 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
19696227 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
19696254 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
19696281 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
19696296 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:19696257 original size:82 final size:81
Alignment explanation
Indices: 19696139--19696294 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
19696129 TGCTATATAA
* *
19696139 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
19696204 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
19696221 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
19696285 CACTTAGTGC
65 CACTTAGTGC
19696295 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:19699947 original size:97 final size:97
Alignment explanation
Indices: 19699776--19699969 Score: 334
Period size: 97 Copynumber: 2.0 Consensus size: 97
19699766 ATTTGAGACT
*
19699776 TTTGTGATCCGAAAACACATGGCACTTCTCACCAAACAAATAATGTCGCCATATTTTCAATGCAA
1 TTTGTGATCCGAAAACACATGGCACTTCTCACCAAACAAATAATGTCGCCATATTTTCAAAGCAA
*
19699841 ACACAATGGCGGCTAGTTCGAGATCATGGGTC
66 ACACAATGGCAGCTAGTTCGAGATCATGGGTC
* * *
19699873 TTTGTGATCCGAAAATACATGGCACTTCTCACCAAACAGATAATGTCGCCATATTTTTAAAGCAA
1 TTTGTGATCCGAAAACACATGGCACTTCTCACCAAACAAATAATGTCGCCATATTTTCAAAGCAA
*
19699938 ACACGATGGCAGCTAGTTCGAGATCATGGGTC
66 ACACAATGGCAGCTAGTTCGAGATCATGGGTC
19699970 GGATAATTCC
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 91 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (97 bp):
TTTGTGATCCGAAAACACATGGCACTTCTCACCAAACAAATAATGTCGCCATATTTTCAAAGCAA
ACACAATGGCAGCTAGTTCGAGATCATGGGTC
Found at i:19703658 original size:43 final size:43
Alignment explanation
Indices: 19703597--19703682 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
19703587 GTCACAGGCA
* * * *
19703597 TCGCATCTATAATAAACTCGGACCACTTAACAAGCTCGGATGC
1 TCGCATCCATAATAAACTCAGACCACTCAACAAGCTCAGATGC
* *
19703640 TCGCATCCATAATGAACTCAGACCACTCAACGAGCTCAGATGC
1 TCGCATCCATAATAAACTCAGACCACTCAACAAGCTCAGATGC
19703683 CACATAACTC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.21
Consensus pattern (43 bp):
TCGCATCCATAATAAACTCAGACCACTCAACAAGCTCAGATGC
Found at i:19712187 original size:35 final size:35
Alignment explanation
Indices: 19712117--19712187 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
19712107 CTCAAGATCA
* **
19712117 TCATCAACATTAGCTCTAAACTCTTCAGCGTCGTG
1 TCATCAACATTAGCTCTAAACTCTTCAACCACGTG
* *
19712152 TCATCAACATTAGCTCTGAATTCTTCAACCACGTG
1 TCATCAACATTAGCTCTAAACTCTTCAACCACGTG
19712187 T
1 T
19712188 TTTCAGATCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.32
Consensus pattern (35 bp):
TCATCAACATTAGCTCTAAACTCTTCAACCACGTG
Found at i:19715579 original size:28 final size:28
Alignment explanation
Indices: 19715514--19715664 Score: 223
Period size: 28 Copynumber: 5.4 Consensus size: 28
19715504 GAGATTGGCG
* * * *
19715514 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
19715543 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
19715571 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
19715599 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
19715627 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
19715654 CTGAGTGTGCG
1 CTAAGTGTGCG
19715665 GACTTAATAT
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
27 24 0.21
28 76 0.66
29 15 0.13
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:19726017 original size:26 final size:26
Alignment explanation
Indices: 19725981--19726032 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
19725971 ATTTCAAGTA
19725981 ACCGAATGGAATACCTAATTCCTTGG
1 ACCGAATGGAATACCTAATTCCTTGG
19726007 ACCGAATGGAATACCTAATTCCTTGG
1 ACCGAATGGAATACCTAATTCCTTGG
19726033 CTTTCTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (26 bp):
ACCGAATGGAATACCTAATTCCTTGG
Found at i:19727807 original size:30 final size:30
Alignment explanation
Indices: 19727772--19727828 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
19727762 CACACAAGTG
*
19727772 TGTTTCTAGGAC-GTGTGTGAGACACGGGCA
1 TGTTTCTAGG-CTGTGTGTGACACACGGGCA
19727802 TGTTTCTAGGCTGTGTGTGACACACGG
1 TGTTTCTAGGCTGTGTGTGACACACGG
19727829 CTTGCCCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.30
Consensus pattern (30 bp):
TGTTTCTAGGCTGTGTGTGACACACGGGCA
Found at i:19739094 original size:6 final size:6
Alignment explanation
Indices: 19739076--19739175 Score: 62
Period size: 6 Copynumber: 16.3 Consensus size: 6
19739066 AAGAAACATT
* * *
19739076 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATCAAA ATTAGT ATCAGGTA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A
* * * * *
19739126 A-CAGA ATCAAA ATTAGA ATCGGT ATCAGGTA A-CAGA ATCAAA ATCAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA
19739174 AT
1 AT
19739176 GTGAATGCAA
Statistics
Matches: 70, Mismatches: 16, Indels: 16
0.69 0.16 0.16
Matches are distributed among these distances:
5 5 0.07
6 56 0.80
7 7 0.10
8 2 0.03
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.21
Consensus pattern (6 bp):
ATCAGA
Found at i:19739175 original size:31 final size:31
Alignment explanation
Indices: 19739096--19739175 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
19739086 GAATCAGAAT
* * *
19739096 CAGAATCAGAATCAAAATTAGTATCAGGTAA
1 CAGAATCAAAATCAGAATCAGTATCAGGTAA
* *
19739127 CAGAATCAAAATTAGAATCGGTATCAGGTAA
1 CAGAATCAAAATCAGAATCAGTATCAGGTAA
19739158 CAGAATCAAAATCAGAAT
1 CAGAATCAAAATCAGAAT
19739176 GTGAATGCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.21
Consensus pattern (31 bp):
CAGAATCAAAATCAGAATCAGTATCAGGTAA
Found at i:19739341 original size:25 final size:26
Alignment explanation
Indices: 19739307--19739406 Score: 114
Period size: 27 Copynumber: 3.8 Consensus size: 26
19739297 GCTCAGTTAT
*
19739307 CAGATATTGT-G-ATAGTCACCAGATA
1 CAGATATTGTGGCATAGCCACCAGA-A
*
19739332 CAGATATTGTGGCAGAGCCACCAGAA
1 CAGATATTGTGGCATAGCCACCAGAA
19739358 CAGATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGGCATAGCCACCAG-AA
* * *
19739386 CAAATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCATAGCCAC
19739407 TTAACAGAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.15
26 8 0.12
27 40 0.62
28 7 0.11
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (26 bp):
CAGATATTGTGGCATAGCCACCAGAA
Found at i:19739397 original size:54 final size:51
Alignment explanation
Indices: 19739307--19739406 Score: 128
Period size: 54 Copynumber: 1.9 Consensus size: 51
19739297 GCTCAGTTAT
* * * * *
19739307 CAGATATTGTGATAGTCACCAGATACAGATATTGTGGCAGAGCCACCAGAA
1 CAGATATTGTGATAGCCACCAGAAACAAATAATGTGGCAAAGCCACCAGAA
19739358 CAGATATTTGTGGCATAGCCACCAGAAACAAATAATGTGGCAAAGCCAC
1 CAGATA-TTGT-G-ATAGCCACCAGAAACAAATAATGTGGCAAAGCCAC
19739407 TTAACAGAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
51 6 0.15
52 4 0.10
53 1 0.02
54 30 0.73
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (51 bp):
CAGATATTGTGATAGCCACCAGAAACAAATAATGTGGCAAAGCCACCAGAA
Found at i:19739598 original size:22 final size:23
Alignment explanation
Indices: 19739564--19739625 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 23
19739554 GCAAATACGT
*
19739564 TTGGCACACAGCCATAAT-TAGG
1 TTGGCACAAAGCCATAATGTAGG
* *
19739586 TTGGCATAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAATGTAGG
*
19739608 TTGACACAAAGCCATAAT
1 TTGGCACAAAGCCATAAT
19739626 CAGAAGGCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 2 0.06
22 29 0.88
23 2 0.06
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (23 bp):
TTGGCACAAAGCCATAATGTAGG
Found at i:19742500 original size:22 final size:22
Alignment explanation
Indices: 19742472--19742594 Score: 69
Period size: 22 Copynumber: 5.3 Consensus size: 22
19742462 ACAAGCATAT
19742472 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
19742494 ATGTGATGAATGTGACC--AT-G-CA
1 ATGTGAT-AA-G-G-CCGAATGGCCA
19742516 TATGTGTGATAAGGCCGAATGGCCA
1 -A--TGTGATAAGGCCGAATGGCCA
* * *
19742541 ATGTGATGAATG-TGAACAT-GCATA
1 ATGTGAT-AAGGCCG-A-ATGGC-CA
19742565 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
19742588 ATGTGAT
1 ATGTGAT
19742595 GAATGTGAAC
Statistics
Matches: 77, Mismatches: 6, Indels: 36
0.65 0.05 0.30
Matches are distributed among these distances:
21 2 0.03
22 24 0.31
23 16 0.21
24 16 0.21
25 17 0.22
26 2 0.03
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:19742679 original size:47 final size:47
Alignment explanation
Indices: 19742400--19742664 Score: 406
Period size: 47 Copynumber: 5.6 Consensus size: 47
19742390 TTAGGATTTT
** * *
19742400 ATGTGATGAATGTGAATGTGTATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
19742447 ATGTGATGAATATGAACAAGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
19742494 ATGTGATGAATGTGACCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
19742541 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
19742588 ATGTGATGAATGTGAACATGCATTTATGTGATAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
19742635 ATGTGATGAACGTGAA-AGTGTATATATGTG
1 ATGTGATGAATGTGAACA-TGCATATATGTG
19742665 GCGAAGCCGA
Statistics
Matches: 200, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
46 1 0.00
47 199 1.00
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:19742711 original size:46 final size:46
Alignment explanation
Indices: 19742658--19742748 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
19742648 GAAAGTGTAT
* * *
19742658 ATATGTGGCGAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGCAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
* * * *
19742704 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGCAAAGCCAAATGGCTAATGCGAAACATGTATGAGATG
19742749 TGTATATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.33, C:0.10, G:0.32, T:0.25
Consensus pattern (46 bp):
ATATGTGGCAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
Found at i:19744210 original size:27 final size:27
Alignment explanation
Indices: 19744125--19744426 Score: 376
Period size: 27 Copynumber: 11.3 Consensus size: 27
19744115 AGGGCAAAAT
* * *
19744125 GGTAATTTTACCCCACA-AGGTATCTT-
1 GGTAATTCTACCCTACAGGGGTAT-TTC
* *
19744151 GGTAATTCCACCCTACAGGGGT-TTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
19744177 AGTAATTCTACCTTATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
19744204 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
19744231 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
19744258 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
19744285 GGTTATTCTACCCTACAGGGGTAATTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
19744312 GATAATTCTAACCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
19744339 GGTAATTCTACCCTATAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
19744366 GGTAATTCTACCCTATAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
19744393 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
19744420 GGTAATT
1 GGTAATT
19744427 TTATAAGCCA
Statistics
Matches: 243, Mismatches: 30, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
25 2 0.01
26 33 0.14
27 208 0.86
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:19744451 original size:81 final size:80
Alignment explanation
Indices: 19744195--19744453 Score: 274
Period size: 81 Copynumber: 3.2 Consensus size: 80
19744185 TACCTTATAG
** * * *
19744195 GGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTTGG
1 GGGTATTTCGGTAATTCTACCCTACAGGGGTATTCCAGTAATTCTACCCTACAGGGGTATTTCGG
* *
19744260 TAATTCTA-CCCTACAA
66 TAATTTTATACC--CAA
* * * *
19744276 GGGTATTTCGGTTATTCTACCCTACAGGGGTAATTCGA-TAATTCTAACCTACAGGGGTATTCCG
1 GGGTATTTCGGTAATTCTACCCTACAGGGGT-ATTCCAGTAATTCTACCCTACAGGGGTATTTCG
*
19744340 GTAA--TTCTACCCTATA
65 GTAATTTTATACCC-A-A
* *
19744356 GGGGTATTCCGGTAATTCTACCCTATAGGGGTATTCCAGTAATTCTACCCTACAGGGGTATTTCG
1 -GGGTATTTCGGTAATTCTACCCTACAGGGGTATTCCAGTAATTCTACCCTACAGGGGTATTTCG
*
19744421 GTAATTTTATAAGCCAA
65 GTAATTTTAT-ACCCAA
* *
19744438 GGGCATTTTGGTAATT
1 GGGTATTTCGGTAATT
19744454 TTACAAACAA
Statistics
Matches: 146, Mismatches: 23, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
78 1 0.01
79 2 0.01
80 8 0.05
81 124 0.85
82 4 0.03
83 4 0.03
84 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (80 bp):
GGGTATTTCGGTAATTCTACCCTACAGGGGTATTCCAGTAATTCTACCCTACAGGGGTATTTCGG
TAATTTTATACCCAA
Done.