Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 64 of 131
Found at i:21176865 original size:20 final size:22
Alignment explanation
Indices: 21176842--21176889 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
21176832 GAGCTGTTAC
21176842 AAAAATAA-T-CAAAATTCACT
1 AAAAATAATTGCAAAATTCACT
* *
21176862 AAAAATAATTGTAAAATTGACT
1 AAAAATAATTGCAAAATTCACT
21176884 AAAAAT
1 AAAAAT
21176890 TAACATGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 15 0.62
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAATAATTGCAAAATTCACT
Found at i:21179397 original size:24 final size:22
Alignment explanation
Indices: 21179356--21179399 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
21179346 CATTATTCAA
*
21179356 ATTTCATATACATGTATCATAC
1 ATTTCATATACATATATCATAC
21179378 ATTTCATATATCAATATATCAT
1 ATTTCATATA-C-ATATATCAT
21179400 GTAACATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 1 0.05
24 8 0.42
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.43
Consensus pattern (22 bp):
ATTTCATATACATATATCATAC
Found at i:21186777 original size:24 final size:22
Alignment explanation
Indices: 21186736--21186779 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
21186726 CATTATTCAA
*
21186736 ATTTCATATACATGTATCATAC
1 ATTTCATATACATATATCATAC
21186758 ATTTCATATATCAATATATCAT
1 ATTTCATATA-C-ATATATCAT
21186780 GTAACATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 1 0.05
24 8 0.42
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.43
Consensus pattern (22 bp):
ATTTCATATACATATATCATAC
Found at i:21189635 original size:25 final size:25
Alignment explanation
Indices: 21189570--21189635 Score: 59
Period size: 25 Copynumber: 2.6 Consensus size: 25
21189560 CGTTACATCA
21189570 TAAGCTC-CTCCGAGCTGAATAATAG
1 TAAGCTCTCT-CGAGCTGAATAATAG
*
21189595 TAAGCTCATGCT--AGCTGAAT-ATCGG
1 TAAGCTC-T-CTCGAGCTGAATAAT-AG
21189620 TAAGCTCTCTCGAGCT
1 TAAGCTCTCTCGAGCT
21189636 AAGAATCGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
23 2 0.06
24 3 0.09
25 27 0.79
28 2 0.06
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (25 bp):
TAAGCTCTCTCGAGCTGAATAATAG
Found at i:21189795 original size:20 final size:20
Alignment explanation
Indices: 21189756--21189792 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
21189746 GGAAATTACA
21189756 CAATTCACAAACATATAATT
1 CAATTCACAAACATATAATT
21189776 CAATTCA-AAACATATAA
1 CAATTCACAAACATATAA
21189793 ATTTACAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (20 bp):
CAATTCACAAACATATAATT
Found at i:21193148 original size:22 final size:22
Alignment explanation
Indices: 21193123--21193169 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
21193113 ACAAGATATA
*
21193123 TGGCAGTTTATATGCAATTATG
1 TGGCAGTTTATATACAATTATG
*
21193145 TGGCAGTTTATCTACAATTATG
1 TGGCAGTTTATATACAATTATG
21193167 TGG
1 TGG
21193170 TGGCTTGTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (22 bp):
TGGCAGTTTATATACAATTATG
Found at i:21200660 original size:50 final size:50
Alignment explanation
Indices: 21200605--21200857 Score: 296
Period size: 50 Copynumber: 5.1 Consensus size: 50
21200595 TATTCCAGAT
** * * **
21200605 ATGGTCTTACATGAGATTTCTCATATCGGTGCCCATTCCATGTCCAAGAC
1 ATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTCCAAGAC
* * *
21200655 ATGGTCTTAC-GGGGAACCTCTCATCTCGGTGCCAATGCCATGTCCCAA-AC
1 ATGGTCTTACATGAG-ACCTCTCATCTCGGTGCCAACGCCATGT-CCAAGAC
* *
21200705 ATGGTCTTACATGAGACCTCTTATCTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTCCAAGAC
* * * *
21200755 AAGGTCTTACATGGGACCCCTTATCTCGGTGCCAACAG-CATGTCCAAGAC
1 ATGGTCTTACATGAGACCTCTCATCTCGGTGCCAAC-GCCATGTCCAAGAC
* * *
21200805 ATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTCCAAGAC
21200855 ATG
1 ATG
21200858 CCAACGCCAT
Statistics
Matches: 178, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
49 6 0.03
50 165 0.93
51 7 0.04
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (50 bp):
ATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTCCAAGAC
Found at i:21200862 original size:22 final size:22
Alignment explanation
Indices: 21200834--21200879 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
21200824 CTTATCTCGG
21200834 TGCCAACGCCATGTCCCAGACA
1 TGCCAACGCCATGTCCCAGACA
21200856 TGCCAACGCCATGTCCCAGACA
1 TGCCAACGCCATGTCCCAGACA
21200878 TG
1 TG
21200880 GTCTTACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.39, G:0.20, T:0.15
Consensus pattern (22 bp):
TGCCAACGCCATGTCCCAGACA
Found at i:21217950 original size:88 final size:88
Alignment explanation
Indices: 21217796--21217971 Score: 262
Period size: 88 Copynumber: 2.0 Consensus size: 88
21217786 GATATTTTGG
* * *
21217796 CCTTGTGATCTTACGAGACTATTGGATATAGTTGCCATACCAAAGGATTGTGAGTACTTACCTTT
1 CCTTATGATCTTACGAGACCATTGGACATAGTTGCCATACCAAAGGATTGTGAGTACTTACCTTT
* *
21217861 GTGATGTGATTTTTAGGCGTTGA
66 GTAATATGATTTTTAGGCGTTGA
* * * *
21217884 CCTTATGATCTTATGAGACCATTGGACATAGTTGGCATACCATAGGATTGTGATTACTTACCTTT
1 CCTTATGATCTTACGAGACCATTGGACATAGTTGCCATACCAAAGGATTGTGAGTACTTACCTTT
*
21217949 GTAATATGATTTTTGGGCGTTGA
66 GTAATATGATTTTTAGGCGTTGA
21217972 GGCCCAGGGA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 78 1.00
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (88 bp):
CCTTATGATCTTACGAGACCATTGGACATAGTTGCCATACCAAAGGATTGTGAGTACTTACCTTT
GTAATATGATTTTTAGGCGTTGA
Found at i:21255368 original size:38 final size:38
Alignment explanation
Indices: 21255294--21255393 Score: 159
Period size: 38 Copynumber: 2.7 Consensus size: 38
21255284 TGCTCTCTTG
*
21255294 TTTCTTTTCTGTCAATTTGCT-CC-CAGTTTATTTTCT
1 TTTCTTTTCTGTCGATTTGCTCCCTCAGTTTATTTTCT
*
21255330 TTTCTTTTCTGTTGATTTGCTCCCTCAGTTTATTTTCT
1 TTTCTTTTCTGTCGATTTGCTCCCTCAGTTTATTTTCT
*
21255368 TTTCTTTTCTGCCGATTTGCTCCCTC
1 TTTCTTTTCTGTCGATTTGCTCCCTC
21255394 TGTCCCTCTG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 19 0.33
37 2 0.03
38 37 0.64
ACGTcount: A:0.08, C:0.25, G:0.10, T:0.57
Consensus pattern (38 bp):
TTTCTTTTCTGTCGATTTGCTCCCTCAGTTTATTTTCT
Found at i:21259251 original size:45 final size:44
Alignment explanation
Indices: 21259151--21259260 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
21259141 NNNNNCATTA
21259151 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
21259190 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
21259235 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
21259261 CCTCTAATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:21259260 original size:16 final size:16
Alignment explanation
Indices: 21259241--21259292 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
21259231 GATTTGCTAT
* *
21259241 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
21259257 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
21259273 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
21259289 TACA
1 TACA
21259293 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:21264235 original size:19 final size:19
Alignment explanation
Indices: 21264211--21264247 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
21264201 TAGACATAAT
21264211 TTTCTTTAAAAACTTGGCG
1 TTTCTTTAAAAACTTGGCG
21264230 TTTCTTTAAAAACTTGGC
1 TTTCTTTAAAAACTTGGC
21264248 TTACTTAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (19 bp):
TTTCTTTAAAAACTTGGCG
Found at i:21274443 original size:13 final size:13
Alignment explanation
Indices: 21274425--21274451 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21274415 CACAAACTTC
21274425 AAAGAAAAAAAGA
1 AAAGAAAAAAAGA
21274438 AAAGAAAAAAAGA
1 AAAGAAAAAAAGA
21274451 A
1 A
21274452 TCGACGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAGA
Found at i:21275804 original size:31 final size:32
Alignment explanation
Indices: 21275745--21275809 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
21275735 GGCAAATTAC
21275745 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
21275777 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
21275808 AA
1 AA
21275810 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:21277274 original size:20 final size:20
Alignment explanation
Indices: 21277228--21277286 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
21277218 GTATAAACTG
* *
21277228 TAATTCATTCATATAACCAG
1 TAATTCATTCATATAAACAA
* * *
21277248 TAGTTCATTCGTATAAATAA
1 TAATTCATTCATATAAACAA
*
21277268 TAATTCATCCATATAAACA
1 TAATTCATTCATATAAACA
21277287 CATATCTTAT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (20 bp):
TAATTCATTCATATAAACAA
Found at i:21277498 original size:23 final size:23
Alignment explanation
Indices: 21277470--21277589 Score: 102
Period size: 23 Copynumber: 5.1 Consensus size: 23
21277460 AGGCTCTATT
21277470 GAGCTGAAATGGTAAGCT-TTGAC
1 GAGCTGAAATGGTAAGCTCTT-AC
*
21277493 GAGCTGAACA--GTAAGCTCATAC
1 GAGCTGAA-ATGGTAAGCTCTTAC
* * *
21277515 GAGCTGAAACGGTAAGCTCTAAT
1 GAGCTGAAATGGTAAGCTCTTAC
* *
21277538 GAGCTGAAAATAGTAGGCTCTTAC
1 GAGCTG-AAATGGTAAGCTCTTAC
*
21277562 GAGCTGAAATATCGGTAAGCTCATAC
1 GAGCTG-AA-AT-GGTAAGCTCTTAC
21277588 GA
1 GA
21277590 ACTGTGGTGA
Statistics
Matches: 78, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
21 1 0.01
22 17 0.22
23 24 0.31
24 22 0.28
25 2 0.03
26 12 0.15
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (23 bp):
GAGCTGAAATGGTAAGCTCTTAC
Found at i:21277509 original size:22 final size:23
Alignment explanation
Indices: 21277491--21277589 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 23
21277481 GTAAGCTTTG
21277491 ACGAGCTG-AACAGTAAGCTCAT
1 ACGAGCTGAAACAGTAAGCTCAT
*
21277513 ACGAGCTGAAACGGTAAGCTC-T
1 ACGAGCTGAAACAGTAAGCTCAT
* * * *
21277535 AATGAGCTGAAAATAGTAGGCTCTT
1 -ACGAGCTG-AAACAGTAAGCTCAT
*
21277560 ACGAGCTGAAATATCGGTAAGCTCAT
1 ACGAGCTG-AA-A-CAGTAAGCTCAT
21277586 ACGA
1 ACGA
21277590 ACTGTGGTGA
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
22 9 0.15
23 18 0.30
24 20 0.33
25 2 0.03
26 12 0.20
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.21
Consensus pattern (23 bp):
ACGAGCTGAAACAGTAAGCTCAT
Found at i:21277519 original size:45 final size:46
Alignment explanation
Indices: 21277453--21277571 Score: 125
Period size: 45 Copynumber: 2.6 Consensus size: 46
21277443 CTAAGCTGAT
* * * *
21277453 AAACAGTAGGCTC-TATTGAGCTGAAATGGTAAGCTTTGACGAGCTG
1 AAACAGTAAGCTCATA-CGAGCTGAAATGGTAAGCTCTAACGAGCTG
* *
21277499 -AACAGTAAGCTCATACGAGCTGAAACGGTAAGCTCTAATGAGCTG
1 AAACAGTAAGCTCATACGAGCTGAAATGGTAAGCTCTAACGAGCTG
* * *
21277544 AAAATAGTAGGCTCTTACGAGCTGAAAT
1 -AAACAGTAAGCTCATACGAGCTGAAAT
21277572 ATCGGTAAGC
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
45 36 0.60
46 2 0.03
47 22 0.37
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (46 bp):
AAACAGTAAGCTCATACGAGCTGAAATGGTAAGCTCTAACGAGCTG
Found at i:21277821 original size:67 final size:67
Alignment explanation
Indices: 21277740--21278125 Score: 555
Period size: 67 Copynumber: 5.8 Consensus size: 67
21277730 AATAATTCAA
* * *
21277740 TTTCTCAAATCACATATATATAATCTATTCAATTAAATACATACATTTAAATACTCAATTTGCAT
1 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
21277805 AC
66 AC
* * * * * *
21277807 CTTCCCAAATCACATATATATAATCGATTTAATTAAATACATACATTTCAATACTCAATTCGCAT
1 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
21277872 AC
66 AC
* * *
21277874 TTTCTCAAAT--CATATATATTATCAATTCAATTAAATACATACATTTAATTACTCAATTCGCAT
1 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
21277937 AC
66 AC
* * *
21277939 TTTCTC-AATCACATACATATAATCGATTTAATTAAATACATACATTTCAATACTCAATTCGCAT
1 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
21278003 AC
66 AC
* * * *
21278005 TTTCTCAAATCATATACATATAATCAATTAAATTAAATACATACATTTAATTACTCAATTC-CCT
1 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
21278069 AC
66 AC
* *
21278071 TTTCTCAAATCACATGCATATAATCAATTGAATTAAATACATACATTTAAATACT
1 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACT
21278126 ATTGCAATTT
Statistics
Matches: 287, Mismatches: 29, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
64 3 0.01
65 56 0.20
66 110 0.38
67 118 0.41
ACGTcount: A:0.41, C:0.19, G:0.02, T:0.37
Consensus pattern (67 bp):
TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
AC
Found at i:21281001 original size:27 final size:27
Alignment explanation
Indices: 21280962--21281094 Score: 147
Period size: 27 Copynumber: 5.1 Consensus size: 27
21280952 CTATTCAGTA
*
21280962 ACAGTACAGTGTGGGCCTTAGCCCAAT
1 ACAGTACAATGTGGGCCTTAGCCCAAT
21280989 ACAGTACAATGT-GGCCTTAGCCCAAT
1 ACAGTACAATGTGGGCCTTAGCCCAAT
21281015 ACAGTAACAATGT-GG-----GCCCAAT
1 ACAGT-ACAATGTGGGCCTTAGCCCAAT
* *
21281037 GCAGTA-ATATGTGGGTCTTAGCCCAAT
1 ACAGTACA-ATGTGGGCCTTAGCCCAAT
*
21281064 ACAGTAACAATGTGGGCCTTCGCCCAAT
1 ACAGT-ACAATGTGGGCCTTAGCCCAAT
21281092 ACA
1 ACA
21281095 ATATCGGTAC
Statistics
Matches: 91, Mismatches: 5, Indels: 19
0.79 0.04 0.17
Matches are distributed among these distances:
20 1 0.01
21 5 0.05
22 13 0.14
26 19 0.21
27 31 0.34
28 21 0.23
29 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (27 bp):
ACAGTACAATGTGGGCCTTAGCCCAAT
Found at i:21281042 original size:48 final size:49
Alignment explanation
Indices: 21280982--21281081 Score: 159
Period size: 49 Copynumber: 2.1 Consensus size: 49
21280972 GTGGGCCTTA
21280982 GCCCAATACAGTACA-ATGT-GGCCTTAGCCCAATACAGTAACAATGTGG
1 GCCCAATACAGTA-ATATGTGGGCCTTAGCCCAATACAGTAACAATGTGG
* *
21281030 GCCCAATGCAGTAATATGTGGGTCTTAGCCCAATACAGTAACAATGTGG
1 GCCCAATACAGTAATATGTGGGCCTTAGCCCAATACAGTAACAATGTGG
21281079 GCC
1 GCC
21281082 TTCGCCCAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
47 1 0.02
48 16 0.33
49 31 0.65
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Consensus pattern (49 bp):
GCCCAATACAGTAATATGTGGGCCTTAGCCCAATACAGTAACAATGTGG
Found at i:21281235 original size:26 final size:26
Alignment explanation
Indices: 21281205--21281305 Score: 130
Period size: 26 Copynumber: 3.9 Consensus size: 26
21281195 AACACACCAA
* * * *
21281205 TATCGCAGAAAAGCTGCCAATAATAT
1 TATCGCAGCAAAGCTGCCAGTAACAG
* *
21281231 TATCGCAGCGAAGCTGCTAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
* *
21281257 TATCTCAGCGAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
21281283 TATCGCAGCAAAGCTGCCAGTAA
1 TATCGCAGCAAAGCTGCCAGTAA
21281306 TAGTGTACTT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 65 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAACAG
Found at i:21281536 original size:27 final size:27
Alignment explanation
Indices: 21281475--21281760 Score: 266
Period size: 27 Copynumber: 10.3 Consensus size: 27
21281465 AGGTATAACA
*
21281475 GTCATATTACCCTATAGGGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGGTATTTCG
* * *
21281503 GTTATTTTACCCTATGGGAGTAATTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
21281530 GTCATTTTACCCTATGGGGGTATTGCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
21281557 GTCATTTTACCTTATGGGTGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * * *
21281584 ATTATTTTACTCTACGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
21281611 GTCATTTTACCCTACGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
*** *
21281638 GTCATTTTACCCTAAACCCTACAAAGGTATTTCA
1 GTCATTTTACCCT--A---T--GGGGGTATTTCG
* *
21281672 GTCATTTTACCCTATAGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
21281699 GTCATATTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
21281726 GTCATTTTACCCTATGGAGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
21281753 GTTATTTT
1 GTCATTTT
21281761 TTTCTACAGG
Statistics
Matches: 212, Mismatches: 39, Indels: 15
0.80 0.15 0.06
Matches are distributed among these distances:
27 175 0.83
28 13 0.06
29 2 0.01
32 1 0.00
34 21 0.10
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:21281667 original size:34 final size:34
Alignment explanation
Indices: 21281619--21281685 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
21281609 CAGTCATTTT
* * **
21281619 ACCCTACGAGGGTATTTTGGTCATTTTACCCTAA
1 ACCCTACAAAGGTATTTCAGTCATTTTACCCTAA
21281653 ACCCTACAAAGGTATTTCAGTCATTTTACCCTA
1 ACCCTACAAAGGTATTTCAGTCATTTTACCCTA
21281686 TAGGGGTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.34
Consensus pattern (34 bp):
ACCCTACAAAGGTATTTCAGTCATTTTACCCTAA
Found at i:21282486 original size:24 final size:22
Alignment explanation
Indices: 21282461--21282507 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
21282451 CCCAAATCCC
21282461 AATATTCCCTCCTCGAATCTCTCCA
1 AATA-TCCCTCCTC-AAT-TCTCCA
*
21282486 AATATCTCTCCTCAATTCTCCA
1 AATATCCCTCCTCAATTCTCCA
21282508 GTGTAAACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 3 0.14
24 8 0.38
25 4 0.19
ACGTcount: A:0.26, C:0.38, G:0.02, T:0.34
Consensus pattern (22 bp):
AATATCCCTCCTCAATTCTCCA
Found at i:21284338 original size:40 final size:40
Alignment explanation
Indices: 21284277--21284513 Score: 291
Period size: 40 Copynumber: 5.9 Consensus size: 40
21284267 CGATTGAAAT
* * * *
21284277 TACCAAAGTATAAACTA-GGGCACGTATGTGCAATCAAGAG
1 TACCGAAGTACAAAC-AGGGGCACATATGTGCAATCAAGGG
*
21284317 TACCGAAGTACAAACAGGGGCACATATGTACAATC-AGGG
1 TACCGAAGTACAAACAGGGGCACATATGTGCAATCAAGGG
* *
21284356 ATA-CGAAAGTACAAACAAGGGCACATATGTGCAATCAGGGG
1 -TACCG-AAGTACAAACAGGGGCACATATGTGCAATCAAGGG
* * * *
21284397 TACCGAAGTACAAATAGAGGCACGTATGTGCAATTAAGGG
1 TACCGAAGTACAAACAGGGGCACATATGTGCAATCAAGGG
* * *
21284437 TACCAAAGTACAAACAGGAGCACATATGTGCAATCAGGGG
1 TACCGAAGTACAAACAGGGGCACATATGTGCAATCAAGGG
*
21284477 TACCGAAGTACAAACAGGGGCACGTATGTGCAATCAA
1 TACCGAAGTACAAACAGGGGCACATATGTGCAATCAA
21284514 TATAATTAAC
Statistics
Matches: 167, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
39 6 0.04
40 156 0.93
41 5 0.03
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (40 bp):
TACCGAAGTACAAACAGGGGCACATATGTGCAATCAAGGG
Found at i:21284349 original size:20 final size:20
Alignment explanation
Indices: 21284324--21284505 Score: 80
Period size: 20 Copynumber: 9.1 Consensus size: 20
21284314 GAGTACCGAA
21284324 GTACAAACAGGGGCACATAT
1 GTACAAACAGGGGCACATAT
* ** *
21284344 GTACAATCAGGGATACGA-AA
1 GTACAAACAGGGGCAC-ATAT
*
21284364 GTACAAACAAGGGCACATAT
1 GTACAAACAGGGGCACATAT
* * * ** *
21284384 GTGCAATCAGGGGTACCGAA
1 GTACAAACAGGGGCACATAT
* * *
21284404 GTACAAATAGAGGCACGTAT
1 GTACAAACAGGGGCACATAT
* ** * * *
21284424 GTGCAATTAAGGGTACCA-AA
1 GTACAAACAGGGGCA-CATAT
*
21284444 GTACAAACAGGAGCACATAT
1 GTACAAACAGGGGCACATAT
* * * ** *
21284464 GTGCAATCAGGGGTACCGAA
1 GTACAAACAGGGGCACATAT
*
21284484 GTACAAACAGGGGCACGTAT
1 GTACAAACAGGGGCACATAT
21284504 GT
1 GT
21284506 GCAATCAATA
Statistics
Matches: 107, Mismatches: 51, Indels: 8
0.64 0.31 0.05
Matches are distributed among these distances:
19 3 0.03
20 102 0.95
21 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.16
Consensus pattern (20 bp):
GTACAAACAGGGGCACATAT
Found at i:21284419 original size:80 final size:78
Alignment explanation
Indices: 21284277--21284512 Score: 337
Period size: 80 Copynumber: 3.0 Consensus size: 78
21284267 CGATTGAAAT
* * * * *
21284277 TACCAAAGTATAAACTAGGGCACGTATGTGCAATCAAGAGTACCGAAGTACAAACAGGGGCACAT
1 TACCAAAGTACAAAC-AGGGCACATATGTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGT
*
21284342 ATGTACAATCAGGG
65 ATGTGCAATCAGGG
* * *
21284356 ATACGAAAGTACAAACAAGGGCACATATGTGCAATCAGGGGTACCGAAGTACAAATAGAGGCACG
1 -TACCAAAGTACAAAC-AGGGCACATATGTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACG
*
21284421 TATGTGCAATTAAGGG
64 TATGTGCAA-TCAGGG
21284437 TACCAAAGTACAAACAGGAGCACATATGTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGT
1 TACCAAAGTACAAACAGG-GCACATATGTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGT
21284502 ATGTGCAATCA
65 ATGTGCAATCA
21284513 ATATAATTAA
Statistics
Matches: 139, Mismatches: 15, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
79 5 0.04
80 129 0.93
81 5 0.04
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (78 bp):
TACCAAAGTACAAACAGGGCACATATGTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTA
TGTGCAATCAGGG
Found at i:21284498 original size:120 final size:120
Alignment explanation
Indices: 21284277--21284512 Score: 350
Period size: 120 Copynumber: 2.0 Consensus size: 120
21284267 CGATTGAAAT
* * *
21284277 TACCAAAGTATAAACTAGGGCACGTATGTGCAATCAAGAGTACCGAAGTACAAACAGGGGCACAT
1 TACCAAAGTACAAACTAGGGCACGTATGTGCAATCAAGAGTACCAAAGTACAAACAGGAGCACAT
21284342 ATGTACAATCAGGGATACGAAAGTACAAACAAGGGCACATATGTGCAATCAGGGG
66 ATGTACAATCAGGGATACGAAAGTACAAACAAGGGCACATATGTGCAATCAGGGG
* * *
21284397 TACCGAAGTACAAA-TAGAGGCACGTATGTGCAATTAAGGGTACCAAAGTACAAACAGGAGCACA
1 TACCAAAGTACAAACTAG-GGCACGTATGTGCAATCAAGAGTACCAAAGTACAAACAGGAGCACA
* * * *
21284461 TATGTGCAATCAGGGGTACCG-AAGTACAAACAGGGGCACGTATGTGCAATCA
65 TATGTACAATCAGGGATA-CGAAAGTACAAACAAGGGCACATATGTGCAATCA
21284513 ATATAATTAA
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
119 3 0.03
120 99 0.95
121 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (120 bp):
TACCAAAGTACAAACTAGGGCACGTATGTGCAATCAAGAGTACCAAAGTACAAACAGGAGCACAT
ATGTACAATCAGGGATACGAAAGTACAAACAAGGGCACATATGTGCAATCAGGGG
Found at i:21287670 original size:15 final size:15
Alignment explanation
Indices: 21287650--21287679 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21287640 ATTATCGTTG
*
21287650 AGACCATGATCATTC
1 AGACCAGGATCATTC
21287665 AGACCAGGATCATTC
1 AGACCAGGATCATTC
21287680 TGTTCTTTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (15 bp):
AGACCAGGATCATTC
Found at i:21309253 original size:26 final size:27
Alignment explanation
Indices: 21309204--21309254 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
21309194 TTCTTCTCTC
21309204 TTTTCTGTTATTTGCTTGCTAGTTTCA
1 TTTTCTGTTATTTGCTTGCTAGTTTCA
21309231 TTTTCTGTT-TTTGCTT-CTGAGTTT
1 TTTTCTGTTATTTGCTTGCT-AGTTT
21309255 GTTTCTTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 2 0.09
26 12 0.52
27 9 0.39
ACGTcount: A:0.08, C:0.14, G:0.16, T:0.63
Consensus pattern (27 bp):
TTTTCTGTTATTTGCTTGCTAGTTTCA
Found at i:21316560 original size:15 final size:15
Alignment explanation
Indices: 21316540--21316575 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
21316530 ATTAATTAAT
21316540 GTTTGATATGAATAA
1 GTTTGATATGAATAA
21316555 GTTTGATATGAATAA
1 GTTTGATATGAATAA
21316570 GTTTGA
1 GTTTGA
21316576 CATTAAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (15 bp):
GTTTGATATGAATAA
Found at i:21329890 original size:25 final size:25
Alignment explanation
Indices: 21329857--21329909 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
21329847 TGAAAGCCGA
* *
21329857 AAAACATCAAGGATCTGCTTATCTG
1 AAAACATCAAGGATCTACTTATCCG
21329882 AAAACATCAAGGATCTACTTATCCG
1 AAAACATCAAGGATCTACTTATCCG
21329907 AAA
1 AAA
21329910 GCACAAGTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.25
Consensus pattern (25 bp):
AAAACATCAAGGATCTACTTATCCG
Found at i:21332501 original size:156 final size:157
Alignment explanation
Indices: 21332221--21332534 Score: 540
Period size: 156 Copynumber: 2.0 Consensus size: 157
21332211 CAAGAAACAT
* *
21332221 AATCATAGTGAGTTAGTCCAGTATGTTGTTCTCTAACACATACTCATGCATCAATTTTGACATCC
1 AATCATAGTGAGTTAGTCCAGTATGTTGTTCTCTAACACATACTCATGAATCAATCTTGACATCC
*
21332286 CTGTGTCAATGAAAACACTTTGCCATCAATCAACTACACATTAGCCTCAATGCATTATCATTGTT
66 CTATGTCAATGAAAACACTTTGCCATCAATCAACTACACATTAGCCTCAATGCATTATCATTGTT
*
21332351 CAAGCCCACAATAATACTTAACTAAGG
131 CAAACCCACAATAATACTTAACTAAGG
* *
21332378 AATCATAGTGAGTTAGTCCAGTATGTTGTTCTCTAATACATACTCATGAATCGATCTTGACATCC
1 AATCATAGTGAGTTAGTCCAGTATGTTGTTCTCTAACACATACTCATGAATCAATCTTGACATCC
**
21332443 CTATG-CAATGAAAACACTTTGTTATCAATCAACTACACATTAGCCTCAATGCATTATCATTGTT
66 CTATGTCAATGAAAACACTTTGCCATCAATCAACTACACATTAGCCTCAATGCATTATCATTGTT
*
21332507 CAAACCCACAATAATACTTGACTAAGG
131 CAAACCCACAATAATACTTAACTAAGG
21332534 A
1 A
21332535 CATTTTAAGA
Statistics
Matches: 148, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
156 83 0.56
157 65 0.44
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.32
Consensus pattern (157 bp):
AATCATAGTGAGTTAGTCCAGTATGTTGTTCTCTAACACATACTCATGAATCAATCTTGACATCC
CTATGTCAATGAAAACACTTTGCCATCAATCAACTACACATTAGCCTCAATGCATTATCATTGTT
CAAACCCACAATAATACTTAACTAAGG
Found at i:21333393 original size:19 final size:20
Alignment explanation
Indices: 21333365--21333408 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
21333355 AATAAAATAA
21333365 TTTCTGGAAAATAATTTACT
1 TTTCTGGAAAATAATTTACT
*
21333385 TTTCT-GAAAATGATTTACT
1 TTTCTGGAAAATAATTTACT
21333404 TTTCT
1 TTTCT
21333409 AGTGTTTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATAATTTACT
Found at i:21336664 original size:16 final size:16
Alignment explanation
Indices: 21336643--21336680 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
21336633 TTTTTTATGC
*
21336643 TTAAAACTGATTGTTA
1 TTAAAACTAATTGTTA
*
21336659 TTAAAATTAATTGTTA
1 TTAAAACTAATTGTTA
21336675 TTAAAA
1 TTAAAA
21336681 TTATATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (16 bp):
TTAAAACTAATTGTTA
Found at i:21336681 original size:16 final size:16
Alignment explanation
Indices: 21336652--21336683 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
21336642 CTTAAAACTG
21336652 ATTGTTATTAAAATTA
1 ATTGTTATTAAAATTA
21336668 ATTGTTATTAAAATTA
1 ATTGTTATTAAAATTA
21336684 TATCAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
ATTGTTATTAAAATTA
Found at i:21338193 original size:25 final size:26
Alignment explanation
Indices: 21338165--21338224 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 26
21338155 AACTAAGCAG
21338165 AATACAGATTGAACATACAACCCA-A
1 AATACAGATTGAACATACAACCCAGA
* *
21338190 AATACAAATTGAACATACAATCCAGA
1 AATACAGATTGAACATACAACCCAGA
21338216 AA-ACAGATT
1 AATACAGATT
21338225 CCAAAATTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 28 0.90
26 3 0.10
ACGTcount: A:0.53, C:0.20, G:0.08, T:0.18
Consensus pattern (26 bp):
AATACAGATTGAACATACAACCCAGA
Found at i:21350051 original size:5 final size:5
Alignment explanation
Indices: 21350043--21350099 Score: 57
Period size: 5 Copynumber: 11.6 Consensus size: 5
21350033 TTAGTTTATT
* *
21350043 TAATA TAATA TAATA TAACA TAATA TATTATA TTATA TAATA -AA-A TAATA
1 TAATA TAATA TAATA TAATA TAATA TA--ATA TAATA TAATA TAATA TAATA
21350093 T-ATA TAA
1 TAATA TAA
21350100 AACATAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
3 1 0.02
4 8 0.19
5 30 0.70
7 4 0.09
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:21352562 original size:16 final size:17
Alignment explanation
Indices: 21352529--21352563 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21352519 TGGCATTTCT
*
21352529 AAATTTAGTTTATTAAC
1 AAATTTAGCTTATTAAC
21352546 AAATTTAGCTT-TTAAC
1 AAATTTAGCTTATTAAC
21352562 AA
1 AA
21352564 TTATTCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (17 bp):
AAATTTAGCTTATTAAC
Found at i:21376460 original size:28 final size:28
Alignment explanation
Indices: 21376423--21376517 Score: 127
Period size: 28 Copynumber: 3.4 Consensus size: 28
21376413 ATACAACATG
* * * *
21376423 CAGTAGCAGTCTGGGCCTAAGCCCTATA
1 CAGTAACAGTATGGGCCTTAGCCCAATA
*
21376451 CAGCAACAGTATGGGCCTTAGCCCAATA
1 CAGTAACAGTATGGGCCTTAGCCCAATA
* *
21376479 TAGTAACAGTGTGGGCCTTAGCCCAATA
1 CAGTAACAGTATGGGCCTTAGCCCAATA
21376507 CAGTAACAGTA
1 CAGTAACAGTA
21376518 CAATGCTGTA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (28 bp):
CAGTAACAGTATGGGCCTTAGCCCAATA
Found at i:21376679 original size:26 final size:26
Alignment explanation
Indices: 21376622--21376698 Score: 91
Period size: 26 Copynumber: 3.0 Consensus size: 26
21376612 ACACCAATAT
* * *
21376622 CACAGCAAGGCTGCCAGTAATAGTGA
1 CACAGCAAAGCTGCCAGTAACAGTAA
**
21376648 TGCAGCAAAGCTGCCAGTAACAGTAA
1 CACAGCAAAGCTGCCAGTAACAGTAA
* *
21376674 CACAGCAAAGTTACCAGTAACAGTA
1 CACAGCAAAGCTGCCAGTAACAGTA
21376699 TATGTGGCAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.39, C:0.23, G:0.22, T:0.16
Consensus pattern (26 bp):
CACAGCAAAGCTGCCAGTAACAGTAA
Found at i:21376949 original size:27 final size:27
Alignment explanation
Indices: 21376876--21376952 Score: 109
Period size: 27 Copynumber: 2.9 Consensus size: 27
21376866 GGTATAACAA
* * *
21376876 TCATTTTACTCTTCAGGGGCATTTCGG
1 TCATTTTACCCTTCGGGGGTATTTCGG
* *
21376903 TCATTTTACCCTTCGAGGGTATTTTGG
1 TCATTTTACCCTTCGGGGGTATTTCGG
21376930 TCATTTTACCCTTCGGGGGTATT
1 TCATTTTACCCTTCGGGGGTATT
21376953 GAGATGAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.43
Consensus pattern (27 bp):
TCATTTTACCCTTCGGGGGTATTTCGG
Found at i:21376998 original size:23 final size:23
Alignment explanation
Indices: 21376964--21377014 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
21376954 AGATGAATAT
*
21376964 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
21376987 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
21377010 AGTAA
1 TGTAA
21377015 GAAAGTTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:21379872 original size:50 final size:50
Alignment explanation
Indices: 21379770--21380307 Score: 722
Period size: 50 Copynumber: 10.6 Consensus size: 50
21379760 TGTGAGCCAG
* * *
21379770 TGTAAGACAATGTTTGGGACATGGCATTGGCATCATTGAGATTACGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAGA-T--GAGAGGTCCCA
* * *
21379826 TATAAGACCATGTTTGGGACATGGCATTGGCATCGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* *
21379876 TGTAAGACCATGTCTGAGACATGGCATTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
21379926 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* *
21379976 TGTAAGACCATGTCTAGGACATGGCCTTGGCACCGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* * *
21380026 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATTAGAGGTCTCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* *
21380076 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGCGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
*
21380126 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* * *
21380176 TGTAAGACCATGTCTAGGACATGCCGTTGGCACC-AGGATGAGAGGCCTCCC-
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGA-GATGAGAGG--TCCCA
* * * **
21380227 -GTAAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAACTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* * * *
21380276 TGTAAGACCATATCTAGGATATGACATTGGCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCA
21380308 GTACAGGAAA
Statistics
Matches: 439, Mismatches: 37, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
48 4 0.01
49 1 0.00
50 394 0.90
51 1 0.00
52 5 0.01
53 4 0.01
56 30 0.07
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.22
Consensus pattern (50 bp):
TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
Found at i:21381871 original size:23 final size:23
Alignment explanation
Indices: 21381835--21381878 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
21381825 GGGATAAATG
*
21381835 TAATATCCCAAAAATTACTACTA
1 TAATACCCCAAAAATTACTACTA
*
21381858 TAATACCCCGAAAATTACTAC
1 TAATACCCCAAAAATTACTAC
21381879 AGTAAGAAAA
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:0.45, C:0.25, G:0.02, T:0.27
Consensus pattern (23 bp):
TAATACCCCAAAAATTACTACTA
Found at i:21387311 original size:16 final size:17
Alignment explanation
Indices: 21387284--21387318 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
21387274 ATACCCCTTT
21387284 CACCTATTCATTCAACA
1 CACCTATTCATTCAACA
*
21387301 CACCT-TTCATTCCACA
1 CACCTATTCATTCAACA
21387317 CA
1 CA
21387319 TTTCTCTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.31, C:0.40, G:0.00, T:0.29
Consensus pattern (17 bp):
CACCTATTCATTCAACA
Found at i:21398418 original size:18 final size:18
Alignment explanation
Indices: 21398395--21398430 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
21398385 CCAACTTAAC
21398395 TTACTATAAGCTAATAAG
1 TTACTATAAGCTAATAAG
21398413 TTACTATAAGCTAATAAG
1 TTACTATAAGCTAATAAG
21398431 AGCAAGAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (18 bp):
TTACTATAAGCTAATAAG
Found at i:21401545 original size:16 final size:15
Alignment explanation
Indices: 21401511--21401551 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
21401501 GGTGATAATA
21401511 ATTAATATATAATTAT
1 ATTAAT-TATAATTAT
*
21401527 ATTTATTATAATGTAT
1 ATTAATTATAAT-TAT
21401543 ATTAATTAT
1 ATTAATTAT
21401552 TATCAACTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTAATTATAATTAT
Found at i:21409802 original size:18 final size:18
Alignment explanation
Indices: 21409779--21409814 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
21409769 CCAACTTAAC
21409779 TTACTATAAGCTAATAAG
1 TTACTATAAGCTAATAAG
21409797 TTACTATAAGCTAATAAG
1 TTACTATAAGCTAATAAG
21409815 AGCAAGAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (18 bp):
TTACTATAAGCTAATAAG
Found at i:21438432 original size:50 final size:51
Alignment explanation
Indices: 21438343--21438526 Score: 156
Period size: 50 Copynumber: 3.5 Consensus size: 51
21438333 TTGTACTACT
* * * * * **
21438343 AATGACATATCCCAGATATGGTCTTAAATGGGAGTTCTCATATCGGTGTCC
1 AATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGTCC
* * *
21438394 -ATTCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTG-CC
1 AATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGTCC
* * * * * **
21438443 AACGCCATGTCTCGGACATTGTCTTACATGGGACCTCTCATAATCTCAATGATGCC
1 AATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCAT-A--TCGGTG-T-CC
21438499 AATGCCATGTCCCAGACATGGTCTTACA
1 AATGCCATGTCCCAGACATGGTCTTACA
21438527 TGAGATCTCT
Statistics
Matches: 102, Mismatches: 24, Indels: 9
0.76 0.18 0.07
Matches are distributed among these distances:
49 2 0.02
50 70 0.69
53 4 0.04
56 26 0.25
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (51 bp):
AATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGTCC
Found at i:21451110 original size:20 final size:20
Alignment explanation
Indices: 21451085--21451135 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
21451075 CATTTTTGGT
*
21451085 TCATTCGAGCTCAAGTTAGC
1 TCATTCGAGCTCAAGTCAGC
21451105 TCATTCGAGCTCAAGTCAGC
1 TCATTCGAGCTCAAGTCAGC
*
21451125 ACATT-GAGCTC
1 TCATTCGAGCTC
21451136 GTTATTAGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (20 bp):
TCATTCGAGCTCAAGTCAGC
Found at i:21451415 original size:41 final size:41
Alignment explanation
Indices: 21451358--21451465 Score: 180
Period size: 41 Copynumber: 2.6 Consensus size: 41
21451348 TTTAATATGT
* *
21451358 CGAATTTAATGCTGCCACTACATGTTATAAATGTGTCTGGA
1 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
21451399 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
1 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
* *
21451440 CGAATTTAATGCTGCTACCACATGTT
1 CGAATTTAATGCTGCCACTACATGTT
21451466 TGGCCGAATT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (41 bp):
CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
Found at i:21462813 original size:50 final size:49
Alignment explanation
Indices: 21462755--21462948 Score: 183
Period size: 50 Copynumber: 3.9 Consensus size: 49
21462745 CATTGAGGTT
* *
21462755 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGAC
** * * * * *
21462805 ATGAGAGGTCCCCCGTAAGACCGTGTTTGGGACATGGCATGGGCACAAAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC-GAC
** * * *
21462855 ATGAGAACTCCCATATAAGACCATATCTGGGATATGGCATTGGCA-GTAC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACG-AC
* * ** *
21462904 AAGAAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
21462949 TGTTATTATC
Statistics
Matches: 114, Mismatches: 28, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
49 39 0.34
50 75 0.66
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (49 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGAC
Found at i:21469995 original size:50 final size:50
Alignment explanation
Indices: 21469905--21470070 Score: 158
Period size: 50 Copynumber: 3.3 Consensus size: 50
21469895 NNNNNNNTCC
* * ** ** *
21469905 GGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCAGGTCT
1 GGGACATGGCATTGGCACCGATATGAGAAATCCCATGTAAGACCATGTCT
* * *
21469955 GGGACATGGCATGGGCACCGATATGAGAAATCCCATGTAAGACCATATTT
1 GGGACATGGCATTGGCACCGATATGAGAAATCCCATGTAAGACCATGTCT
* **
21470005 GGGATATGGCATTGGCA--G-TACAAGAAACGTCCCATGTAAGACCATGTCT
1 GGGACATGGCATTGGCACCGATATGAGAAA--TCCCATGTAAGACCATGTCT
* *
21470054 GAGACATGGCTTTGGCA
1 GGGACATGGCATTGGCA
21470071 TGTTATTATT
Statistics
Matches: 95, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
47 7 0.07
48 1 0.01
49 32 0.34
50 55 0.58
ACGTcount: A:0.28, C:0.22, G:0.30, T:0.20
Consensus pattern (50 bp):
GGGACATGGCATTGGCACCGATATGAGAAATCCCATGTAAGACCATGTCT
Found at i:21470063 original size:49 final size:49
Alignment explanation
Indices: 21469941--21470070 Score: 138
Period size: 49 Copynumber: 2.6 Consensus size: 49
21469931 GAGGTCCCCC
* * **
21469941 GTAAGACCAGGTCTGGGACATGGCATGGGCACCGATATGAGAAATCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCA-CGATACAAGAAATCCCAT
* * *
21469991 GTAAGACCATATTTGGGATATGGCATTGGCA-G-TACAAGAAACGTCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACGATACAAGAAA--TCCCAT
* *
21470040 GTAAGACCATGTCTGAGACATGGCTTTGGCA
1 GTAAGACCATGTCTGGGACATGGCATTGGCA
21470071 TGTTATTATT
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
47 7 0.11
48 1 0.02
49 32 0.48
50 26 0.39
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (49 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCACGATACAAGAAATCCCAT
Found at i:21471608 original size:32 final size:31
Alignment explanation
Indices: 21471567--21471683 Score: 153
Period size: 32 Copynumber: 3.6 Consensus size: 31
21471557 GCGATGCTAA
*
21471567 TGATGGCTTTGTGCCAGTCATAGTACCGTTAC
1 TGATGGCTTTGTGCGA-TCATAGTACCGTTAC
*
21471599 TGATGGCTTTGTTTCGATCATAGTACCGTTAC
1 TGATGGCTTTG-TGCGATCATAGTACCGTTAC
*
21471631 TGATGGCTTTGTGCTGATCATATTACCGTTAC
1 TGATGGCTTTGTGC-GATCATAGTACCGTTAC
* *
21471663 CGATGGCTGTGTGTCGATCAT
1 TGATGGCTTTGTG-CGATCAT
21471684 TTCACTATTA
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
31 2 0.03
32 70 0.92
33 4 0.05
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.38
Consensus pattern (31 bp):
TGATGGCTTTGTGCGATCATAGTACCGTTAC
Found at i:21471745 original size:32 final size:31
Alignment explanation
Indices: 21471567--21471747 Score: 141
Period size: 32 Copynumber: 5.7 Consensus size: 31
21471557 GCGATGCTAA
21471567 TGATGGCTTTGTGCC-AGTCATAGTACCGTTAC
1 TGATGGCTTTGTGCCGA-TCATA-TACCGTTAC
**
21471599 TGATGGCTTTGTTTCGATCATAGTACCGTTAC
1 TGATGGCTTTGTGCCGATCATA-TACCGTTAC
*
21471631 TGATGGCTTTGTGCTGATCATATTACCGTTAC
1 TGATGGCTTTGTGCCGATCATA-TACCGTTAC
* * * * **
21471663 CGATGGCTGTGTGTCGATCATTTCACTATTAC
1 TGATGGCTTTGTGCCGATCATAT-ACCGTTAC
* * * * * *
21471695 AGATTG-TTGTGTGTCGGTCATATCACTGCTAC
1 TGATGGCTT-TGTGCCGATCATAT-ACCGTTAC
*
21471727 TGATGGCTTTGTGCCGGTCAT
1 TGATGGCTTTGTGCCGATCAT
21471748 GATGCCTATG
Statistics
Matches: 122, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
31 2 0.02
32 117 0.96
33 3 0.02
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (31 bp):
TGATGGCTTTGTGCCGATCATATACCGTTAC
Found at i:21483801 original size:29 final size:29
Alignment explanation
Indices: 21483766--21483835 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
21483756 TGATCGACCA
* *
21483766 ATGAAAAGGGATAGCTTTGGTTATCGATT
1 ATGAAAAGGGATAGCTTCGATTATCGATT
**
21483795 ATGAAAATAGATAGCTTCGATTATCGATT
1 ATGAAAAGGGATAGCTTCGATTATCGATT
21483824 ATGAAAAGGGAT
1 ATGAAAAGGGAT
21483836 GGTGACGACC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.31
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGATTATCGATT
Found at i:21483855 original size:29 final size:29
Alignment explanation
Indices: 21483823--21483993 Score: 200
Period size: 29 Copynumber: 5.9 Consensus size: 29
21483813 GATTATCGAT
21483823 TATGAAAAGGGATGGTGACGACCATCAAC
1 TATGAAAAGGGATGGTGACGACCATCAAC
* * * *
21483852 TATGAAAAGGGATGGTAATGACCATGAAA
1 TATGAAAAGGGATGGTGACGACCATCAAC
*
21483881 TATGAAAAGGGATAGTGACGACCATCAAC
1 TATGAAAAGGGATGGTGACGACCATCAAC
* * *
21483910 TATGAAAAGGGATGGTGACAACCATCGAT
1 TATGAAAAGGGATGGTGACGACCATCAAC
**
21483939 TAATGAAAAGGGATGGTTTCGACCATCGAA-
1 T-ATGAAAAGGGATGGTGACGACCATC-AAC
* **
21483969 TATGAAAATGGATGGTTTCGACCAT
1 TATGAAAAGGGATGGTGACGACCAT
21483994 TGAATATGAA
Statistics
Matches: 122, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
29 98 0.80
30 23 0.19
31 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.22
Consensus pattern (29 bp):
TATGAAAAGGGATGGTGACGACCATCAAC
Found at i:21483924 original size:58 final size:56
Alignment explanation
Indices: 21483823--21484024 Score: 208
Period size: 58 Copynumber: 3.5 Consensus size: 56
21483813 GATTATCGAT
*
21483823 TATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGGGATGGTAATGACCATGAAA
1 TATGAAAAGGGATAGTGACGACCATCAACTATGAAAAGGGATGGT-ATGACCATG-AA
** *
21483881 TATGAAAAGGGATAGTGACGACCATCAACTATGAAAAGGGATGGTGACAACCATCGAT
1 TATGAAAAGGGATAGTGACGACCATCAACTATGAAAAGGGATGGT-ATGACCAT-GAA
* ** * *
21483939 TAATGAAAAGGGATGGTTTCGACCATCGAA-TATGAAAATGGATGGTTTCGACCATTGAA
1 T-ATGAAAAGGGATAGTGACGACCATC-AACTATGAAAAGGGATGGTAT-GACCA-TGAA
* * * *
21483998 TATGAAAATGGACAGTTACTACCATCA
1 TATGAAAAGGGATAGTGACGACCATCA
21484025 TTTAGAACAC
Statistics
Matches: 121, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
57 1 0.01
58 72 0.60
59 45 0.37
60 3 0.02
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (56 bp):
TATGAAAAGGGATAGTGACGACCATCAACTATGAAAAGGGATGGTATGACCATGAA
Found at i:21484021 original size:29 final size:29
Alignment explanation
Indices: 21483817--21484023 Score: 105
Period size: 29 Copynumber: 7.1 Consensus size: 29
21483807 AGCTTCGATT
* * ** *
21483817 ATCGATTATGAAAAGGGATGGTGACGACC
1 ATCGAATATGAAAATGGACAGTTACGACC
* ** * *
21483846 ATC-AACTATGAAAAGGGATGGTAATGACC
1 ATCGAA-TATGAAAATGGACAGTTACGACC
* * *
21483875 AT-GAAATATGAAAAGGGATAGTGACGACC
1 ATCG-AATATGAAAATGGACAGTTACGACC
* ** * *
21483904 ATC-AACTATGAAAAGGGATGGTGACAACC
1 ATCGAA-TATGAAAATGGACAGTTACGACC
* * ** *
21483933 ATCGATTAATGAAAAGGGATGGTTTCGACC
1 ATCGAAT-ATGAAAATGGACAGTTACGACC
** *
21483963 ATCGAATATGAAAATGGATGGTTTCGACC
1 ATCGAATATGAAAATGGACAGTTACGACC
* *
21483992 ATTGAATATGAAAATGGACAGTTACTACC
1 ATCGAATATGAAAATGGACAGTTACGACC
21484021 ATC
1 ATC
21484024 ATTTAGAACA
Statistics
Matches: 151, Mismatches: 20, Indels: 14
0.82 0.11 0.08
Matches are distributed among these distances:
28 3 0.02
29 120 0.79
30 28 0.19
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.23
Consensus pattern (29 bp):
ATCGAATATGAAAATGGACAGTTACGACC
Found at i:21484022 original size:88 final size:88
Alignment explanation
Indices: 21483823--21484023 Score: 203
Period size: 88 Copynumber: 2.3 Consensus size: 88
21483813 GATTATCGAT
** * * *
21483823 TATGAAAAGGGATGGTGACGACCATCAACT-ATGAAAAGGGATGGTAATGACCATGAAATATGAA
1 TATGAAAAGGGACAGTGACAACCATCGATTAATGAAAAGGGATGGTAATGACCATGAAATATGAA
21483887 AAGGGATAGTGACGACCATCAAC
66 AAGGGATAGTGACGACCATCAAC
** *
21483910 TATGAAAAGGGATGGTGACAACCATCGATTAATGAAAAGGGATGGT-TTCGACCATCG-AATATG
1 TATGAAAAGGGACAGTGACAACCATCGATTAATGAAAAGGGATGGTAAT-GACCAT-GAAATATG
* * ** *
21483973 AAAATGGATGGTTTCGACCATTGAA-
64 AAAAGGGATAGTGACGACCA-TCAAC
* * *
21483998 TATGAAAATGGACAGTTACTACCATC
1 TATGAAAAGGGACAGTGACAACCATC
21484024 ATTTAGAACA
Statistics
Matches: 96, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
87 28 0.29
88 64 0.67
89 4 0.04
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (88 bp):
TATGAAAAGGGACAGTGACAACCATCGATTAATGAAAAGGGATGGTAATGACCATGAAATATGAA
AAGGGATAGTGACGACCATCAAC
Found at i:21492837 original size:50 final size:50
Alignment explanation
Indices: 21492728--21492911 Score: 158
Period size: 51 Copynumber: 3.7 Consensus size: 50
21492718 AGTTGCTAGG
* * *
21492728 TCACGTGTGTAGTACTATGTGTAGGCTACTATGTGTACCGGAATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAATGATAGA
* * * * *
21492778 TCGCATGTGTAGCACTATGTGCA-GCTACTATGCGTACCGG-ATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAAT-G-ATAGA
* * * * * * *
21492828 TCACGTGTGTAGTACTTTATGCAGGCTACTACGTGTATCGG-ATGAAAATGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAATG-ATA-GA
* *
21492879 TCACATGTGTAGTACTATGTGTAGGCTACTATG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATG
21492912 TGAACCGGGT
Statistics
Matches: 104, Mismatches: 26, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
48 2 0.02
49 17 0.16
50 40 0.38
51 45 0.43
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAATGATAGA
Found at i:21497581 original size:20 final size:20
Alignment explanation
Indices: 21497556--21497778 Score: 123
Period size: 20 Copynumber: 11.2 Consensus size: 20
21497546 AAATGAAGAA
21497556 GTGCCCCTGAATGCACATCT
1 GTGCCCCTGAATGCACATCT
** * *
21497576 GTGCCCCTGTTTGCACTTCG
1 GTGCCCCTGAATGCACATCT
*
21497596 GTGCCTCTGAATGCACATCT
1 GTGCCCCTGAATGCACATCT
* * * * * *
21497616 ATGCCTCT-ATTTACACTTCA
1 GTGCCCCTGA-ATGCACATCT
* *
21497636 GTG-CCCTAAATGCACATTT
1 GTGCCCCTGAATGCACATCT
** *
21497655 GTGCCCCTGTTTGCACTTC-
1 GTGCCCCTGAATGCACATCT
21497674 GATGCCCCTGAATGCACATCT
1 G-TGCCCCTGAATGCACATCT
* * ** * *
21497695 ATG-CCTTGTTTGCACTTCA
1 GTGCCCCTGAATGCACATCT
* *
21497714 GTGCCCCTAAATGCACATTT
1 GTGCCCCTGAATGCACATCT
** * *
21497734 GTGCCCCTGTTTTCACTTC-
1 GTGCCCCTGAATGCACATCT
21497753 GCTGCCCCTGAATGCACATCT
1 G-TGCCCCTGAATGCACATCT
*
21497774 ATGCC
1 GTGCC
21497779 TTATTTGCAC
Statistics
Matches: 141, Mismatches: 54, Indels: 16
0.67 0.26 0.08
Matches are distributed among these distances:
19 27 0.19
20 114 0.81
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.32
Consensus pattern (20 bp):
GTGCCCCTGAATGCACATCT
Found at i:21497600 original size:40 final size:40
Alignment explanation
Indices: 21497556--21497841 Score: 312
Period size: 40 Copynumber: 7.2 Consensus size: 40
21497546 AAATGAAGAA
*
21497556 GTGCCCCTGAATGCACATCTGTGCCCCTGTTTGCACTTCG
1 GTGCCCCTGAATGCACATCTATGCCCCTGTTTGCACTTCG
* * * * *
21497596 GTGCCTCTGAATGCACATCTATGCCTCTATTTACACTTCA
1 GTGCCCCTGAATGCACATCTATGCCCCTGTTTGCACTTCG
* * *
21497636 GTG-CCCTAAATGCACATTTGTGCCCCTGTTTGCACTTCG
1 GTGCCCCTGAATGCACATCTATGCCCCTGTTTGCACTTCG
* * *
21497675 ATGCCCCTGAATGCACATCTATG-CCTTGTTTGCACTTCA
1 GTGCCCCTGAATGCACATCTATGCCCCTGTTTGCACTTCG
* * * *
21497714 GTGCCCCTAAATGCACATTTGTGCCCCTGTTTTCACTTCG
1 GTGCCCCTGAATGCACATCTATGCCCCTGTTTGCACTTCG
* * *
21497754 CTGCCCCTGAATGCACATCTATG-CCTTATTTGCACTTCG
1 GTGCCCCTGAATGCACATCTATGCCCCTGTTTGCACTTCG
* * * *
21497793 GTGCCCCT-AATCGCACAT-TCATGCTCCTGATTGCAATTTG
1 GTGCCCCTGAAT-GCACATCT-ATGCCCCTGTTTGCACTTCG
21497833 GTGCCCCTG
1 GTGCCCCTG
21497842 TTAAGCATCT
Statistics
Matches: 199, Mismatches: 41, Indels: 11
0.79 0.16 0.04
Matches are distributed among these distances:
38 4 0.02
39 92 0.46
40 103 0.52
ACGTcount: A:0.17, C:0.32, G:0.18, T:0.33
Consensus pattern (40 bp):
GTGCCCCTGAATGCACATCTATGCCCCTGTTTGCACTTCG
Found at i:21497660 original size:79 final size:79
Alignment explanation
Indices: 21497555--21497811 Score: 401
Period size: 79 Copynumber: 3.3 Consensus size: 79
21497545 AAAATGAAGA
* * * *
21497555 AGTGCCCCTGAATGCACATCTGTGCCCCTGTTTGCACTTCGGTGCCTCTGAATGCACATCTATGC
1 AGTGCCCCTAAATGCACATTTGTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACATCTATGC
*
21497620 CTCTATTTACACTTC
66 CT-TATTTGCACTTC
21497635 AGTG-CCCTAAATGCACATTTGTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACATCTATGC
1 AGTGCCCCTAAATGCACATTTGTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACATCTATGC
*
21497699 CTTGTTTGCACTTC
66 CTTATTTGCACTTC
* *
21497713 AGTGCCCCTAAATGCACATTTGTGCCCCTGTTTTCACTTCGCTGCCCCTGAATGCACATCTATGC
1 AGTGCCCCTAAATGCACATTTGTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACATCTATGC
21497778 CTTATTTGCACTTC
66 CTTATTTGCACTTC
*
21497792 GGTGCCCCT-AATCGCACATT
1 AGTGCCCCTAAAT-GCACATT
21497812 CATGCTCCTG
Statistics
Matches: 165, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
78 17 0.10
79 144 0.87
80 4 0.02
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.33
Consensus pattern (79 bp):
AGTGCCCCTAAATGCACATTTGTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACATCTATGC
CTTATTTGCACTTC
Found at i:21497838 original size:79 final size:79
Alignment explanation
Indices: 21497555--21497841 Score: 391
Period size: 79 Copynumber: 3.6 Consensus size: 79
21497545 AAAATGAAGA
* *
21497555 AGTGCCCCTGAATGCACA-TCTGTGCCCCTGTTTGCACTTCGGTGCCTCTGAATGCACATCTATG
1 AGTGCCCCTAAATGCACATTC-GTGCCCCTGTTTGCACTTCGGTGCCCCTGAATGCACATCTATG
*
21497619 CCTCTATTTACACTTC
65 CCT-TATTTGCACTTC
* *
21497635 AGTG-CCCTAAATGCACATTTGTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACATCTATGC
1 AGTGCCCCTAAATGCACATTCGTGCCCCTGTTTGCACTTCGGTGCCCCTGAATGCACATCTATGC
*
21497699 CTTGTTTGCACTTC
66 CTTATTTGCACTTC
* * *
21497713 AGTGCCCCTAAATGCACATTTGTGCCCCTGTTTTCACTTCGCTGCCCCTGAATGCACATCTATGC
1 AGTGCCCCTAAATGCACATTCGTGCCCCTGTTTGCACTTCGGTGCCCCTGAATGCACATCTATGC
21497778 CTTATTTGCACTTC
66 CTTATTTGCACTTC
* * * * * *
21497792 GGTGCCCCT-AATCGCACATTCATGCTCCTGATTGCAATTTGGTGCCCCTG
1 AGTGCCCCTAAAT-GCACATTCGTGCCCCTGTTTGCACTTCGGTGCCCCTG
21497842 TTAAGCATCT
Statistics
Matches: 186, Mismatches: 18, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
78 17 0.09
79 164 0.88
80 5 0.03
ACGTcount: A:0.17, C:0.32, G:0.18, T:0.33
Consensus pattern (79 bp):
AGTGCCCCTAAATGCACATTCGTGCCCCTGTTTGCACTTCGGTGCCCCTGAATGCACATCTATGC
CTTATTTGCACTTC
Found at i:21506695 original size:24 final size:25
Alignment explanation
Indices: 21506668--21506717 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 25
21506658 AAATTGGAAA
21506668 AAAAAT-GAGAAAGAA-AAAGAAAAG
1 AAAAATAGA-AAAGAAGAAAGAAAAG
*
21506692 -AAAATAGAAAAGAAGAAAGGAAAG
1 AAAAATAGAAAAGAAGAAAGAAAAG
21506716 AA
1 AA
21506718 TGAGGTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
23 11 0.50
24 10 0.45
25 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (25 bp):
AAAAATAGAAAAGAAGAAAGAAAAG
Found at i:21506715 original size:12 final size:11
Alignment explanation
Indices: 21506664--21506717 Score: 56
Period size: 12 Copynumber: 4.7 Consensus size: 11
21506654 AGGAAAATTG
*
21506664 GAAAA-AAAAT
1 GAAAAGAAAAA
21506674 GAGAAAGAAAAA
1 GA-AAAGAAAAA
21506686 GAAAAGAAAATA
1 GAAAAGAAAA-A
21506698 GAAAAGAAGAAA
1 GAAAAGAA-AAA
*
21506710 GGAAAGAA
1 GAAAAGAA
21506718 TGAGGTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
10 2 0.05
11 11 0.29
12 23 0.61
13 2 0.05
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (11 bp):
GAAAAGAAAAA
Found at i:21509385 original size:13 final size:13
Alignment explanation
Indices: 21509369--21509416 Score: 64
Period size: 13 Copynumber: 3.7 Consensus size: 13
21509359 ATGAAATATT
21509369 TTAAAATAAATTG
1 TTAAAATAAATTG
21509382 TT-AAATATAATT-
1 TTAAAATA-AATTG
21509394 TTAAAATAAATTG
1 TTAAAATAAATTG
21509407 TTAAATATAA
1 TTAAA-ATAA
21509417 TTTTACATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
12 11 0.35
13 16 0.52
14 4 0.13
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (13 bp):
TTAAAATAAATTG
Found at i:21509397 original size:12 final size:12
Alignment explanation
Indices: 21509366--21509421 Score: 62
Period size: 12 Copynumber: 4.5 Consensus size: 12
21509356 TTAATGAAAT
21509366 ATTTTAAAATAA
1 ATTTTAAAATAA
21509378 ATTGTT-AAATATA
1 ATT-TTAAAATA-A
21509391 ATTTTAAAATAA
1 ATTTTAAAATAA
21509403 ATTGTT-AAATATA
1 ATT-TTAAAATA-A
21509416 ATTTTA
1 ATTTTA
21509422 CATTTTATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
12 21 0.55
13 17 0.45
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:21509399 original size:25 final size:25
Alignment explanation
Indices: 21509366--21509421 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
21509356 TTAATGAAAT
21509366 ATTTTAAAATAAATTGTTAAATATA
1 ATTTTAAAATAAATTGTTAAATATA
21509391 ATTTTAAAATAAATTGTTAAATATA
1 ATTTTAAAATAAATTGTTAAATATA
21509416 ATTTTA
1 ATTTTA
21509422 CATTTTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
ATTTTAAAATAAATTGTTAAATATA
Found at i:21509418 original size:13 final size:13
Alignment explanation
Indices: 21509372--21509418 Score: 64
Period size: 12 Copynumber: 3.8 Consensus size: 13
21509362 AAATATTTTA
21509372 AAATA-AATTGTT
1 AAATATAATTGTT
21509384 AAATATAATT-TT
1 AAATATAATTGTT
21509396 AAA-ATAAATTGTT
1 AAATAT-AATTGTT
21509409 AAATATAATT
1 AAATATAATT
21509419 TTACATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 2 0.06
12 14 0.45
13 13 0.42
14 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (13 bp):
AAATATAATTGTT
Found at i:21520530 original size:53 final size:50
Alignment explanation
Indices: 21520367--21520541 Score: 233
Period size: 50 Copynumber: 3.4 Consensus size: 50
21520357 GGGAATGAGA
21520367 TCCCATGTAAGACCATGTCTGGGACATGGCGTAGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTAGGCACCGAGATGAGAGG
*
21520417 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTAGGCACCGAGATGAGAGG
** * * * **
21520467 TCCCCCGTAAGACCAAGTCTGGGACATGGTGGCATAGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACA---TGGCGTAGGCACCGAGATGAGAGG
* *
21520520 TCTCATGTAAGACCATATCTGG
1 TCCCATGTAAGACCATGTCTGG
21520542 AATATGACAT
Statistics
Matches: 108, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
50 72 0.67
53 36 0.33
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.20
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCGTAGGCACCGAGATGAGAGG
Found at i:21520555 original size:103 final size:100
Alignment explanation
Indices: 21520373--21520556 Score: 242
Period size: 103 Copynumber: 1.8 Consensus size: 100
21520363 GAGATCCCAT
* * ** *
21520373 GTAAGACCATGTCTGGGACATGGCGTAGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTG
1 GTAAGACCAAGTCTGGGACATGGCATAGGCACCGAGATGAGAACTCCCATGTAAGACCATATCTG
* * *
21520438 GGACATGGCGTTGGCACCGAGATGAGAGGTCCCCC
66 GAACATGACATTGGCACCGAGATGAGAGGTCCCCC
* *
21520473 GTAAGACCAAGTCTGGGACATGGTGGCATAGGCACCGATATGAGAACTCTCATGTAAGACCATAT
1 GTAAGACCAAGTCTGGGACA---TGGCATAGGCACCGAGATGAGAACTCCCATGTAAGACCATAT
*
21520538 CTGGAATATGACATTGGCA
63 CTGGAACATGACATTGGCA
21520557 GTAAAGAAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
100 19 0.27
103 51 0.73
ACGTcount: A:0.28, C:0.22, G:0.30, T:0.20
Consensus pattern (100 bp):
GTAAGACCAAGTCTGGGACATGGCATAGGCACCGAGATGAGAACTCCCATGTAAGACCATATCTG
GAACATGACATTGGCACCGAGATGAGAGGTCCCCC
Found at i:21522517 original size:50 final size:50
Alignment explanation
Indices: 21522440--21522685 Score: 303
Period size: 50 Copynumber: 4.9 Consensus size: 50
21522430 TTTTCTGTAT
* * * * ** *
21522440 TGCCAATGCCATATCCCAAATATGGTCTTACATAGGATTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATAGGACCTCTCATCTCGG
* * * * * ***
21522490 TGCCCATGCCATCTCCTAGACAAGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATAGGACCTCTCATCTCGG
21522540 TGCCAACGCCATGTCCCAGACATGGTCTTACATAGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATAGGACCTCTCATCTCGG
* * *
21522590 CGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATAGGACCTCTCATCTCGG
* * *
21522640 TGCGAACGCCATGTCCCATACATGGTCTTACATGGGACCTCTCATC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATAGGACCTCTCATC
21522686 ATGGCTCACA
Statistics
Matches: 170, Mismatches: 26, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 170 1.00
ACGTcount: A:0.22, C:0.32, G:0.20, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATAGGACCTCTCATCTCGG
Found at i:21522685 original size:100 final size:100
Alignment explanation
Indices: 21522392--21522685 Score: 342
Period size: 100 Copynumber: 3.0 Consensus size: 100
21522382 ATAATAAAAA
* ** * *
21522392 GCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA--TGTTTTCT-GTATTGCCAATGCCATAT
1 GCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG-A-TGCCAACGCCATGT
* ** * *
21522454 CCCAAATATGGTCTTACATAGGATTTCTCATATCGGT
64 CCCAAACATGGTCTTACATAGGACCTCTCATCTCGGC
* * * * * ** *
21522491 GCCCATGCCATCTCCTAGACAAGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCC
1 GCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATGCCAACGCCATGTCC
*
21522556 CAGACATGGTCTTACATAGGACCTCTCATCTCGGC
66 CAAACATGGTCTTACATAGGACCTCTCATCTCGGC
* *
21522591 GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATGCGAACGCCATGTCC
1 GCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATGCCAACGCCATGTCC
* *
21522656 CATACATGGTCTTACATGGGACCTCTCATC
66 CAAACATGGTCTTACATAGGACCTCTCATC
21522686 ATGGCTCACA
Statistics
Matches: 162, Mismatches: 30, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
99 29 0.18
100 127 0.78
101 5 0.03
102 1 0.01
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (100 bp):
GCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATGCCAACGCCATGTCC
CAAACATGGTCTTACATAGGACCTCTCATCTCGGC
Found at i:21525872 original size:27 final size:26
Alignment explanation
Indices: 21525842--21526224 Score: 363
Period size: 27 Copynumber: 14.2 Consensus size: 26
21525832 TCACACTGTT
* *
21525842 ATGACCAAAATACTTCCATAGGGTAAA
1 ATGACCGAAATAC-CCCATAGGGTAAA
* *
21525869 ATGACCAAAATACCCCCATAGGGTAGA
1 ATGACCGAAATA-CCCCATAGGGTAAA
21525896 ATGACCGAAATACCTCCATAGGGTAAA
1 ATGACCGAAATACC-CCATAGGGTAAA
*
21525923 ATGACTGAAATACCCTCAT-GTGGTAAA
1 ATGACCGAAATACCC-CATAG-GGTAAA
*
21525950 ATGATCGAAATACCCTCATAGGGTAAA
1 ATGACCGAAATACCC-CATAGGGTAAA
*
21525977 ATGACCGAAATACCCCCATAGGATAAA
1 ATGACCGAAATA-CCCCATAGGGTAAA
* * * *
21526004 ATAATCGGAATACCCCTATAAGGTAAA
1 ATGACCGAAATACCCC-ATAGGGTAAA
* * *
21526031 ATGATCGAAATACCCTTATAGGGTAGA
1 ATGACCGAAATACCC-CATAGGGTAAA
* * * *
21526058 CTAACTGAAATACCCCCATAGGCTAAA
1 ATGACCGAAATA-CCCCATAGGGTAAA
* *
21526085 ATGACTGAAATACCCCCATAGGATAAA
1 ATGACCGAAATA-CCCCATAGGGTAAA
* *
21526112 ATGACTGGAATACCCCCATAGGGTAAA
1 ATGACCGAAATA-CCCCATAGGGTAAA
*
21526139 ATGACCGAAATACCCTCATAGGGTAGA
1 ATGACCGAAATACCC-CATAGGGTAAA
* * * *
21526166 ATAACTGAAATACTCCCATAGGCTAAC
1 ATGACCGAAATAC-CCCATAGGGTAAA
* *
21526193 ATGATCAAAATACCCCTATAGGGTAAA
1 ATGACCGAAATACCCC-ATAGGGTAAA
21526220 ATGAC
1 ATGAC
21526225 TATTATACCT
Statistics
Matches: 298, Mismatches: 46, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
26 14 0.05
27 274 0.92
28 10 0.03
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (26 bp):
ATGACCGAAATACCCCATAGGGTAAA
Found at i:21525980 original size:81 final size:80
Alignment explanation
Indices: 21525857--21526224 Score: 427
Period size: 81 Copynumber: 4.5 Consensus size: 80
21525847 CAAAATACTT
* * * *
21525857 CCATAGGGTAAAATGACCAAAATACCCCCATAGGGTAGAATGACCGAAATACCTCCATAGGGTAA
1 CCATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAA
21525922 AATGACTGAAATACC
66 AATGACTGAAATACC
* *
21525937 CTCAT-GTGGTAAAATGATCGAAATACCCTCATAGGGTAAAATGACCGAAATACCCCCATAGGAT
1 C-CATAG-GGTAAAATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGT
* *
21526001 AAAAT-AATCGGAATACC
64 AAAATGACT-GAAATACC
* ** * * * * *
21526018 CCTATAAGGTAAAATGATCGAAATACCCTTATAGGGTAGACTAACTGAAATACCCCCATAGGCTA
1 CC-ATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTA
21526083 AAATGACTGAAATACCC
65 AAATGACTGAAATA-CC
* * *
21526100 CCATAGGATAAAATGA-CTGGAATACCCCCATAGGGTAAAATGACCGAAATACCCTCATAGGGTA
1 CCATAGGGTAAAATGATC-GAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTA
* *
21526164 GAATAACTGAAATACTC
65 AAATGACTGAAATAC-C
* * * *
21526181 CCATAGGCTAACATGATCAAAATACCCCTATAGGGTAAAATGAC
1 CCATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGAC
21526225 TATTATACCT
Statistics
Matches: 243, Mismatches: 35, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
80 7 0.03
81 229 0.94
82 7 0.03
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (80 bp):
CCATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAA
AATGACTGAAATACC
Found at i:21526251 original size:108 final size:107
Alignment explanation
Indices: 21525849--21526224 Score: 452
Period size: 108 Copynumber: 3.5 Consensus size: 107
21525839 GTTATGACCA
* * * *
21525849 AAATACTTCCATAGGGTAAAATGACCAAAATACCCCCATAGGGTAGAATGACCGAAATACCTCCA
1 AAATACTCCCATAGGCTAAAATGACCAAAATACCCCCATAGGATAAAATGACCGAAATACC-CCA
* * *
21525914 TAGGGTAAAATGACTGAAATACCCTCAT-GTGGTAAAATGA-TCG
65 TAGGGTAAAATGACCGAAATACCCTCATAG-GGTAGAATAACT-G
* * * * *
21525957 AAATAC-CCTCATAGGGTAAAATGACCGAAATACCCCCATAGGATAAAATAATCGGAATACCCCT
1 AAATACTCC-CATAGGCTAAAATGACCAAAATACCCCCATAGGATAAAATGACCGAAATACCCC-
* * * *
21526021 ATAAGGTAAAATGATCGAAATACCCTTATAGGGTAGACTAACTG
64 ATAGGGTAAAATGACCGAAATACCCTCATAGGGTAGAATAACTG
* ** * *
21526065 AAATACCCCCATAGGCTAAAATGACTGAAATACCCCCATAGGATAAAATGACTGGAATACCCCCA
1 AAATACTCCCATAGGCTAAAATGACCAAAATACCCCCATAGGATAAAATGACCGAAATA-CCCCA
21526130 TAGGGTAAAATGACCGAAATACCCTCATAGGGTAGAATAACTG
65 TAGGGTAAAATGACCGAAATACCCTCATAGGGTAGAATAACTG
* * * *
21526173 AAATACTCCCATAGGCTAACATGATCAAAATACCCCTATAGGGTAAAATGAC
1 AAATACTCCCATAGGCTAAAATGACCAAAATACCCCCATAGGATAAAATGAC
21526225 TATTATACCT
Statistics
Matches: 232, Mismatches: 30, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
107 3 0.01
108 221 0.95
109 8 0.03
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (107 bp):
AAATACTCCCATAGGCTAAAATGACCAAAATACCCCCATAGGATAAAATGACCGAAATACCCCAT
AGGGTAAAATGACCGAAATACCCTCATAGGGTAGAATAACTG
Found at i:21529720 original size:28 final size:28
Alignment explanation
Indices: 21529680--21529737 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
21529670 AAGATGAGGT
21529680 AACTTAGTCATGTGTGCCTATCAAGGAG
1 AACTTAGTCATGTGTGCCTATCAAGGAG
21529708 AACTTAGTCATGTGTGCCTATCAAGGAG
1 AACTTAGTCATGTGTGCCTATCAAGGAG
21529736 AA
1 AA
21529738 TTTCCTAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (28 bp):
AACTTAGTCATGTGTGCCTATCAAGGAG
Found at i:21531301 original size:20 final size:20
Alignment explanation
Indices: 21531228--21531301 Score: 50
Period size: 21 Copynumber: 3.8 Consensus size: 20
21531218 TGTTAAGAAG
21531228 AAATTTTCTA-GTTAAGAA-TT
1 AAATTTT-TATGTTAA-AATTT
*
21531248 AAATTTTT-T-TTTAAATTT
1 AAATTTTTATGTTAAAATTT
* *
21531266 -CATTTGTTCTGTTTAAAATTT
1 AAATTT-TTATG-TTAAAATTT
21531287 AAATTTTTATGTTAA
1 AAATTTTTATGTTAA
21531302 TAAAGGGGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
17 6 0.14
18 7 0.17
19 2 0.05
20 11 0.26
21 12 0.29
22 4 0.10
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55
Consensus pattern (20 bp):
AAATTTTTATGTTAAAATTT
Found at i:21552147 original size:25 final size:26
Alignment explanation
Indices: 21552094--21552147 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
21552084 TTCTCCTAAA
* *
21552094 TTTCAATTTTATTTAATTATTTAATT
1 TTTCAATTTTATTGAATTATTAAATT
21552120 TTTCAA-TTTATTGAATTA-TAAATAT
1 TTTCAATTTTATTGAATTATTAAAT-T
21552145 TTT
1 TTT
21552148 ATACTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 4 0.16
25 15 0.60
26 6 0.24
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTCAATTTTATTGAATTATTAAATT
Found at i:21553850 original size:50 final size:50
Alignment explanation
Indices: 21553763--21553860 Score: 133
Period size: 50 Copynumber: 2.0 Consensus size: 50
21553753 TTATTAGATA
* * ** *
21553763 TCCCACGTAAGACCATGTCTGGGATATGGTGTTGGCACCGAGATGAGAGG
1 TCCCACGTAAGACCATGTATGGGACATGGCATAGGCACCGAGATGAGAGG
* *
21553813 TCCCCCGTAAGACCATGTATGGGACATGGCATAGGCACCGATATGAGA
1 TCCCACGTAAGACCATGTATGGGACATGGCATAGGCACCGAGATGAGA
21553861 ACTCTCATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.27, C:0.22, G:0.31, T:0.20
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTATGGGACATGGCATAGGCACCGAGATGAGAGG
Found at i:21553941 original size:49 final size:50
Alignment explanation
Indices: 21553819--21553945 Score: 125
Period size: 49 Copynumber: 2.6 Consensus size: 50
21553809 GAGGTCCCCC
* ** * * *
21553819 GTAAGACCATGTATGGGACATGGCATAGGCACCGATATGAGAACTCTCAT
1 GTAAGACCATGTCTGGGACATGGCATTTGCACAGACAGGAGAACTCTCAT
* * * * *
21553869 ATAAGACCATATCCGGGATATGGCATTTGCA-ATACAGGA-AACATCTCAT
1 GTAAGACCATGTCTGGGACATGGCATTTGCACAGACAGGAGAAC-TCTCAT
21553918 GTAAGACCATGTCTGGGACATGGC-TTTG
1 GTAAGACCATGTCTGGGACATGGCATTTG
21553946 GCATGTTATT
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
48 7 0.11
49 30 0.49
50 24 0.39
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATTTGCACAGACAGGAGAACTCTCAT
Found at i:21554175 original size:20 final size:20
Alignment explanation
Indices: 21554150--21554198 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
21554140 TGGGTTATTT
21554150 AAGTAAGCAAGTAAATAAAC
1 AAGTAAGCAAGTAAATAAAC
* *
21554170 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAATAAAC
21554190 AA-TAAGCAA
1 AAGTAAGCAA
21554199 AGACCATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.59, C:0.06, G:0.20, T:0.14
Consensus pattern (20 bp):
AAGTAAGCAAGTAAATAAAC
Found at i:21558179 original size:21 final size:21
Alignment explanation
Indices: 21558150--21558191 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
21558140 TATTAATTCA
21558150 TAATATAA-TTAATTTTAATTT
1 TAATATAATTTAA-TTTAATTT
*
21558171 TAATCTAATTTAATTTAATTT
1 TAATATAATTTAATTTAATTT
21558192 AGGTTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATATAATTTAATTTAATTT
Found at i:21561365 original size:27 final size:27
Alignment explanation
Indices: 21561335--21561504 Score: 134
Period size: 27 Copynumber: 6.3 Consensus size: 27
21561325 TGTCAAGAAT
*
21561335 GGAATGCCTTTGTGGTG-AATTATGAAA
1 GGAAAGCCTTTGTGGTGCAA-TATGAAA
21561362 GG-AA-CACTTTGTGGTGCAATATGAAA
1 GGAAAGC-CTTTGTGGTGCAATATGAAA
* *
21561388 GGAAAGCCTTTATGGCGCAATATGAAA
1 GGAAAGCCTTTGTGGTGCAATATGAAA
* * * *
21561415 -GAAATGTCGTTGTGGCG-AATTATAAAA
1 GGAAA-GCCTTTGTGGTGCAA-TATGAAA
* * * *
21561442 GGAACGTCTATGTGGTGCAATATAAAA
1 GGAAAGCCTTTGTGGTGCAATATGAAA
* * *
21561469 GGAAAGCCTTTTTAGCGCAATATGAAA
1 GGAAAGCCTTTGTGGTGCAATATGAAA
*
21561496 GGAACGCCT
1 GGAAAGCCT
21561505 CTATGGAGAA
Statistics
Matches: 116, Mismatches: 19, Indels: 16
0.77 0.13 0.11
Matches are distributed among these distances:
25 1 0.01
26 26 0.22
27 83 0.72
28 6 0.05
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.26
Consensus pattern (27 bp):
GGAAAGCCTTTGTGGTGCAATATGAAA
Found at i:21561478 original size:81 final size:80
Alignment explanation
Indices: 21561344--21561496 Score: 234
Period size: 81 Copynumber: 1.9 Consensus size: 80
21561334 TGGAATGCCT
* * * * *
21561344 TTGTGGTGAATTATGAAAGGAACACTTTGTGGTGCAATATGAAAGGAAAGCCTTTATGGCGCAAT
1 TTGTGGCGAATTATAAAAGGAACACTATGTGGTGCAATATAAAAGGAAAGCCTTTATAGCGCAAT
21561409 ATGAAAGAAATGTCG
66 ATGAAAGAAATGTCG
* *
21561424 TTGTGGCGAATTATAAAAGGAACGTCTATGTGGTGCAATATAAAAGGAAAGCCTTTTTAGCGCAA
1 TTGTGGCGAATTATAAAAGGAAC-ACTATGTGGTGCAATATAAAAGGAAAGCCTTTATAGCGCAA
21561489 TATGAAAG
65 TATGAAAG
21561497 GAACGCCTCT
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
80 21 0.32
81 44 0.68
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.27
Consensus pattern (80 bp):
TTGTGGCGAATTATAAAAGGAACACTATGTGGTGCAATATAAAAGGAAAGCCTTTATAGCGCAAT
ATGAAAGAAATGTCG
Found at i:21563388 original size:18 final size:18
Alignment explanation
Indices: 21563347--21563389 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
21563337 ATTCTTCATA
21563347 TTCATCTTTACCTTGAGC
1 TTCATCTTTACCTTGAGC
* * * *
21563365 TCCATCTTTATCTTTATC
1 TTCATCTTTACCTTGAGC
21563383 TTCATCT
1 TTCATCT
21563390 CATTCATCCA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.28, G:0.05, T:0.51
Consensus pattern (18 bp):
TTCATCTTTACCTTGAGC
Found at i:21565888 original size:2 final size:2
Alignment explanation
Indices: 21565877--21565909 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
21565867 TCGATCTAAA
*
21565877 AT AT -T AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21565910 CAATTGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
AT
Found at i:21570506 original size:41 final size:42
Alignment explanation
Indices: 21570460--21570545 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 42
21570450 CTCATTTGAC
*
21570460 TTTTGATTTAATTAAATTATGA-AAAGGTTTGATGATAAG-GT
1 TTTTGATTTAATTAAATTATGACAAA-GTTTCATGATAAGTGT
* * *
21570501 TTTTGATTTAATTTATTTATTACAAAGTTTCATGATAAGTGT
1 TTTTGATTTAATTAAATTATGACAAAGTTTCATGATAAGTGT
21570543 TTT
1 TTT
21570546 GTGAATAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
41 31 0.79
42 8 0.21
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.50
Consensus pattern (42 bp):
TTTTGATTTAATTAAATTATGACAAAGTTTCATGATAAGTGT
Found at i:21572163 original size:333 final size:334
Alignment explanation
Indices: 21571690--21572354 Score: 1323
Period size: 333 Copynumber: 2.0 Consensus size: 334
21571680 ATATAATTAT
21571690 TTTTAATTAAATCTATACTTCAAATGAGTTGAATAATTAAATATATTTTTATTATATATTGAATG
1 TTTTAATTAAATCTATACTTCAAATGAGTTGAATAATTAAATATATTTTTATTATATATTGAATG
21571755 TGTGTTTATCCATGTCTTGTTTTTTTAAATTAAAAAATAAATTGCTTAAACAACAATATATATCA
66 TGTGTTTATCCATGTCTTGTTTTTTTAAATTAAAAAATAAATTGCTTAAACAACAATATATATCA
21571820 TTTAGCTTTATTATAGAAATTTAATAATTAATAATTCCTAACTACGTCTTTTAATAAAAGCCAAT
131 TTTAGCTTTATTATAGAAATTTAATAATTAATAATTCCTAACTACGTCTTTTAATAAAAGCCAAT
21571885 ATATTTAATTTTAAAAAATAATTTAGATTTTTATTATCTTATTAATTAGTGAATAAAAGCAGCAA
196 ATATTTAATTTTAAAAAATAATTTAGATTTTTATTATCTTATTAATTAGTGAATAAAAGCAGCAA
21571950 ATCAAAATAATTTTCATGTAAAACCTTAAAAGAATGAATACAATAAAACTCAAGGACATATATGC
261 ATCAAAATAATTTTCATGTAAAACCTTAAAAGAATGAATACAATAAAACTCAAGGACATATATGC
21572015 AAATGTTAA
326 AAATGTTAA
21572024 TTTTAATT-AATCTATACTTCAAATGAGTTGAATAATTAAATATATTTTTATTATATATTGAATG
1 TTTTAATTAAATCTATACTTCAAATGAGTTGAATAATTAAATATATTTTTATTATATATTGAATG
21572088 TGTGTTTATCCATGTCTTGTTTTTTTAAATTAAAAAATAAATTGCTTAAACAACAATATATATCA
66 TGTGTTTATCCATGTCTTGTTTTTTTAAATTAAAAAATAAATTGCTTAAACAACAATATATATCA
21572153 TTTAGCTTTATTATAGAAATTTAATAATTAATAATTCCTAACTACGTCTTTTAATAAAAGCCAAT
131 TTTAGCTTTATTATAGAAATTTAATAATTAATAATTCCTAACTACGTCTTTTAATAAAAGCCAAT
21572218 ATATTTAATTTTAAAAAATAATTTAGATTTTTATTATCTTATTAATTAGTGAATAAAAGCAGCAA
196 ATATTTAATTTTAAAAAATAATTTAGATTTTTATTATCTTATTAATTAGTGAATAAAAGCAGCAA
21572283 ATCAAAATAATTTTCATGTAAAACCTTAAAAGAATGAATACAATAAAACTCAAGGACATATATGC
261 ATCAAAATAATTTTCATGTAAAACCTTAAAAGAATGAATACAATAAAACTCAAGGACATATATGC
21572348 AAATGTT
326 AAATGTT
21572355 GAAAGTTAGA
Statistics
Matches: 331, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
333 323 0.98
334 8 0.02
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (334 bp):
TTTTAATTAAATCTATACTTCAAATGAGTTGAATAATTAAATATATTTTTATTATATATTGAATG
TGTGTTTATCCATGTCTTGTTTTTTTAAATTAAAAAATAAATTGCTTAAACAACAATATATATCA
TTTAGCTTTATTATAGAAATTTAATAATTAATAATTCCTAACTACGTCTTTTAATAAAAGCCAAT
ATATTTAATTTTAAAAAATAATTTAGATTTTTATTATCTTATTAATTAGTGAATAAAAGCAGCAA
ATCAAAATAATTTTCATGTAAAACCTTAAAAGAATGAATACAATAAAACTCAAGGACATATATGC
AAATGTTAA
Found at i:21574201 original size:17 final size:17
Alignment explanation
Indices: 21574179--21574217 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
21574169 AAGTTAGATA
*
21574179 AAATAATTAAAATAAAT
1 AAATAACTAAAATAAAT
*
21574196 AAATAACTAAGATAAAT
1 AAATAACTAAAATAAAT
21574213 AAATA
1 AAATA
21574218 GAACAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (17 bp):
AAATAACTAAAATAAAT
Found at i:21575145 original size:27 final size:27
Alignment explanation
Indices: 21575115--21575169 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
21575105 CATCGATACT
21575115 CATAGGAAGGTGTATCGAAACTTCGTA
1 CATAGGAAGGTGTATCGAAACTTCGTA
*
21575142 CATAGGAAGGTGTATCGAGACTTCGTA
1 CATAGGAAGGTGTATCGAAACTTCGTA
21575169 C
1 C
21575170 TGTAAGTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.25
Consensus pattern (27 bp):
CATAGGAAGGTGTATCGAAACTTCGTA
Found at i:21576657 original size:20 final size:22
Alignment explanation
Indices: 21576609--21576657 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
21576599 GTGATAAAGT
*
21576609 CTCAATTAAGGATAATTATTGA
1 CTCAATTAAGGATAATTAGTGA
* *
21576631 CTTAATT-AGG-TAATTAGTGG
1 CTCAATTAAGGATAATTAGTGA
21576651 CTCAATT
1 CTCAATT
21576658 GATAATAGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 14 0.61
21 3 0.13
22 6 0.26
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (22 bp):
CTCAATTAAGGATAATTAGTGA
Found at i:21577144 original size:33 final size:33
Alignment explanation
Indices: 21577103--21577174 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
21577093 AGTATTCTAT
* *
21577103 TTTTTGTAGATAATTAACTATTTTAATTTTGAA
1 TTTTTGTAGATAATTAAATATTTTAATTTTAAA
* *
21577136 TTTTTGTAGTTAATTAAATATTTTTATTTTAAA
1 TTTTTGTAGATAATTAAATATTTTAATTTTAAA
21577169 TATTTT
1 T-TTTT
21577175 TACTTACCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.88
34 4 0.12
ACGTcount: A:0.32, C:0.01, G:0.07, T:0.60
Consensus pattern (33 bp):
TTTTTGTAGATAATTAAATATTTTAATTTTAAA
Found at i:21578521 original size:27 final size:27
Alignment explanation
Indices: 21578470--21578521 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
21578460 CAAAATTGGC
*
21578470 AATCCTAGTTCACCAACCTATTGGCAA
1 AATCCTAGTTCACCAACCTACTGGCAA
*
21578497 AATCCT-GTTCACCAAACGTACTGGC
1 AATCCTAGTTCACC-AACCTACTGGC
21578522 TAACCCTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.25
Consensus pattern (27 bp):
AATCCTAGTTCACCAACCTACTGGCAA
Found at i:21584913 original size:55 final size:54
Alignment explanation
Indices: 21584847--21584983 Score: 141
Period size: 55 Copynumber: 2.5 Consensus size: 54
21584837 GGTATAGGTT
*
21584847 TCACACAGCCTGCGACACGGCCGTGTGACCGCATTTCGAATA-TACACAAGATCTA
1 TCACACAGCCTGCGACACGGCCGTGTGACCGCATTTCGAATATTACAC-A-ATCAA
* * * ** ** * *
21584902 TCACACGGCCTGTGACATGATCGTGTGAGGGTATTTCGATTATTACACAATCAA
1 TCACACAGCCTGCGACACGGCCGTGTGACCGCATTTCGAATATTACACAATCAA
* *
21584956 GCACACAGCTTGCGACACGGCCGTGTGA
1 TCACACAGCCTGCGACACGGCCGTGTGA
21584984 AATTATTTCG
Statistics
Matches: 64, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
54 25 0.39
55 34 0.53
56 5 0.08
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (54 bp):
TCACACAGCCTGCGACACGGCCGTGTGACCGCATTTCGAATATTACACAATCAA
Found at i:21592893 original size:6 final size:6
Alignment explanation
Indices: 21592882--21592913 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
21592872 GAGTATATCA
21592882 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
21592914 CAAATCCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:21595709 original size:54 final size:54
Alignment explanation
Indices: 21595638--21595747 Score: 157
Period size: 54 Copynumber: 2.0 Consensus size: 54
21595628 AATTGAGTTA
* * * *
21595638 AATAATTAAGCTTTATTAAAATATGAAATAGAATAAAAGGATAAAACACACTTG
1 AATAATTAAACTCTATTAAAATATAAAATAGAATAAAAGAATAAAACACACTTG
** *
21595692 AATAATTAAACTCTATTAAAATATAAAATAGAATAGGAGAATAAAACGCACTTG
1 AATAATTAAACTCTATTAAAATATAAAATAGAATAAAAGAATAAAACACACTTG
21595746 AA
1 AA
21595748 CATGATTGAT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.55, C:0.08, G:0.11, T:0.26
Consensus pattern (54 bp):
AATAATTAAACTCTATTAAAATATAAAATAGAATAAAAGAATAAAACACACTTG
Found at i:21596630 original size:13 final size:11
Alignment explanation
Indices: 21596594--21596624 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
21596584 CCGTCCGTAT
21596594 TAATTTTTATA
1 TAATTTTTATA
*
21596605 TTATTTTTATA
1 TAATTTTTATA
21596616 TAATTTTTA
1 TAATTTTTA
21596625 AATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:21596825 original size:14 final size:14
Alignment explanation
Indices: 21596802--21596838 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
21596792 TACAATATCC
*
21596802 AAATAATAACAACA
1 AAATAGTAACAACA
21596816 AAATAGTAACAACA
1 AAATAGTAACAACA
*
21596830 TAATAGTAA
1 AAATAGTAA
21596839 AATGGTAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.65, C:0.11, G:0.05, T:0.19
Consensus pattern (14 bp):
AAATAGTAACAACA
Found at i:21598098 original size:20 final size:20
Alignment explanation
Indices: 21598064--21598117 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
21598054 AATTATTGTT
* * *
21598064 TTTTTTTACTATTTTCTTGC
1 TTTTTTTATTGTTTTCTTAC
*
21598084 TTTTTTTATTGTTTTGTTAC
1 TTTTTTTATTGTTTTCTTAC
*
21598104 -TATTTTATTGTTTT
1 TTTTTTTATTGTTTT
21598118 TTTATCACTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.11, C:0.07, G:0.07, T:0.74
Consensus pattern (20 bp):
TTTTTTTATTGTTTTCTTAC
Found at i:21598107 original size:31 final size:30
Alignment explanation
Indices: 21598064--21598122 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
21598054 AATTATTGTT
* *
21598064 TTTTTTTACTATTTTCTTGCTTTTTTTATTG
1 TTTTGTTACTATTTTATTG-TTTTTTTATTG
21598095 TTTTGTTACTATTTTATTGTTTTTTTAT
1 TTTTGTTACTATTTTATTGTTTTTTTAT
21598123 CACTATTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.75
Consensus pattern (30 bp):
TTTTGTTACTATTTTATTGTTTTTTTATTG
Found at i:21602110 original size:21 final size:21
Alignment explanation
Indices: 21602086--21602134 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
21602076 TGTAAATATT
21602086 TTATTAAATATTTACGAAGTG
1 TTATTAAATATTTACGAAGTG
*
21602107 TTATTAAATATTTATGAAGTG
1 TTATTAAATATTTACGAAGTG
21602128 TTATTAA
1 TTATTAA
21602135 GGTTGTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.47
Consensus pattern (21 bp):
TTATTAAATATTTACGAAGTG
Found at i:21607804 original size:20 final size:20
Alignment explanation
Indices: 21607774--21607811 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21607764 TTGAAAGAAA
21607774 AACTCAAAGAGAA-TTGATG
1 AACTCAAAGAGAAGTTGATG
21607793 AACTCAAAAGAGAAGTTGA
1 AACTC-AAAGAGAAGTTGA
21607812 ATAATACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.50, C:0.11, G:0.21, T:0.18
Consensus pattern (20 bp):
AACTCAAAGAGAAGTTGATG
Found at i:21611190 original size:18 final size:19
Alignment explanation
Indices: 21611162--21611197 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
21611152 TTGATCGAAA
21611162 GGATGTTGAATTATACTTT
1 GGATGTTGAATTATACTTT
*
21611181 GGAT-TTGAATTTTACTT
1 GGATGTTGAATTATACTT
21611198 GCCAACCCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (19 bp):
GGATGTTGAATTATACTTT
Found at i:21620016 original size:50 final size:50
Alignment explanation
Indices: 21619906--21620105 Score: 206
Period size: 50 Copynumber: 3.9 Consensus size: 50
21619896 ACATTTGGGT
* * *
21619906 GATGAGA--TCCCATGTAAGACCATGTTTGGAACATGGCATTGGCATCATTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA
* *
21619957 GATTATGAGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
1 G---ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
** *
21620010 GATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* ** * * *
21620060 TATGAGAACTCCCATGTAAGACCATATCTGGGATATGACATTGGCA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
21620106 GTACAAGAAA
Statistics
Matches: 125, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
50 81 0.65
51 1 0.01
53 3 0.02
54 6 0.05
55 1 0.01
56 33 0.26
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
Found at i:21624832 original size:16 final size:17
Alignment explanation
Indices: 21624804--21624836 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
21624794 AAGAATAGGA
21624804 ATAAGTTAGAAAATTAG
1 ATAAGTTAGAAAATTAG
21624821 ATAAGTTA-AAAATTAG
1 ATAAGTTAGAAAATTAG
21624837 CAATCGTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30
Consensus pattern (17 bp):
ATAAGTTAGAAAATTAG
Found at i:21636240 original size:16 final size:16
Alignment explanation
Indices: 21636219--21636252 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
21636209 AGCTAATAGA
21636219 ATTCAATAAACTTTAT
1 ATTCAATAAACTTTAT
21636235 ATTCAATAAACTTTAT
1 ATTCAATAAACTTTAT
21636251 AT
1 AT
21636253 GAAATTGTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTCAATAAACTTTAT
Found at i:21647307 original size:4 final size:4
Alignment explanation
Indices: 21647298--21647327 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
21647288 ATTATACAGC
21647298 AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
21647328 AGAAATCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:21649287 original size:18 final size:17
Alignment explanation
Indices: 21649247--21649290 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
21649237 TAGAATACAT
*
21649247 AAAAAAATATAAAATTC
1 AAAAAAATAAAAAATTC
*
21649264 AGAAAATATAAAAAATTCC
1 A-AAAAAATAAAAAATT-C
21649283 AAAAAAAT
1 AAAAAAAT
21649291 TAAATTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 19 0.86
19 2 0.09
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.20
Consensus pattern (17 bp):
AAAAAAATAAAAAATTC
Found at i:21651479 original size:15 final size:15
Alignment explanation
Indices: 21651459--21651492 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
21651449 AAAAGAACAC
*
21651459 AAAAGAGATCCTAAA
1 AAAAGAGATCCCAAA
21651474 AAAAGAGATCCCAAA
1 AAAAGAGATCCCAAA
21651489 AAAA
1 AAAA
21651493 ACTTAGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.65, C:0.15, G:0.12, T:0.09
Consensus pattern (15 bp):
AAAAGAGATCCCAAA
Found at i:21654573 original size:4 final size:4
Alignment explanation
Indices: 21654564--21654615 Score: 54
Period size: 4 Copynumber: 13.0 Consensus size: 4
21654554 AAAGGAGAGG
* *
21654564 GAAA GAAA GAAA GAAA GAAA GGAGAG GAAA GAAA G-AA -AAA GAAG GAAA
1 GAAA GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA
21654612 GAAA
1 GAAA
21654616 AGGAAAGGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
3 4 0.10
4 31 0.77
5 4 0.10
6 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:21654595 original size:18 final size:18
Alignment explanation
Indices: 21654572--21654626 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 18
21654562 GGGAAAGAAA
21654572 GAAAGAAAGAAAGGAGAG
1 GAAAGAAAGAAAGGAGAG
*
21654590 GAAAGAAAGAAA-AAGAAG
1 GAAAGAAAGAAAGGAG-AG
21654608 GAAAGAAAAGGAAAGGAGA
1 GAAAG-AAA-GAAAGGAGA
21654627 AGAGAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 2 0.06
18 19 0.61
19 3 0.10
20 5 0.16
21 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (18 bp):
GAAAGAAAGAAAGGAGAG
Found at i:21654633 original size:36 final size:34
Alignment explanation
Indices: 21654565--21654637 Score: 85
Period size: 36 Copynumber: 2.1 Consensus size: 34
21654555 AAGGAGAGGG
21654565 AAAGAAAGAAAGAAAGAAAGGAGAGGAAAGAAAGAA
1 AAAGAAAGAAAGAAAGAAAGGAGA-GAAAGAAA-AA
* *
21654601 AAAGAAGGAAAGAAAAGGAAAGGAGA-AGAGAAAAA
1 AAAGAAAGAAAG-AAA-GAAAGGAGAGAAAGAAAAA
21654636 AA
1 AA
21654638 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
35 4 0.12
36 17 0.52
37 3 0.09
38 9 0.27
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (34 bp):
AAAGAAAGAAAGAAAGAAAGGAGAGAAAGAAAAA
Found at i:21661914 original size:18 final size:18
Alignment explanation
Indices: 21661860--21661914 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
21661850 CTCCTTTCCT
* *
21661860 TTTCTTTCCTTCTTTTTC
1 TTTCTTTCCCTCTCTTTC
21661878 TTTCTTT-CCTCTCATTTC
1 TTTCTTTCCCTCTC-TTTC
*
21661896 TTTCTTTCCCTCTCCTTC
1 TTTCTTTCCCTCTCTTTC
21661914 T
1 T
21661915 GCCCCCCCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 4 0.12
18 22 0.69
19 6 0.19
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTCTTTCCCTCTCTTTC
Done.