Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 84 of 128
Found at i:27723846 original size:25 final size:26
Alignment explanation
Indices: 27723812--27723863 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
27723802 TATGTAGATG
*
27723812 ATTATTGTT-ATTAAATTTTAATAAA
1 ATTATTGTTAAATAAATTTTAATAAA
*
27723837 ATTATTGTTAAATATATTTTAATAAA
1 ATTATTGTTAAATAAATTTTAATAAA
27723863 A
1 A
27723864 ACAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (26 bp):
ATTATTGTTAAATAAATTTTAATAAA
Found at i:27724837 original size:56 final size:57
Alignment explanation
Indices: 27724770--27724885 Score: 164
Period size: 57 Copynumber: 2.1 Consensus size: 57
27724760 AAAAAAATTA
27724770 AATATAACCAATT-AAA-ACTTCTCTCAAACCGAGAAAAAACCTAAAAGTCAATCCAT
1 AATATAACCAATTAAAATACTTCTCTCAAACCGAGAAAAAA-CTAAAAGTCAATCCAT
* * * * *
27724826 AATATAACCAATTAAAATACTTTTGTTAAACCGAGAAAAGATTAAAAGTCAATCCAT
1 AATATAACCAATTAAAATACTTCTCTCAAACCGAGAAAAAACTAAAAGTCAATCCAT
27724883 AAT
1 AAT
27724886 TGCGACAGTG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
56 13 0.25
57 21 0.40
58 19 0.36
ACGTcount: A:0.50, C:0.18, G:0.07, T:0.25
Consensus pattern (57 bp):
AATATAACCAATTAAAATACTTCTCTCAAACCGAGAAAAAACTAAAAGTCAATCCAT
Found at i:27735237 original size:7 final size:7
Alignment explanation
Indices: 27735225--27735265 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
27735215 CAAAGAAGAT
27735225 AAAGAGA
1 AAAGAGA
*
27735232 AAAGAGC
1 AAAGAGA
27735239 AAAGAGA
1 AAAGAGA
27735246 AAAGAGA
1 AAAGAGA
27735253 AAAGAGA
1 AAAGAGA
27735260 AAAGAG
1 AAAGAG
27735266 TTTATTACAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.68, C:0.02, G:0.29, T:0.00
Consensus pattern (7 bp):
AAAGAGA
Found at i:27735251 original size:21 final size:22
Alignment explanation
Indices: 27735215--27735265 Score: 77
Period size: 21 Copynumber: 2.3 Consensus size: 22
27735205 AGGAAAAATA
27735215 CAAAGAAGATAAAGAGAAAAGAG
1 CAAAG-AGATAAAGAGAAAAGAG
27735238 CAAAGAGA-AAAGAGAAAAGAG
1 CAAAGAGATAAAGAGAAAAGAG
*
27735259 AAAAGAG
1 CAAAGAG
27735266 TTTATTACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 19 0.70
22 3 0.11
23 5 0.19
ACGTcount: A:0.67, C:0.04, G:0.27, T:0.02
Consensus pattern (22 bp):
CAAAGAGATAAAGAGAAAAGAG
Found at i:27742340 original size:25 final size:25
Alignment explanation
Indices: 27742292--27742337 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
27742282 GATAACTTTG
27742292 AATTTTGAGGATTTTTATATTTTAA
1 AATTTTGAGGATTTTTATATTTTAA
27742317 AATTTTGA-GATTTTT-TATTTT
1 AATTTTGAGGATTTTTATATTTT
27742338 TTATTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 7 0.33
25 8 0.38
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (25 bp):
AATTTTGAGGATTTTTATATTTTAA
Found at i:27742345 original size:14 final size:14
Alignment explanation
Indices: 27742328--27742378 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
27742318 ATTTTGAGAT
*
27742328 TTTTTATTTTT-TA
1 TTTTTATTTTTGAA
27742341 TTTTTATTTTTGAA
1 TTTTTATTTTTGAA
* *
27742355 TTTTGAATTTTGAA
1 TTTTTATTTTTGAA
27742369 TTTTTATTTT
1 TTTTTATTTT
27742379 ATTTTTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
13 11 0.34
14 21 0.66
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.75
Consensus pattern (14 bp):
TTTTTATTTTTGAA
Found at i:27742358 original size:28 final size:29
Alignment explanation
Indices: 27742319--27742378 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
27742309 TATTTTAAAA
** **
27742319 TTTTGAGATTTTTTATTTTTTATTTTTAT
1 TTTTGAGATTTTGAATTTTGAATTTTTAT
27742348 TTTTGA-ATTTTGAATTTTGAATTTTTAT
1 TTTTGAGATTTTGAATTTTGAATTTTTAT
27742376 TTT
1 TTT
27742379 ATTTTTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 21 0.78
29 6 0.22
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (29 bp):
TTTTGAGATTTTGAATTTTGAATTTTTAT
Found at i:27742373 original size:8 final size:7
Alignment explanation
Indices: 27742288--27742372 Score: 53
Period size: 7 Copynumber: 11.4 Consensus size: 7
27742278 TTTTGATAAC
27742288 TTTGAAT
1 TTTGAAT
27742295 TTTGAGGAT
1 TTTGA--AT
*
27742304 TTTTATAT
1 TTTGA-AT
*
27742312 TTTAAAAT
1 TTT-GAAT
27742320 TTTGAGAT
1 TTTGA-AT
**
27742328 TTTTTAT
1 TTTGAAT
**
27742335 TTTTTAT
1 TTTGAAT
* *
27742342 TTTTATT
1 TTTGAAT
27742349 TTTGAAT
1 TTTGAAT
27742356 TTTGAAT
1 TTTGAAT
27742363 TTTGAAT
1 TTTGAAT
27742370 TTT
1 TTT
27742373 TATTTTATTT
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
7 42 0.66
8 15 0.23
9 7 0.11
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.65
Consensus pattern (7 bp):
TTTGAAT
Found at i:27760237 original size:119 final size:120
Alignment explanation
Indices: 27759958--27760255 Score: 318
Period size: 120 Copynumber: 2.5 Consensus size: 120
27759948 TTCGTCCGGA
** * *
27759958 CTAAACCTTTAAAATGACATCAGGTTAC-CAGTTTAGGCTAAACTTATGTCCCAAGTATTCTCGA
1 CTAAACCTTTAAAATGACATCAGGTTACTC-GTCCAGGCTAAACCTATGTCCCAAGTATCCTCGA
* ** *
27760022 AACATCAATCATTTGTCCTAGCTGAAAATATATACATAACAGATTACTCGTTCGAG
65 AACATCAATCACTCATCCGAGCTGAAAATATATACATAACAGATTACTCGTTCGAG
* * ** * *
27760078 CTAAATCTTTAAAACGACATCAGGTTACTAATCCAGGCTAAACCTATGTCCTAAGTATCCTCGAC
1 CTAAACCTTTAAAATGACATCAGGTTACTCGTCCAGGCTAAACCTATGTCCCAAGTATCCTCGAA
** ** *
27760143 ACATCAATTGCTCATCCGAGCTG-AAATATATACATGTCAGGTTACAT-GTTC-AG
66 ACATCAATCACTCATCCGAGCTGAAAATATATACATAACAGATTAC-TCGTTCGAG
* * * *
27760196 TCTAAACCTTTAAATTGACATCAGGTTACTCGTCC-GAGCTAAACCTGTGTCACAAATATC
1 -CTAAACCTTTAAAATGACATCAGGTTACTCGTCCAG-GCTAAACCTATGTCCCAAGTATC
27760256 TTTGGTGTAC
Statistics
Matches: 146, Mismatches: 28, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
118 3 0.02
119 71 0.49
120 72 0.49
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (120 bp):
CTAAACCTTTAAAATGACATCAGGTTACTCGTCCAGGCTAAACCTATGTCCCAAGTATCCTCGAA
ACATCAATCACTCATCCGAGCTGAAAATATATACATAACAGATTACTCGTTCGAG
Found at i:27761343 original size:19 final size:19
Alignment explanation
Indices: 27761319--27761358 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
27761309 CTTACATAGT
*
27761319 AATTAATTAATCTTAATTA
1 AATTAATTAAACTTAATTA
27761338 AATTAATTAAACTTAATTA
1 AATTAATTAAACTTAATTA
27761357 AA
1 AA
27761359 ACTAAACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTAATTAAACTTAATTA
Found at i:27761358 original size:10 final size:10
Alignment explanation
Indices: 27761321--27761358 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
27761311 TACATAGTAA
*
27761321 TTAATTAATC
1 TTAATTAAAC
27761331 TTAATTAAA-
1 TTAATTAAAC
27761340 TTAATTAAAC
1 TTAATTAAAC
27761350 TTAATTAAA
1 TTAATTAAA
27761359 ACTAAACATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 9 0.35
10 17 0.65
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (10 bp):
TTAATTAAAC
Found at i:27765767 original size:24 final size:24
Alignment explanation
Indices: 27765740--27765795 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
27765730 AAACTTAATT
27765740 CTAATCAAAGGC-AAATATATTATG
1 CTAAT-AAAGGCTAAATATATTATG
* *
27765764 CTAATAAATGCTAAATATATTATA
1 CTAATAAAGGCTAAATATATTATG
*
27765788 CTCATAAA
1 CTAATAAA
27765796 TACTAAATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.32
Consensus pattern (24 bp):
CTAATAAAGGCTAAATATATTATG
Found at i:27765796 original size:24 final size:24
Alignment explanation
Indices: 27765752--27765803 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
27765742 AATCAAAGGC
* *
27765752 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
27765776 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
27765800 AAAT
1 AAAT
27765804 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:27767646 original size:17 final size:17
Alignment explanation
Indices: 27767623--27767863 Score: 188
Period size: 17 Copynumber: 13.8 Consensus size: 17
27767613 TTTAAAAAAA
27767623 CCGTGTTTCAAAAATCTT
1 CCGTGTTTCAAAAAT-TT
27767641 CC-TGTTTTCAAAAA-TT
1 CCGTG-TTTCAAAAATTT
27767657 CCGGTGTTTCAAAAATCTT
1 CC-GTGTTTCAAAAAT-TT
27767676 -CGTGTTTTC-AAAATTT
1 CCGTG-TTTCAAAAATTT
*
27767692 CCGGTGTTTTAAAAATTT
1 CC-GTGTTTCAAAAATTT
* *
27767710 TCGTGTTTTCAAAAAATTC
1 CCGTG-TTTC-AAAAATTT
27767729 CCGTGTTTCAAAAATTT
1 CCGTGTTTCAAAAATTT
* * * *
27767746 TCATGTTTTCAACAATTC
1 CCGTG-TTTCAAAAATTT
*
27767764 CCGTGTTTCACAAATTT
1 CCGTGTTTCAAAAATTT
27767781 CCGTGTTTTCAAAAATTT
1 CCGTG-TTTCAAAAATTT
* *
27767799 TCGTGTTTTAAAAATTT
1 CCGTGTTTCAAAAATTT
** *
27767816 TTGTG-TTCTTAAAA-TT
1 CCGTGTTTC-AAAAATTT
* *
27767832 CTCGTATTTCAAAAGTTT
1 C-CGTGTTTCAAAAATTT
*
27767850 TCGTGTTTCAAAAA
1 CCGTGTTTCAAAAA
27767864 AAATTCTCAT
Statistics
Matches: 177, Mismatches: 29, Indels: 35
0.73 0.12 0.15
Matches are distributed among these distances:
16 10 0.06
17 85 0.48
18 69 0.39
19 13 0.07
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (17 bp):
CCGTGTTTCAAAAATTT
Found at i:27767651 original size:18 final size:17
Alignment explanation
Indices: 27767628--27767815 Score: 152
Period size: 18 Copynumber: 10.7 Consensus size: 17
27767618 AAAAACCGTG
27767628 TTTCAAAAATCTTCCTGT
1 TTTCAAAAAT-TTCCTGT
*
27767646 TTTCAAAAA-TTCCGGT
1 TTTCAAAAATTTCCTGT
*
27767662 GTTTCAAAAATCTTCGTGT
1 -TTTCAAAAAT-TTCCTGT
27767681 TTTC-AAAATTTCCGGTGT
1 TTTCAAAAATTTCC--TGT
*
27767699 TTT-AAAAATTTTCGTGT
1 TTTCAAAAA-TTTCCTGT
* *
27767716 TTTCAAAAAATTCCCGT
1 TTTCAAAAATTTCCTGT
*
27767733 GTTTCAAAAATTTTCATGT
1 -TTTCAAAAA-TTTCCTGT
* *
27767752 TTTCAACAA-TTCCCGT
1 TTTCAAAAATTTCCTGT
*
27767768 GTTTCACAAATTTCCGTGT
1 -TTTCAAAAATTTCC-TGT
*
27767787 TTTCAAAAATTTTCGTGT
1 TTTCAAAAA-TTTCCTGT
27767805 TTT-AAAAATTT
1 TTTCAAAAATTT
27767816 TTGTGTTCTT
Statistics
Matches: 137, Mismatches: 19, Indels: 30
0.74 0.10 0.16
Matches are distributed among these distances:
16 17 0.12
17 37 0.27
18 63 0.46
19 20 0.15
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (17 bp):
TTTCAAAAATTTCCTGT
Found at i:27767814 original size:35 final size:35
Alignment explanation
Indices: 27767623--27767863 Score: 281
Period size: 35 Copynumber: 6.9 Consensus size: 35
27767613 TTTAAAAAAA
* *
27767623 CCGTGTTTCAAAAATCTTCCTGTTTTCAAAAATTC
1 CCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATTC
* * *
27767658 CGGTGTTTCAAAAATCTTCGTGTTTTCAAAATTTC
1 CCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATTC
* *
27767693 CGGTGTTTTAAAAATTTTCGTGTTTTCAAAAAATTC
1 CCGTGTTTCAAAAATTTTCGTGTTTTC-AAAAATTC
* *
27767729 CCGTGTTTCAAAAATTTTCATGTTTTCAACAATTC
1 CCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATTC
* * *
27767764 CCGTGTTTCACAAATTTCCGTGTTTTCAAAAATTT
1 CCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATTC
* * *
27767799 TCGTGTTTTAAAAATTTTTGTGTTCTT--AAAATTC
1 CCGTGTTTCAAAAATTTTCGTGTT-TTCAAAAATTC
* * *
27767833 TCGTATTTCAAAAGTTTTCGTG-TTTCAAAAA
1 CCGTGTTTCAAAAATTTTCGTGTTTTCAAAAA
27767864 AAATTCTCAT
Statistics
Matches: 177, Mismatches: 25, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
32 2 0.01
33 1 0.01
34 28 0.16
35 113 0.64
36 33 0.19
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (35 bp):
CCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATTC
Found at i:27769919 original size:24 final size:24
Alignment explanation
Indices: 27769876--27769989 Score: 85
Period size: 24 Copynumber: 4.8 Consensus size: 24
27769866 TGTTTTTAAA
* *
27769876 AATATATATATTTAATTTTAAATCT
1 AATAT-TATTTTTAAATTTAAATCT
** *
27769901 AATATTATTTTTATGTTT-AAGCTT
1 AATATTATTTTTAAATTTAAATC-T
*
27769925 AATATTATTTTTAAATTTATCATC-
1 AATATTATTTTTAAATTTA-AATCT
*
27769949 AATATTA-TTTT-AATTTACAATGT
1 AATATTATTTTTAAATTTA-AATCT
*
27769972 ATTATTA-TTTTAAATTTA
1 AATATTATTTTTAAATTTA
27769990 TCTTGTATTT
Statistics
Matches: 72, Mismatches: 12, Indels: 11
0.76 0.13 0.12
Matches are distributed among these distances:
22 8 0.11
23 17 0.24
24 40 0.56
25 5 0.07
26 2 0.03
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.55
Consensus pattern (24 bp):
AATATTATTTTTAAATTTAAATCT
Found at i:27769996 original size:24 final size:24
Alignment explanation
Indices: 27769927--27770117 Score: 169
Period size: 24 Copynumber: 8.0 Consensus size: 24
27769917 TTAAGCTTAA
* *
27769927 TATTATTTTTAAATTTATCAT-CAA
1 TATTA-TTTTAAATTTATCATGTAT
27769951 TATTATTTT-AATTTA-CAATGTAT
1 TATTATTTTAAATTTATC-ATGTAT
*
27769974 TATTATTTTAAATTTATCTTGTATT
1 TATTATTTTAAATTTATCATGTA-T
*
27769999 TGTTA-TTTAAATTTATCATGTAT
1 TATTATTTTAAATTTATCATGTAT
* *
27770022 TATTATTTTAAGTTTATCACGTAT
1 TATTATTTTAAATTTATCATGTAT
* * *
27770046 T-TTCATTTTGAATCTATCAAGTAT
1 TATT-ATTTTAAATTTATCATGTAT
* * *
27770070 TATTATTTTTTAACTTATCATTTAT
1 TATTA-TTTTAAATTTATCATGTAT
* *
27770095 TATTA-TTTAAAGTTACCATGTAT
1 TATTATTTTAAATTTATCATGTAT
27770118 CGTTTTATAC
Statistics
Matches: 137, Mismatches: 21, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
21 1 0.01
22 8 0.06
23 35 0.26
24 66 0.48
25 27 0.20
ACGTcount: A:0.31, C:0.07, G:0.05, T:0.56
Consensus pattern (24 bp):
TATTATTTTAAATTTATCATGTAT
Found at i:27770444 original size:12 final size:12
Alignment explanation
Indices: 27770413--27770444 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
27770403 TTATTTCAAT
*
27770413 TTATTATATATA
1 TTATTATTTATA
27770425 TTATTATTTATA
1 TTATTATTTATA
27770437 TTATTATT
1 TTATTATT
27770445 AAACTTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTATTATTTATA
Found at i:27770870 original size:17 final size:18
Alignment explanation
Indices: 27770832--27770874 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
27770822 ATTATTGCTC
* *
27770832 TTATGTGTATTGTATTGC
1 TTATTTGTATTGTATTGA
27770850 TTATTTGTATT-TATTGA
1 TTATTTGTATTGTATTGA
27770867 TTATTTGT
1 TTATTTGT
27770875 CGCTCATTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.19, C:0.02, G:0.16, T:0.63
Consensus pattern (18 bp):
TTATTTGTATTGTATTGA
Found at i:27772625 original size:24 final size:24
Alignment explanation
Indices: 27772598--27772645 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
27772588 TCTAATCGAA
*
27772598 GTTAAATATATTATGCTAATAAAT
1 GTTAAATATATTATACTAATAAAT
*
27772622 GTTAAATATATTATACTCATAAAT
1 GTTAAATATATTATACTAATAAAT
27772646 ACTAAATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (24 bp):
GTTAAATATATTATACTAATAAAT
Found at i:27772651 original size:24 final size:24
Alignment explanation
Indices: 27772600--27772652 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
27772590 TAATCGAAGT
* **
27772600 TAAATATATTATGCTAATAAATGT
1 TAAATATATTATACTAATAAATAC
*
27772624 TAAATATATTATACTCATAAATAC
1 TAAATATATTATACTAATAAATAC
27772648 TAAAT
1 TAAAT
27772653 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.40
Consensus pattern (24 bp):
TAAATATATTATACTAATAAATAC
Found at i:27776409 original size:3 final size:3
Alignment explanation
Indices: 27776396--27776441 Score: 74
Period size: 3 Copynumber: 14.7 Consensus size: 3
27776386 TTGAAGCTGT
27776396 AGA AGGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGAA AGA AG
1 AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AG
27776442 GGGTTTTGGG
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 35 0.85
4 6 0.15
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:27776465 original size:21 final size:21
Alignment explanation
Indices: 27776441--27776483 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
27776431 GAAGAAAGAA
*
27776441 GGGGTTTTGGGGGGGGGGGGG
1 GGGGTGTTGGGGGGGGGGGGG
27776462 GGGGTGTTGGGGGGGGGGGGG
1 GGGGTGTTGGGGGGGGGGGGG
27776483 G
1 G
27776484 AGGTCATTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.84, T:0.16
Consensus pattern (21 bp):
GGGGTGTTGGGGGGGGGGGGG
Found at i:27779923 original size:20 final size:22
Alignment explanation
Indices: 27779898--27779938 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
27779888 TTTGCTTCAA
*
27779898 TTTAAT-TTTT-ATTACTTTTC
1 TTTAATATTTTCAATACTTTTC
27779918 TTTAATATTTTCAATACTTTT
1 TTTAATATTTTCAATACTTTT
27779939 AAAACCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 4 0.22
22 8 0.44
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTAATATTTTCAATACTTTTC
Found at i:27786879 original size:29 final size:30
Alignment explanation
Indices: 27786837--27786895 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
27786827 GAATTGGATC
* *
27786837 AAATCAAAATTTCATGTATAAAATTACACA
1 AAATCAAAAGTTCATATATAAAATTACACA
* *
27786867 AAATC-AAAGTTCATATATACAATTGCACA
1 AAATCAAAAGTTCATATATAAAATTACACA
27786896 TTAAACCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (30 bp):
AAATCAAAAGTTCATATATAAAATTACACA
Found at i:27787987 original size:18 final size:17
Alignment explanation
Indices: 27787929--27787988 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 17
27787919 ATTATGTCAA
*
27787929 TAAATAATT-TAAAAAT
1 TAAAAAATTATAAAAAT
*
27787945 TATAAACAATTATAAAAAA
1 TA-AAA-AATTATAAAAAT
* *
27787964 TGAAAAGTTCATAAAAAT
1 TAAAAAATT-ATAAAAAT
27787982 TAAAAAA
1 TAAAAAA
27787989 GAAAAAGTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
16 2 0.06
17 5 0.15
18 19 0.58
19 7 0.21
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.28
Consensus pattern (17 bp):
TAAAAAATTATAAAAAT
Found at i:27794264 original size:8 final size:8
Alignment explanation
Indices: 27794251--27794292 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
27794241 GTGTAAATGT
27794251 AAATAAAA
1 AAATAAAA
*
27794259 AAATAACA
1 AAATAAAA
*
27794267 AAATAACA
1 AAATAAAA
*
27794275 AAA-AAGA
1 AAATAAAA
27794282 AAATAAAA
1 AAATAAAA
27794290 AAA
1 AAA
27794293 GATGAAGCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.83, C:0.05, G:0.02, T:0.10
Consensus pattern (8 bp):
AAATAAAA
Found at i:27795011 original size:44 final size:43
Alignment explanation
Indices: 27794894--27795012 Score: 166
Period size: 44 Copynumber: 2.7 Consensus size: 43
27794884 TCCACTGCAT
* * * *
27794894 CTTGTCGCTTCGATCCACTTCCTTGCAACCTCTGAGAGATTCGA
1 CTTGTAGCTTCAATCCACTT-ATTGCAACTTCTGAGAGATTCGA
*
27794938 CTTGTAGCTCCAATCCACTTTATTGCAACTTCTGAGAGATTCGA
1 CTTGTAGCTTCAATCCAC-TTATTGCAACTTCTGAGAGATTCGA
27794982 CTTGTAGCTTCAATCCACTCTATTGCAACTT
1 CTTGTAGCTTCAATCCACT-TATTGCAACTT
27795013 TAGGGGGACG
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
43 1 0.01
44 64 0.96
45 2 0.03
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.34
Consensus pattern (43 bp):
CTTGTAGCTTCAATCCACTTATTGCAACTTCTGAGAGATTCGA
Found at i:27795377 original size:44 final size:44
Alignment explanation
Indices: 27795329--27795442 Score: 142
Period size: 44 Copynumber: 2.6 Consensus size: 44
27795319 TTTTAATCCT
* * *
27795329 CTCCACTGCAACTTTAGGGAGATAGGA-TTAGTAGCTTCAGTCT-G
1 CTCCACTGCAACTTCAGGGAGATAAGACTT-GTAGCTTCA-ACTGG
* *
27795373 CTCCACTGTAACTTCAGGGAGATAAGACTTGTATCTTCAACTGG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAACTGG
*
27795417 CCCCACTGCAACTTCAGGGAGATAAG
1 CTCCACTGCAACTTCAGGGAGATAAG
27795443 GTTTGATATG
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
43 2 0.03
44 57 0.93
45 2 0.03
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAACTGG
Found at i:27795784 original size:89 final size:89
Alignment explanation
Indices: 27795667--27795973 Score: 461
Period size: 89 Copynumber: 3.4 Consensus size: 89
27795657 AGGACTAGTT
* * * *
27795667 TTCGATTTGCTTCACTGCCAGTATAGGAAGACAAGATCTGCTGCTTTTAGTCTACTCCGCTGCAA
1 TTCGATCTGCTTCACTGCCGGTACAGGAAGACAAGATCTGCTACTTTTAGTCTACTCCGCTGCAA
27795732 ACTCAGGGAGGTCAGGCTTGTGTC
66 ACTCAGGGAGGTCAGGCTTGTGTC
** * * *
27795756 TTCGATCTGCTTTGCTACCGGTACAGGAAGACAAGATCTGCTACTTTTAGTCTGCTCCACTGCAA
1 TTCGATCTGCTTCACTGCCGGTACAGGAAGACAAGATCTGCTACTTTTAGTCTACTCCGCTGCAA
27795821 ACTCAGGGAGGTCAGGCTTGTGTC
66 ACTCAGGGAGGTCAGGCTTGTGTC
* * *
27795845 TTCGATCTGCTTCCCTGCCGGTACAGGAAGACAAGATCTGCTACTTATAGTCTGCTCCGCTGCAA
1 TTCGATCTGCTTCACTGCCGGTACAGGAAGACAAGATCTGCTACTTTTAGTCTACTCCGCTGCAA
* * * *
27795910 ACTTAGGGAGATCAGGCTGGTGCC
66 ACTCAGGGAGGTCAGGCTTGTGTC
*
27795934 TTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTG
1 TTCGATCTGCTTCACTGCCGGTACAGGAAGACAAGATCTG
27795974 TTGCTTCTAT
Statistics
Matches: 198, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
89 198 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (89 bp):
TTCGATCTGCTTCACTGCCGGTACAGGAAGACAAGATCTGCTACTTTTAGTCTACTCCGCTGCAA
ACTCAGGGAGGTCAGGCTTGTGTC
Found at i:27797366 original size:17 final size:17
Alignment explanation
Indices: 27797344--27797390 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
27797334 TTGGCCTCTC
27797344 TTTTTTCTTTTTCTTCT
1 TTTTTTCTTTTTCTTCT
*
27797361 TTTTTT-TATTTTCTTTT
1 TTTTTTCT-TTTTCTTCT
27797378 TTATTTTCTTTTT
1 TT-TTTTCTTTTT
27797391 GTTTTTAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.04
17 16 0.62
18 8 0.31
19 1 0.04
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTCTTTTTCTTCT
Found at i:27797377 original size:12 final size:12
Alignment explanation
Indices: 27797362--27797390 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
27797352 TTTTCTTCTT
27797362 TTTTTTATTTTC
1 TTTTTTATTTTC
27797374 TTTTTTATTTTC
1 TTTTTTATTTTC
27797386 TTTTT
1 TTTTT
27797391 GTTTTTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTATTTTC
Found at i:27797395 original size:17 final size:16
Alignment explanation
Indices: 27797346--27797397 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
27797336 GGCCTCTCTT
*
27797346 TTTTCTTTTTCTTCTTTT
1 TTTTCTTTTT-TT-TTTA
*
27797364 TTTTATTTTCTTTTTTA
1 TTTTCTTTT-TTTTTTA
27797381 TTTTCTTTTTGTTTTTA
1 TTTTCTTTTT-TTTTTA
27797398 ACATTCTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 1 0.03
17 17 0.59
18 10 0.34
19 1 0.03
ACGTcount: A:0.06, C:0.10, G:0.02, T:0.83
Consensus pattern (16 bp):
TTTTCTTTTTTTTTTA
Found at i:27797396 original size:12 final size:11
Alignment explanation
Indices: 27797344--27797396 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 11
27797334 TTGGCCTCTC
27797344 TTTTTTCTTTT
1 TTTTTTCTTTT
27797355 TCTTCTTT-TTTT
1 T-TT-TTTCTTTT
*
27797367 TATTTTCTTTT
1 TTTTTTCTTTT
27797378 TTATTTTCTTTT
1 TT-TTTTCTTTT
27797390 TGTTTTT
1 T-TTTTT
27797397 AACATTCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
10 3 0.09
11 7 0.20
12 21 0.60
13 4 0.11
ACGTcount: A:0.04, C:0.09, G:0.02, T:0.85
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:27804179 original size:30 final size:31
Alignment explanation
Indices: 27804113--27804179 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
27804103 AGTTTAATTG
*
27804113 TAATTTTTAAAAATTTTCAAAGGCTTAATAA
1 TAATTTTTAAAAATTTTCAAAGGCCTAATAA
27804144 TAATTTTT-AAAATTTT-AAAGGGCCTAACTAA
1 TAATTTTTAAAAATTTTCAAA-GGCCTAA-TAA
27804175 -AATTT
1 TAATTT
27804180 AAAAAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
29 3 0.09
30 19 0.58
31 11 0.33
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.42
Consensus pattern (31 bp):
TAATTTTTAAAAATTTTCAAAGGCCTAATAA
Found at i:27804279 original size:13 final size:14
Alignment explanation
Indices: 27804255--27804285 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
27804245 CGAGATTGTC
27804255 TGACAGAATGACTT
1 TGACAGAATGACTT
27804269 TGACA-AATGACTT
1 TGACAGAATGACTT
27804282 TGAC
1 TGAC
27804286 TACCTCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (14 bp):
TGACAGAATGACTT
Found at i:27813609 original size:43 final size:43
Alignment explanation
Indices: 27813561--27813645 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
27813551 TATGTGATTG
27813561 ATATTGAAATGGAAAAGATGAGAAATGCATATGAGATGAGAAA
1 ATATTGAAATGGAAAAGATGAGAAATGCATATGAGATGAGAAA
* *
27813604 ATATTGAAATGGCAAAGATGAGAAATGTATATGAGATGAGAA
1 ATATTGAAATGGAAAAGATGAGAAATGCATATGAGATGAGAA
27813646 GTGAAATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.49, C:0.02, G:0.26, T:0.22
Consensus pattern (43 bp):
ATATTGAAATGGAAAAGATGAGAAATGCATATGAGATGAGAAA
Found at i:27813642 original size:18 final size:19
Alignment explanation
Indices: 27813619--27813669 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
27813609 GAAATGGCAA
*
27813619 AGATGAGAAATG-TATATG
1 AGATGAGAAATGAAATATG
*
27813637 AGATGAGAAGTGAAATATG
1 AGATGAGAAATGAAATATG
*
27813656 AAATGATGAAATGA
1 AGATGA-GAAATGA
27813670 GATGTGAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 11 0.41
19 10 0.37
20 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (19 bp):
AGATGAGAAATGAAATATG
Found at i:27813669 original size:27 final size:27
Alignment explanation
Indices: 27813634--27813688 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
27813624 AGAAATGTAT
*
27813634 ATGAGATGAGAAGTGAAA-TATGAAATG
1 ATGAAATGAGAAGTGAAACT-TGAAATG
*
27813661 ATGAAATGAGATGTGAAACTTGAAATG
1 ATGAAATGAGAAGTGAAACTTGAAATG
27813688 A
1 A
27813689 ATCCAAGTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.27, T:0.24
Consensus pattern (27 bp):
ATGAAATGAGAAGTGAAACTTGAAATG
Found at i:27815538 original size:25 final size:25
Alignment explanation
Indices: 27815504--27815557 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
27815494 AGGGTCACAC
*
27815504 GGCCGTGTCACACACCCGTGTGCCA
1 GGCCGTGTCACACACCCATGTGCCA
** *
27815529 GGCCGTGTCATGCGCCCATGTGCCA
1 GGCCGTGTCACACACCCATGTGCCA
27815554 GGCC
1 GGCC
27815558 ATGTAGCTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.13, C:0.39, G:0.31, T:0.17
Consensus pattern (25 bp):
GGCCGTGTCACACACCCATGTGCCA
Found at i:27819409 original size:18 final size:18
Alignment explanation
Indices: 27819374--27819418 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
27819364 GCAATAAGTG
*
27819374 ACGTTTTGAAAATTAATA
1 ACGTTTTGAAAATGAATA
27819392 ACGTTTTGAAAGA-GAATA
1 ACGTTTTGAAA-ATGAATA
27819410 AC-TTTTGAA
1 ACGTTTTGAA
27819419 TACGAATCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 7 0.28
18 17 0.68
19 1 0.04
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.36
Consensus pattern (18 bp):
ACGTTTTGAAAATGAATA
Found at i:27836949 original size:113 final size:114
Alignment explanation
Indices: 27836746--27836968 Score: 439
Period size: 113 Copynumber: 2.0 Consensus size: 114
27836736 GCTTTGATTA
27836746 GTGATGAAGGTTCTCATTTTGACCGCAAATTAGTTGCTACTGCCTTGAATAAATATGGGGTTAAA
1 GTGATGAAGGTTCTCATTTTGACCGCAAATTAGTTGCTACTGCCTTGAATAAATATGGGGTTAAA
27836811 CATAAAATTGCCACGTCATATCATTCCCAGACAAATGGACAAGTTTTTG
66 CATAAAATTGCCACGTCATATCATTCCCAGACAAATGGACAAGTTTTTG
27836860 GTGA-GAAGGTTCTCATTTTGACCGCAAATTAGTTGCTACTGCCTTGAATAAATATGGGGTTAAA
1 GTGATGAAGGTTCTCATTTTGACCGCAAATTAGTTGCTACTGCCTTGAATAAATATGGGGTTAAA
27836924 CATAAAATTGCCACGTCATATCATTCCCAGACAAATGGACAAGTT
66 CATAAAATTGCCACGTCATATCATTCCCAGACAAATGGACAAGTT
27836969 GAGGTCTATA
Statistics
Matches: 109, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
113 105 0.96
114 4 0.04
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (114 bp):
GTGATGAAGGTTCTCATTTTGACCGCAAATTAGTTGCTACTGCCTTGAATAAATATGGGGTTAAA
CATAAAATTGCCACGTCATATCATTCCCAGACAAATGGACAAGTTTTTG
Found at i:27854448 original size:20 final size:20
Alignment explanation
Indices: 27854410--27854448 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
27854400 ATTTTTTCTA
*
27854410 TTTATTTTTCTATTTTTATT
1 TTTATTTTTCTATTGTTATT
27854430 TTTATTTTTTCT-TTGTTAT
1 TTTA-TTTTTCTATTGTTAT
27854449 CAAATTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTATTTTTCTATTGTTATT
Found at i:27857958 original size:129 final size:129
Alignment explanation
Indices: 27857797--27858059 Score: 490
Period size: 129 Copynumber: 2.0 Consensus size: 129
27857787 GAATACACAA
*
27857797 TCAACATCACCTTTTACAATTTCACCATAAAAAAGAATGTACACTAAAAACACTGAGTTATTCAT
1 TCAACATCACCTTTTACAATTTCACCATAAAAAAGAATGTACACTAAAAACACTAAGTTATTCAT
* *
27857862 CTTCACCAGAATTTTTGAGCTGTCCTACTAAACACAACAATTTCTCTCTTTTCTTCTCTTCATT
66 CTTCACCAGAATTTTTGAGCTCTCCTACTAAACACAACAATTTCTCTCTTTTCTTCTCTTCAGT
*
27857926 TCAACATTACCTTTTACAATTTCACCATAAAAAAGAATGTACACTAAAAACACTAAGTTATTCAT
1 TCAACATCACCTTTTACAATTTCACCATAAAAAAGAATGTACACTAAAAACACTAAGTTATTCAT
27857991 CTTCACCAGAATTTTTGAGCTCTCCTACTAAACACAACAATTTCTCTCTTTTCTTCTCTTCAGT
66 CTTCACCAGAATTTTTGAGCTCTCCTACTAAACACAACAATTTCTCTCTTTTCTTCTCTTCAGT
27858055 TCAAC
1 TCAAC
27858060 TGTTACAAAA
Statistics
Matches: 130, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
129 130 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.35
Consensus pattern (129 bp):
TCAACATCACCTTTTACAATTTCACCATAAAAAAGAATGTACACTAAAAACACTAAGTTATTCAT
CTTCACCAGAATTTTTGAGCTCTCCTACTAAACACAACAATTTCTCTCTTTTCTTCTCTTCAGT
Found at i:27860130 original size:28 final size:27
Alignment explanation
Indices: 27860080--27860132 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
27860070 CGTATGTGAA
*
27860080 ATAATTTAAAATAAAAATTAAAAAAAC
1 ATAATTTAAAATAAAAATCAAAAAAAC
27860107 ATAATTTTAAAATTAAAAA-CAAAAAA
1 ATAA-TTTAAAA-TAAAAATCAAAAAA
27860133 TAAAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 13 0.57
29 6 0.26
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (27 bp):
ATAATTTAAAATAAAAATCAAAAAAAC
Found at i:27861135 original size:69 final size:69
Alignment explanation
Indices: 27861024--27861154 Score: 246
Period size: 69 Copynumber: 1.9 Consensus size: 69
27861014 CAGAGCTACA
27861024 TTGAATTTAGTATAACAATTGCTCTTCTCGTTGAGAGAAAAATCATAAAGTGACTTTCCTGACTT
1 TTGAATTTAGTATAACAATTGCTCTTCTCGTTGAGAGAAAAATCATAAAGTGACTTTCCTGACTT
27861089 TAGG
66 TAGG
27861093 TTGAATTTAGTATAACAATTGCTCTTCTCAG-TGAGAGAAAAATCATAAAGTGACTTTCCTGA
1 TTGAATTTAGTATAACAATTGCTCTTCTC-GTTGAGAGAAAAATCATAAAGTGACTTTCCTGA
27861155 GAAGATGATA
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
69 60 0.98
70 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (69 bp):
TTGAATTTAGTATAACAATTGCTCTTCTCGTTGAGAGAAAAATCATAAAGTGACTTTCCTGACTT
TAGG
Found at i:27862434 original size:13 final size:13
Alignment explanation
Indices: 27862391--27862435 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
27862381 TCAAGCATGA
27862391 TATTTCTGTATCTG
1 TATTT-TGTATCTG
** *
27862405 TATACTGTTTCTG
1 TATTTTGTATCTG
27862418 TATTTTGTATCTG
1 TATTTTGTATCTG
27862431 TATTT
1 TATTT
27862436 GGGGTGGAGT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
13 22 0.88
14 3 0.12
ACGTcount: A:0.16, C:0.11, G:0.13, T:0.60
Consensus pattern (13 bp):
TATTTTGTATCTG
Found at i:27870273 original size:17 final size:17
Alignment explanation
Indices: 27870251--27870285 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
27870241 ACGGATTAGG
27870251 TGATATGTTTTATGAAA
1 TGATATGTTTTATGAAA
27870268 TGATATGTTTTATGAAA
1 TGATATGTTTTATGAAA
27870285 T
1 T
27870286 TTTATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (17 bp):
TGATATGTTTTATGAAA
Found at i:27871024 original size:5 final size:5
Alignment explanation
Indices: 27871011--27871041 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
27871001 ACGTAAGTTC
*
27871011 TTAAA TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT T
27871042 ACTATTTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TTAAT
Found at i:27871178 original size:45 final size:45
Alignment explanation
Indices: 27871129--27871247 Score: 132
Period size: 45 Copynumber: 2.6 Consensus size: 45
27871119 ATCAAACAAG
* * * *
27871129 TAAGACCATAGATGAAAGACACTATGGCACTAT-ACCAGAATCAAA
1 TAAGACCATAGTTGAAAGACACTATGACAATATGACCAAAAT-AAA
* * * * *
27871174 TAAGACCATAGTTGAAAAAAATTATGACAATATGACGAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGACAATATGACCAAAATAAA
*
27871219 TAAGAACATAGTTGAAAGACACTATGACA
1 TAAGACCATAGTTGAAAGACACTATGACA
27871248 TCTTTGAGCA
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
45 54 0.90
46 6 0.10
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACTATGACAATATGACCAAAATAAA
Found at i:27873270 original size:27 final size:26
Alignment explanation
Indices: 27873240--27873303 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 26
27873230 TTTATTGAGG
*
27873240 TTATTAGTTTATCACTAAATGAATATT
1 TTATTAGTTTATCAATAAATGAATA-T
*
27873267 TTATTAGTTTATCAATAAATTAATAT
1 TTATTAGTTTATCAATAAATGAATAT
*
27873293 TTATTAATTTA
1 TTATTAGTTTA
27873304 AAGAATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 11 0.32
27 23 0.68
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (26 bp):
TTATTAGTTTATCAATAAATGAATAT
Found at i:27873453 original size:34 final size:33
Alignment explanation
Indices: 27873381--27873446 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 33
27873371 TGAATCAAAG
* * *
27873381 TTAATTGGTTCATGTAACAAAAAAAGAGAGTTAA
1 TTAATTGATTCATGTAACAAAAAAAAAAAG-TAA
27873415 TTAATTGATTCATGTAACTAAAAAGAAAAAAG
1 TTAATTGATTCATGTAAC-AAAAA-AAAAAAG
27873447 ATTTAATGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
34 17 0.63
35 5 0.19
36 5 0.19
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (33 bp):
TTAATTGATTCATGTAACAAAAAAAAAAAGTAA
Found at i:27875979 original size:30 final size:30
Alignment explanation
Indices: 27875943--27876006 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
27875933 GTCTTAAATT
27875943 GTGTAACTCACTGACTTAGAT-CACACGCCC
1 GTGTAACTCACTGACTT-GATACACACGCCC
** *
27875973 GTGTAACTTTCTGACTTGATACACACGGCC
1 GTGTAACTCACTGACTTGATACACACGCCC
27876003 GTGT
1 GTGT
27876007 GCCAGACCGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 3 0.10
30 27 0.90
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (30 bp):
GTGTAACTCACTGACTTGATACACACGCCC
Found at i:27876030 original size:42 final size:42
Alignment explanation
Indices: 27875983--27876090 Score: 171
Period size: 42 Copynumber: 2.6 Consensus size: 42
27875973 GTGTAACTTT
* *
27875983 CTGACTTGATACACACGGCCGTGTGCCAGACCGTGTGGCTCA
1 CTGACTTGATACACACGGCCGTGTGCCAAACCGTGTGACTCA
*
27876025 CTGACTTGATACAGACGGCCGTGTGCCAAACCGTGTGACTCA
1 CTGACTTGATACACACGGCCGTGTGCCAAACCGTGTGACTCA
* *
27876067 CTAACTTGATACACACGGTCGTGT
1 CTGACTTGATACACACGGCCGTGT
27876091 CATAGACCGT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.22, C:0.29, G:0.26, T:0.23
Consensus pattern (42 bp):
CTGACTTGATACACACGGCCGTGTGCCAAACCGTGTGACTCA
Found at i:27876100 original size:42 final size:42
Alignment explanation
Indices: 27875986--27876102 Score: 157
Period size: 42 Copynumber: 2.8 Consensus size: 42
27875976 TAACTTTCTG
* * *
27875986 ACTTGATACACACGGCCGTGTGCCAGACCGTGTGGCTCACTG
1 ACTTGATACACACGGCCGTGTGCAAGACCGTGTGACTCACTA
*
27876028 ACTTGATACAGACGGCCGTGTGCCAA-ACCGTGTGACTCACTA
1 ACTTGATACACACGGCCGTGTG-CAAGACCGTGTGACTCACTA
*
27876070 ACTTGATACACACGGTCGTGT-CATAGACCGTGT
1 ACTTGATACACACGGCCGTGTGCA-AGACCGTGT
27876103 ATGGCACACA
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
40 2 0.03
41 1 0.02
42 61 0.92
43 2 0.03
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.23
Consensus pattern (42 bp):
ACTTGATACACACGGCCGTGTGCAAGACCGTGTGACTCACTA
Found at i:27884328 original size:45 final size:45
Alignment explanation
Indices: 27884272--27884525 Score: 262
Period size: 45 Copynumber: 5.6 Consensus size: 45
27884262 GAAATACGAG
*
27884272 TAAGACCATAATTGAAAGACACTATAGCACTATACCAGAAATGAA
1 TAAGACCATAATTGAAAGACACTATGGCACTATACCAGAAATGAA
* * * * *
27884317 AAAGACGATAATTGAAAGACACAATGGCACTATATCAAAAATGAA
1 TAAGACCATAATTGAAAGACACTATGGCACTATACCAGAAATGAA
* * * * *
27884362 TAAGATCATAGTTAAAAGACACTATGACACTATACCGGAAATGAA
1 TAAGACCATAATTGAAAGACACTATGGCACTATACCAGAAATGAA
**
27884407 TAAGACCATAGCTGAAAGACACTATGGCACTATACCA-AAATCGAA
1 TAAGACCATAATTGAAAGACACTATGGCACTATACCAGAAAT-GAA
* * * * * * **
27884452 TAAGACCACAGTTGAAAAACATTGTGGCAATATGA-TGGAAATGAA
1 TAAGACCATAATTGAAAGACACTATGGCACTAT-ACCAGAAATGAA
*
27884497 TAAGACCATAGTTGAAA-AGCACTATGGCA
1 TAAGACCATAATTGAAAGA-CACTATGGCA
27884526 TCATGTCAAA
Statistics
Matches: 173, Mismatches: 32, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
44 5 0.03
45 163 0.94
46 5 0.03
ACGTcount: A:0.47, C:0.16, G:0.17, T:0.20
Consensus pattern (45 bp):
TAAGACCATAATTGAAAGACACTATGGCACTATACCAGAAATGAA
Found at i:27884520 original size:135 final size:135
Alignment explanation
Indices: 27884272--27884522 Score: 319
Period size: 135 Copynumber: 1.9 Consensus size: 135
27884262 GAAATACGAG
* * * *
27884272 TAAGACCATAATTGAAAGACACTATAGCACTATACCAGAAATGAAAAAGACGATAATTGAAAGAC
1 TAAGACCATAACTGAAAGACACTATAGCACTATACCAGAAATGAAAAAGACCACAATTGAAAAAC
* *
27884337 ACAATGGCACTATATCAAAAATGAATAAGATCATAGTTAAAAGACACTATGACACTATACCGGAA
66 ACAATGGCAATATATCAAAAATGAATAAGACCATAGTTAAAAGACACTATGACACTATACCGGAA
27884402 ATGAA
131 ATGAA
* * * *
27884407 TAAGACCATAGCTGAAAGACACTATGGCACTATACCA-AAATCGAATAAGACCACAGTTGAAAAA
1 TAAGACCATAACTGAAAGACACTATAGCACTATACCAGAAAT-GAAAAAGACCACAATTGAAAAA
*** **
27884471 CATTGTGGCAATATGAT-GGAAATGAATAAGACCATAGTTGAAAAG-CACTATG
65 CACAATGGCAATAT-ATCAAAAATGAATAAGACCATAGTT-AAAAGACACTATG
27884523 GCATCATGTC
Statistics
Matches: 98, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
134 4 0.04
135 87 0.89
136 7 0.07
ACGTcount: A:0.47, C:0.16, G:0.17, T:0.20
Consensus pattern (135 bp):
TAAGACCATAACTGAAAGACACTATAGCACTATACCAGAAATGAAAAAGACCACAATTGAAAAAC
ACAATGGCAATATATCAAAAATGAATAAGACCATAGTTAAAAGACACTATGACACTATACCGGAA
ATGAA
Found at i:27888778 original size:19 final size:19
Alignment explanation
Indices: 27888754--27888793 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
27888744 AAAAGTACCT
*
27888754 AAAAAATACTATGACAAGA
1 AAAAAATACTACGACAAGA
27888773 AAAAAATACTACGACAAGA
1 AAAAAATACTACGACAAGA
27888792 AA
1 AA
27888794 TATGAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.65, C:0.12, G:0.10, T:0.12
Consensus pattern (19 bp):
AAAAAATACTACGACAAGA
Found at i:27897526 original size:63 final size:63
Alignment explanation
Indices: 27897457--27897581 Score: 162
Period size: 63 Copynumber: 2.0 Consensus size: 63
27897447 TGTTTAGTCT
* * * *
27897457 GGTTCATCTGATGATAAAGGTTTGTATATTTCTA-TAATGAAACCAAGTTTTGTTTGAATGTCC
1 GGTTCATCTAATGACAAAGATTTGTATATTTCAATTAATGAAACCAAGTTTT-TTTGAATGTCC
* * * *
27897520 GGTTCATCTAATGACAAAGATTTTTATGTTTCAATTGATGAAACTAAGTTTTTTTGAATGTC
1 GGTTCATCTAATGACAAAGATTTGTATATTTCAATTAATGAAACCAAGTTTTTTTGAATGTC
27897582 TGGATTGTAG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
63 38 0.72
64 15 0.28
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (63 bp):
GGTTCATCTAATGACAAAGATTTGTATATTTCAATTAATGAAACCAAGTTTTTTTGAATGTCC
Found at i:27903086 original size:65 final size:65
Alignment explanation
Indices: 27902982--27903111 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
27902972 CATGTCAAGA
27902982 AAGGAAAGCCTTTGTGACACAATATGAAAGTAAAGCATTTGTGGTGAATTATGAAAATAACGCCT
1 AAGGAAAGCCTTTGTGACACAATATGAAAGTAAAGCATTTGTGGTGAATTATGAAAATAACGCCT
27903047 AAGGAAAGCCTTTGTGACACAATATGAAAGTAAAGCATTTGTGGTGAATTATGAAAATAACGCCT
1 AAGGAAAGCCTTTGTGACACAATATGAAAGTAAAGCATTTGTGGTGAATTATGAAAATAACGCCT
27903112 TTCTAGCACA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (65 bp):
AAGGAAAGCCTTTGTGACACAATATGAAAGTAAAGCATTTGTGGTGAATTATGAAAATAACGCCT
Found at i:27903138 original size:27 final size:28
Alignment explanation
Indices: 27903047--27903198 Score: 100
Period size: 27 Copynumber: 5.6 Consensus size: 28
27903037 AATAACGCCT
27903047 AAGGAAAGCCTTTGT-GACACAATATGA
1 AAGGAAAGCCTTTGTGGACACAATATGA
* * ** *
27903074 AAGTAAAGCATTTGTGGTGA-ATTATGA
1 AAGGAAAGCCTTTGTGGACACAATATGA
** * * *
27903101 AAATAACGCCTTTCTAG-CACAATATGA
1 AAGGAAAGCCTTTGTGGACACAATATGA
* * *
27903128 AAGGAAAGCCTTTATGG-CGCAATATAA
1 AAGGAAAGCCTTTGTGGACACAATATGA
* *
27903155 AAGGAACGCTTTTGTGG-CA-AATCATGA
1 AAGGAAAGCCTTTGTGGACACAAT-ATGA
* *
27903182 AGGGATAGCCTTTGTGG
1 AAGGAAAGCCTTTGTGG
27903199 CAAACCCTGC
Statistics
Matches: 94, Mismatches: 28, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
26 4 0.04
27 88 0.94
28 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (28 bp):
AAGGAAAGCCTTTGTGGACACAATATGA
Found at i:27903163 original size:54 final size:54
Alignment explanation
Indices: 27903047--27903199 Score: 143
Period size: 54 Copynumber: 2.8 Consensus size: 54
27903037 AATAACGCCT
* * * *
27903047 AAGGAAAGCCTTTGTGACACAATATGAAAGTAAAGCATTTGTGGTGAATTATGAA
1 AAGGAACGCCTTTGTG-CACAATATGAAAGGAAAGCCTTTGTGGCGAATTATGAA
* * *
27903102 AA-TAACGCCTTTCTAGCACAATATGAAAGGAAAGCCTTTATGGCGCAA-TAT-AA
1 AAGGAACGCCTTTGT-GCACAATATGAAAGGAAAGCCTTTGTGGCG-AATTATGAA
* * *
27903155 AAGGAACGCTTTTGTGGCA-AATCATGAAGGGATAGCCTTTGTGGC
1 AAGGAACGCCTTTGT-GCACAAT-ATGAAAGGAAAGCCTTTGTGGC
27903200 AAACCCTGCA
Statistics
Matches: 80, Mismatches: 14, Indels: 9
0.78 0.14 0.09
Matches are distributed among these distances:
53 7 0.09
54 68 0.85
55 5 0.06
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (54 bp):
AAGGAACGCCTTTGTGCACAATATGAAAGGAAAGCCTTTGTGGCGAATTATGAA
Found at i:27903199 original size:27 final size:27
Alignment explanation
Indices: 27903165--27903225 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
27903155 AAGGAACGCT
*
27903165 TTTGTGGCAAATCATG-AAGGGATAGCC
1 TTTGTGGCAAACCATGCAA-GGATAGCC
* *
27903192 TTTGTGGCAAACCCTGCAATGATAGCC
1 TTTGTGGCAAACCATGCAAGGATAGCC
27903219 TTTGTGG
1 TTTGTGG
27903226 TAATAGTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 28 0.93
28 2 0.07
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.30
Consensus pattern (27 bp):
TTTGTGGCAAACCATGCAAGGATAGCC
Found at i:27906490 original size:49 final size:49
Alignment explanation
Indices: 27906417--27906543 Score: 123
Period size: 50 Copynumber: 2.6 Consensus size: 49
27906407 CAAACACTAC
* * * * * * * *
27906417 TTATGAAAATAAGTAATTGT-TAAAAAAGTTATTTTTCAGATTCTTTTAG
1 TTATGAAAATTAGT-ATTTTCTAAAAAAATTATCTGTCAAATTCATTTAA
27906466 TTATGAAAATTAGTATTTTCTAAAAATAATTATCTGTCAAATTCATTTAA
1 TTATGAAAATTAGTATTTTCTAAAAA-AATTATCTGTCAAATTCATTTAA
* *
27906516 TTATAAAAAATT-GTATTTGCTAAAAAAA
1 TTAT-GAAAATTAGTATTTTCTAAAAAAA
27906544 AAATGGTCAT
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
48 4 0.06
49 21 0.32
50 34 0.52
51 6 0.09
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (49 bp):
TTATGAAAATTAGTATTTTCTAAAAAAATTATCTGTCAAATTCATTTAA
Found at i:27912910 original size:29 final size:29
Alignment explanation
Indices: 27912865--27912922 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
27912855 TATTCCCTAA
27912865 CGAATTTCTATCAAAATCACAATTTTAGT
1 CGAATTTCTATCAAAATCACAATTTTAGT
*
27912894 CGAATTTCTATCGAAATCACAATTTTAGT
1 CGAATTTCTATCAAAATCACAATTTTAGT
27912923 TAATTCAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (29 bp):
CGAATTTCTATCAAAATCACAATTTTAGT
Found at i:27915753 original size:15 final size:16
Alignment explanation
Indices: 27915726--27915759 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
27915716 CCCTTTTCTC
*
27915726 TTCTTTATAATTTTTT
1 TTCTTTATAATTTGTT
27915742 TTCTTT-TAATTTGTT
1 TTCTTTATAATTTGTT
27915757 TTC
1 TTC
27915760 ATAAACTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.15, C:0.09, G:0.03, T:0.74
Consensus pattern (16 bp):
TTCTTTATAATTTGTT
Found at i:27919971 original size:18 final size:18
Alignment explanation
Indices: 27919948--27920008 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
27919938 CAATTTAAGT
27919948 TGAGCTCGCATCTTTTTA-
1 TGAGCTCGCA-CTTTTTAG
27919966 TGAGCTCGCAC-TTTTAG
1 TGAGCTCGCACTTTTTAG
*
27919983 TTGAGCTCGCAAC-TTTTGG
1 -TGAGCTCGC-ACTTTTTAG
27920002 TGAGCTC
1 TGAGCTC
27920009 ACAAATGTAG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
16 5 0.13
17 1 0.03
18 26 0.67
19 7 0.18
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (18 bp):
TGAGCTCGCACTTTTTAG
Found at i:27928268 original size:24 final size:24
Alignment explanation
Indices: 27928235--27928286 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
27928225 TTCGTAGGTC
*
27928235 AAATAAATTATA-TCAATAAATGCT
1 AAATAAATTATACT-AATAAATACT
*
27928259 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
27928283 AAAT
1 AAAT
27928287 CTTCTCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:27931845 original size:27 final size:27
Alignment explanation
Indices: 27931810--27931879 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
27931800 GAATAAATTC
27931810 AAGGTGTCAATCTTTCTTTTCTTTCAA
1 AAGGTGTCAATCTTTCTTTTCTTTCAA
*
27931837 AAGGCGTCAATCTTTCTTTTCTTTCAA
1 AAGGTGTCAATCTTTCTTTTCTTTCAA
*
27931864 AAGGTTTCAATCTTTC
1 AAGGTGTCAATCTTTC
27931880 ATACGTTTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (27 bp):
AAGGTGTCAATCTTTCTTTTCTTTCAA
Found at i:27935632 original size:34 final size:34
Alignment explanation
Indices: 27935589--27935660 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 34
27935579 ACATGTACAT
*
27935589 TTTAGAATATACATAT-ATTTTCTATA-TAT-TATAA
1 TTTAAAATATACAT-TCATTTT-TATAGTATATAT-A
27935623 TTTAAAATATACATTCATTTTTATAGTATATATA
1 TTTAAAATATACATTCATTTTTATAGTATATATA
27935657 TTTA
1 TTTA
27935661 CATTTTTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
33 5 0.15
34 26 0.76
35 3 0.09
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (34 bp):
TTTAAAATATACATTCATTTTTATAGTATATATA
Found at i:27941406 original size:132 final size:132
Alignment explanation
Indices: 27941093--27942163 Score: 1402
Period size: 132 Copynumber: 7.9 Consensus size: 132
27941083 CTACATAGAC
* * * *
27941093 AGTGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGATTACAGTGGAGTATATTGAAGCCA
1 AGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
* *
27941158 GTAATTCTA-TCTCTCTGGACAGCAGTGGAATAGATTGAAGTTTAAAGATTTCAGATCTTGTCTC
66 GTAATTCTACT-TCCCTGGGCAGCAGTGGAATAGATT---G----AAGATTTCAGATCTTGTCTC
*
27941222 CCCAAGCAGT
123 CCTAAGCAGT
*
27941232 AGTGGAGCAGATCAAAGATGG-TGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
1 AGTGGAGCAGATCAAAGATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
27941296 AGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGC
65 AGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGC
*
27941361 GGT
130 AGT
* * *
27941364 AGTGGAGCAGATCAAAGATGG-TGAATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGAC
1 AGTGGAGCAGATCAAAGATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
* * * * *
27941428 AGTAATTCTACTTCTCTGAGCAGTAGTGGAGTAGATTGAAGATTTCAGATATTGTCTCCCTAAGC
65 AGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGC
*
27941493 GGT
130 AGT
* *
27941496 AGTGGAGCAGATCAAAGATGGCAGATTTTACCTTCCTGTGGTTACAGCGGAGTACATTGAAGCCA
1 AGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
* * * * *
27941561 GTAATTCTACTTCCCTGGACAGCAGCGGAATAGATTGAAGATTTCAGATATTGCCTTCCT--GCA
66 GTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCA
27941624 -T
131 GT
* * *
27941625 AGACAGCGAAGCAGATCAAAGATGGCAGATTTTACCTTCCTGTGGTTACAGCGGAGTACATTGAA
1 AG--TG-G-AGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAA
*
27941690 GCCAGTAATTCTACTTCCCTAGGCAGCAGTGGAATAGATTGAAGATTGAAGATTTCAGATCTTGT
62 GCCAGTAATTCTACTTCCCTGGGCAGCAGTGG---A-A-T--AGATTGAAGATTTCAGATCTTGT
27941755 CTCCCTAAGCAGT
120 CTCCCTAAGCAGT
27941768 AGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
1 AGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
*
27941833 -TAAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGC
66 GT-AATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGC
27941897 AGT
130 AGT
27941900 AGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
1 AGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
** *
27941965 GTAATTCTACTTCCCTAAGCAGCAGTGGAATAGATTGAAGATTGAAGATTTCAGATCTTATCTCC
66 GTAATTCTACTTCCCTGGGCAGCAGTGG---A-A-T--AGATTGAAGATTTCAGATCTTGTCTCC
*
27942030 CTAAACAGT
124 CTAAGCAGT
* * * * * *
27942039 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTTCCTGAGGTTACAGTGAAGTATATTGAAGCCA
1 AGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
** * * * *
27942104 GTAATTCTA-TCTCCCTGGGCAATAGTGGAATGGATTGAAGATTACAGGTCTTATCTCCCT
66 GTAATTCTACT-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCT
27942164 GAAGTTGCTG
Statistics
Matches: 845, Mismatches: 60, Indels: 61
0.87 0.06 0.06
Matches are distributed among these distances:
129 3 0.00
130 2 0.00
131 1 0.00
132 414 0.49
133 87 0.10
134 2 0.00
135 3 0.00
136 5 0.01
137 2 0.00
138 4 0.00
139 287 0.34
140 28 0.03
141 1 0.00
142 3 0.00
143 3 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
AGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
GTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCA
GT
Found at i:27942002 original size:536 final size:540
Alignment explanation
Indices: 27941069--27942146 Score: 1672
Period size: 536 Copynumber: 2.0 Consensus size: 540
27941059 TTGAGGATAG
* * *
27941069 CAGATTTTTCCTTCCTACATAGACAGTGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGA
1 CAGATATTGCCTTCCTACATAGACAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGA
* * * *
27941134 TTACAGTGGAGTATATTGAAGCCAGTAATTCTATCTCTCTGGACAGCAGTGGAATAGATTGAAGT
66 TTACAGCGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGACAGCAGTGGAATAGATTGAAGA
*
27941199 TTAAAGATTTCAGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACC
131 TTAAAGATTTCAGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGAGAATTTTACC
*
27941264 TCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATA
196 TCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATA
* *
27941329 GATTGAAGATTTCAGATCTTGTCTCCCTAAGCGGTAGTGGAGCAGATCAAAGATGGTGAATTTTA
261 GATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGAGAATTTTA
* * *
27941394 CCTCCCTGTGGTTACAGTAGAGTACATTGAAGACAGTAATTCTACTTCTCTGAGCAGTAGTGG-A
326 CCTCCCTGTGGTTACAGTAGAGTACATTGAAGACAGTAATTCTACTTCCCTAAGCAGCAGTGGAA
* * *
27941458 G--T-AGATTGAAGATTTCAGATATTGTCTCCCTAAGCGGTAGTGGAGCAGATCAAAGATGGCAG
391 GATTAAGATTGAAGATTTCAGATATTATCTCCCTAAACAGTAGTGGAGCAGATCAAAGATGGCAG
* * *
27941520 ATTTTACCTTCCTGTGGTTACAGCGGAGTACATTGAAGCCAGTAATTCTA-CTTCCCTGGACAGC
456 ATTTTACCTTCCTGAGGTTACAGCGAAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGACAAC
27941584 AGCGGAATAGATTGAAGATTT
520 AGCGGAATAGATTGAAGATTT
* * * *
27941605 CAGATATTGCCTTCCTGCATAGACAGCGAAGCAGATCAAAGATGGCAGATTTTACCTTCCTGTGG
1 CAGATATTGCCTTCCTACATAGACAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGA
27941670 TTACAGCGGAGTACATTGAAGCCAGTAATTCTA-CTTCCCTAGG-CAGCAGTGGAATAGATTGAA
66 TTACAGCGGAGTACATTGAAGCCAGTAATTCTATC-TCCCT-GGACAGCAGTGGAATAGATTGAA
* *
27941733 GATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAG-ATTTT
129 GATTAAAGATTTCAGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGG-AGAATTTT
27941797 ACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA-TAAATTCTACTTCCCTGGGCAGCAGCGG
193 ACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGT-AATTCTACTTCCCTGGGCAGCAGCGG
27941861 AATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAG-A
257 AATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGG-AGAA
* *
27941925 TTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTAAGCAGCAG
321 TTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGACAGTAATTCTACTTCCCTAAGCAGCAG
* *
27941990 TGGAATAGATTGAAGATTGAAGATTTCAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAA
386 TGG-A-AGATT-AAGATTGAAGATTTCAGATATTATCTCCCTAAACAGTAGTGGAGCAGATCAAA
* * *
27942055 GATGGCGGATTTTACCTTCCTGAGGTTACAGTGAAGTATATTGAAGCCAGTAATTCTATCTCCCT
448 GATGGCAGATTTTACCTTCCTGAGGTTACAGCGAAGTACATTGAAGCCAGTAATTCTATCTCCCT
* * * *
27942120 GGGCAATAGTGGAATGGATTGAAGATT
513 GGACAACAGCGGAATAGATTGAAGATT
27942147 ACAGGTCTTA
Statistics
Matches: 492, Mismatches: 37, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
535 2 0.00
536 355 0.72
537 4 0.01
539 2 0.00
541 1 0.00
543 127 0.26
544 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (540 bp):
CAGATATTGCCTTCCTACATAGACAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGA
TTACAGCGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGACAGCAGTGGAATAGATTGAAGA
TTAAAGATTTCAGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGAGAATTTTACC
TCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATA
GATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGAGAATTTTA
CCTCCCTGTGGTTACAGTAGAGTACATTGAAGACAGTAATTCTACTTCCCTAAGCAGCAGTGGAA
GATTAAGATTGAAGATTTCAGATATTATCTCCCTAAACAGTAGTGGAGCAGATCAAAGATGGCAG
ATTTTACCTTCCTGAGGTTACAGCGAAGTACATTGAAGCCAGTAATTCTATCTCCCTGGACAACA
GCGGAATAGATTGAAGATTT
Found at i:27943023 original size:6 final size:6
Alignment explanation
Indices: 27942981--27943009 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
27942971 CTTAGTTTCG
27942981 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
27943010 TCCCTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:27943604 original size:3 final size:3
Alignment explanation
Indices: 27943585--27943646 Score: 103
Period size: 3 Copynumber: 21.7 Consensus size: 3
27943575 TTACTGTTTA
27943585 ATT ATT -TT -TT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
27943630 ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
27943647 AATCATTATC
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 6 0.11
3 51 0.89
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:27946166 original size:13 final size:13
Alignment explanation
Indices: 27946147--27946189 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
27946137 TTAAAATTAA
27946147 CAAAACACTTTTC
1 CAAAACACTTTTC
*
27946160 CACAACACTTTT-
1 CAAAACACTTTTC
27946172 CAAAAGCACTTTTC
1 CAAAA-CACTTTTC
27946186 CAAA
1 CAAA
27946190 CCAAGCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 4 0.15
13 18 0.69
14 4 0.15
ACGTcount: A:0.40, C:0.30, G:0.02, T:0.28
Consensus pattern (13 bp):
CAAAACACTTTTC
Found at i:27955862 original size:25 final size:24
Alignment explanation
Indices: 27955837--27955897 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 24
27955827 CTTTTTTTAT
27955837 ATTTTTTATAATTTTTTAAAAATATA
1 ATTTTTTA-AA-TTTTTAAAAATATA
* *
27955863 AATTTTGAAATTTTTAAAAATATTA
1 ATTTTTTAAATTTTTAAAAATA-TA
27955888 ATTTTTTAAA
1 ATTTTTTAAA
27955898 ATATAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 12 0.40
25 12 0.40
26 6 0.20
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTTTTTAAATTTTTAAAAATATA
Found at i:27955881 original size:24 final size:24
Alignment explanation
Indices: 27955849--27955925 Score: 89
Period size: 24 Copynumber: 3.5 Consensus size: 24
27955839 TTTTTATAAT
27955849 TTTTTAAAAATATAAATTTTGAAA
1 TTTTTAAAAATATAAATTTTGAAA
27955873 TTTTT-AAAA-AT--A--TT--AA
1 TTTTTAAAAATATAAATTTTGAAA
*
27955889 TTTTTTAAAATATAAATTTTGAAA
1 TTTTTAAAAATATAAATTTTGAAA
27955913 TTTTTAAAAATAT
1 TTTTTAAAAATAT
27955926 TTTTAATTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 16
0.72 0.02 0.26
Matches are distributed among these distances:
16 7 0.16
17 4 0.09
18 4 0.09
20 2 0.05
22 4 0.09
23 4 0.09
24 19 0.43
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (24 bp):
TTTTTAAAAATATAAATTTTGAAA
Found at i:27955890 original size:16 final size:16
Alignment explanation
Indices: 27955870--27955908 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
27955860 ATAAATTTTG
27955870 AAATTTTTAAAAATAT
1 AAATTTTTAAAAATAT
* *
27955886 TAATTTTTTAAAATAT
1 AAATTTTTAAAAATAT
27955902 AAATTTT
1 AAATTTT
27955909 GAAATTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AAATTTTTAAAAATAT
Found at i:27955902 original size:40 final size:41
Alignment explanation
Indices: 27955845--27955926 Score: 157
Period size: 40 Copynumber: 2.0 Consensus size: 41
27955835 ATATTTTTTA
27955845 TAATTTTTTAAAAATATAAATTTTGAAATTTTTAAAAATAT
1 TAATTTTTTAAAAATATAAATTTTGAAATTTTTAAAAATAT
27955886 TAATTTTTT-AAAATATAAATTTTGAAATTTTTAAAAATAT
1 TAATTTTTTAAAAATATAAATTTTGAAATTTTTAAAAATAT
27955926 T
1 T
27955927 TTTAATTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 32 0.78
41 9 0.22
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (41 bp):
TAATTTTTTAAAAATATAAATTTTGAAATTTTTAAAAATAT
Found at i:27955935 original size:18 final size:19
Alignment explanation
Indices: 27955904--27955952 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
27955894 TAAAATATAA
27955904 ATTTTGAAATTTTTAAAAAT-
1 ATTTTG-AA-TTTTAAAAATG
*
27955924 ATTTTTAATTTTAAAAATG
1 ATTTTGAATTTTAAAAATG
27955943 ATTTTGAATT
1 ATTTTGAATT
27955953 ATTTTGTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 10 0.38
19 11 0.42
20 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
ATTTTGAATTTTAAAAATG
Found at i:27957756 original size:3 final size:3
Alignment explanation
Indices: 27957748--27957787 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
27957738 AGTCAAAGCA
27957748 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
27957788 CTTGATTCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:27957978 original size:3 final size:3
Alignment explanation
Indices: 27957964--27958004 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
27957954 TTTGTAAGCA
*
27957964 ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
27958005 TGATTCTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
ATT
Found at i:27962081 original size:3 final size:3
Alignment explanation
Indices: 27962073--27962112 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
27962063 TTTCAACTTT
27962073 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
27962113 ATTACAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:27972592 original size:30 final size:28
Alignment explanation
Indices: 27972528--27972592 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 28
27972518 AATGGAAAGT
*
27972528 AAAGAAAAAGAAAAAACAAAGAAAATAA
1 AAAGAAAAAGAAAAAACAAAAAAAATAA
27972556 ATAAGAAATAAGAAAAAA-AAACAAAAATAA
1 A-AAGAAA-AAGAAAAAACAAA-AAAAATAA
27972586 GAAAGAA
1 -AAAGAA
27972593 CGTTAATTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 1 0.03
29 9 0.28
30 21 0.66
31 1 0.03
ACGTcount: A:0.80, C:0.03, G:0.11, T:0.06
Consensus pattern (28 bp):
AAAGAAAAAGAAAAAACAAAAAAAATAA
Found at i:27983890 original size:45 final size:45
Alignment explanation
Indices: 27983820--27983934 Score: 117
Period size: 45 Copynumber: 2.6 Consensus size: 45
27983810 TATACGCCTA
* * *
27983820 AAATGAGTAAGAACC-TAGTTAAAAGACACTATGGTATCATGATTA-
1 AAATGAGTAAG-ACCATAGTTGAAAGACACTATAGCATCATGA-TAG
* *** *
27983865 AGATGAGTAAGACCATAGTTGAAAGATGTTATAGCATCGTGATAG
1 AAATGAGTAAGACCATAGTTGAAAGACACTATAGCATCATGATAG
*
27983910 AAATGAGTAAGACCATAGCTGAAAG
1 AAATGAGTAAGACCATAGTTGAAAG
27983935 GCGCTATGAC
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
44 5 0.09
45 53 0.91
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.24
Consensus pattern (45 bp):
AAATGAGTAAGACCATAGTTGAAAGACACTATAGCATCATGATAG
Found at i:27984231 original size:27 final size:27
Alignment explanation
Indices: 27984180--27984232 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
27984170 GATGACACAT
* *
27984180 TAAACACGGGATAGTTCGACGGGACAA
1 TAAACACGAGATAGTTCGACAGGACAA
* *
27984207 TAAACACGAGATAGTTTGCCAGGACA
1 TAAACACGAGATAGTTCGACAGGACA
27984233 CTACACTCAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (27 bp):
TAAACACGAGATAGTTCGACAGGACAA
Found at i:27987939 original size:257 final size:256
Alignment explanation
Indices: 27987483--27987993 Score: 959
Period size: 257 Copynumber: 2.0 Consensus size: 256
27987473 TAAATAATTT
27987483 AAAAAAATTAATAATTTTAAAATCATTTACTGACGTGGCATATAAGACAAAATAGTGCCATGTCA
1 AAAAAAATTAATAATTTTAAAATCATTTACTGACGTGGCATATAAGACAAAATAGTGCCATGTCA
27987548 CCATTTAAAAATATTTAGACTGCCACGTCAGCGGTTTATGTTGACCATTAGTCAACTAACTATCA
66 CCATTTAAAAATATTTAGACTGCCACGTCAGCGGTTTATGTTGACCATTAGTCAACTAACTATCA
*
27987613 CGTCAGCATGTCCGTTAAAATCAGACCAATTTGACTAAAAAACTTAGGTGTTAAAGTGCTCAAAA
131 CGTCAGCATGTCCGTTAAAAACAGACCAATTTGACTAAAAAACTTAGGTGTTAAAGTGCTC-AAA
*
27987678 AAAAAATGGCCAAAGTGATCAAACAACCAAACTTTAGGGGATGTTTTTAGTATTATGCCTAC
195 AAAAAATGGCCAAAGTGACCAAACAACCAAACTTTAGGGGATGTTTTTAGTATTATGCCTAC
*
27987740 AAAAAAATTAATAATTTTAAAATCATTTGCTGACGTGGCATATAAGACAAAATAGTGCCATGTCA
1 AAAAAAATTAATAATTTTAAAATCATTTACTGACGTGGCATATAAGACAAAATAGTGCCATGTCA
*
27987805 CCATTTAAAAATATTTGGACTGCCACGTCAGCGGTTTATGTTGACCATTAGTCAACTAACTATCA
66 CCATTTAAAAATATTTAGACTGCCACGTCAGCGGTTTATGTTGACCATTAGTCAACTAACTATCA
27987870 CGTCAGCATGTCCGTTAAAAACAGACCAATTTGACTAAAAAACTTAGGTGTTAAAGTGCTCAAAA
131 CGTCAGCATGTCCGTTAAAAACAGACCAATTTGACTAAAAAACTTAGGTGTTAAAGTGCTCAAAA
* *
27987935 AAAAATGGCCAAAGTGACCAAACAACCAAACTTTAGGGGCTGTTTTTGGTATTATGCCT
196 AAAAATGGCCAAAGTGACCAAACAACCAAACTTTAGGGGATGTTTTTAGTATTATGCCT
27987994 TCAATATTTA
Statistics
Matches: 248, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
256 60 0.24
257 188 0.76
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (256 bp):
AAAAAAATTAATAATTTTAAAATCATTTACTGACGTGGCATATAAGACAAAATAGTGCCATGTCA
CCATTTAAAAATATTTAGACTGCCACGTCAGCGGTTTATGTTGACCATTAGTCAACTAACTATCA
CGTCAGCATGTCCGTTAAAAACAGACCAATTTGACTAAAAAACTTAGGTGTTAAAGTGCTCAAAA
AAAAATGGCCAAAGTGACCAAACAACCAAACTTTAGGGGATGTTTTTAGTATTATGCCTAC
Found at i:27990114 original size:40 final size:40
Alignment explanation
Indices: 27990070--27990164 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 40
27990060 TCTTGAATAA
* *
27990070 GTGCTCCTGATAGTAC-TTTCGTCCTCCTGTTAGCACTACG
1 GTGCTCCTGATAGCACATTT-GTCCTCCTGTTAGCACCACG
* * * * *
27990110 GTGCTCTTAATAGCACATTTGTGCTCCTTTTAGCACCACT
1 GTGCTCCTGATAGCACATTTGTCCTCCTGTTAGCACCACG
*
27990150 TTGCTCCTGATAGCA
1 GTGCTCCTGATAGCA
27990165 TATTCATGCT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
40 41 0.93
41 3 0.07
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.36
Consensus pattern (40 bp):
GTGCTCCTGATAGCACATTTGTCCTCCTGTTAGCACCACG
Found at i:27990810 original size:2 final size:2
Alignment explanation
Indices: 27990803--27990844 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
27990793 GGTTTGTAAA
27990803 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
27990845 ATTTGAGATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:28000349 original size:108 final size:111
Alignment explanation
Indices: 28000160--28000376 Score: 413
Period size: 108 Copynumber: 2.0 Consensus size: 111
28000150 TAGTTCTGCC
28000160 ATCTGCAATGCATCATCCAATATATATATATATATATATTTATATATGAAATGCAATATTAACCA
1 ATCTGCAATGCATCATCCAATATATATATATATATATATTTATATATGAAATGCAATATTAACCA
28000225 AATTTTTTGAAGAAAAAAATGCATGTTATGATTGTTGTAGGAAGCA
66 AATTTTTTGAAGAAAAAAATGCATGTTATGATTGTTGTAGGAAGCA
28000271 ATCTGCAA-GCATCATCC-A-ATATATATATATATATATTTATATATGAAATGCAATATTAACCA
1 ATCTGCAATGCATCATCCAATATATATATATATATATATTTATATATGAAATGCAATATTAACCA
28000333 AATTTTTTGAAGAAAAAAATGCATGTTATGATTGTTGTAGGAAG
66 AATTTTTTGAAGAAAAAAATGCATGTTATGATTGTTGTAGGAAG
28000377 TTAGGGTTAT
Statistics
Matches: 106, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
108 88 0.83
109 1 0.01
110 9 0.08
111 8 0.08
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (111 bp):
ATCTGCAATGCATCATCCAATATATATATATATATATATTTATATATGAAATGCAATATTAACCA
AATTTTTTGAAGAAAAAAATGCATGTTATGATTGTTGTAGGAAGCA
Found at i:28008280 original size:22 final size:22
Alignment explanation
Indices: 28008255--28008296 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
28008245 TATTAAATTT
28008255 AAAATAATATAATAT-AATTTAA
1 AAAATAATATAA-ATGAATTTAA
28008277 AAAATAATATAAATGAATTT
1 AAAATAATATAAATGAATTT
28008297 GGATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAATAATATAAATGAATTTAA
Found at i:28010225 original size:147 final size:147
Alignment explanation
Indices: 28009958--28010243 Score: 493
Period size: 147 Copynumber: 1.9 Consensus size: 147
28009948 CAATAAAGCT
28009958 CAGTGGTACTTTCATGATTCAAGTAACAAATAAGCATATTCAATATAGAAATTCAATCAATATAT
1 CAGTGGTACTTTCATGATTCAAGTAACAAATAAGCATATTCAATATAGAAATTCAATCAATATAT
* *
28010023 GTCACAATTCAACCAAATAAATTTGCATATTCAATACTCAAATATCATACTTTTACTCCATTTCA
66 GCCACAATTCAACCAAATAAATTTGCATATTCAATACTCAAATATCATACTTTTACACCATTTCA
28010088 ATTGATGATTAAACTAG
131 ATTGATGATTAAACTAG
*
28010105 CAGTGGTACTTTCATGATTCAAGTCACAAATAAGCATACTT-AATATAGAAATTCAATCAATATA
1 CAGTGGTACTTTCATGATTCAAGTAACAAATAAGCATA-TTCAATATAGAAATTCAATCAATATA
* * * *
28010169 TGCCACAATTCAACCAGATCACTTTGCATATTCAATACTCAAATATCATACTTTTACACCGTTTC
65 TGCCACAATTCAACCAAATAAATTTGCATATTCAATACTCAAATATCATACTTTTACACCATTTC
28010234 AATTGATGAT
130 AATTGATGAT
28010244 CAAAATAGAA
Statistics
Matches: 131, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
147 129 0.98
148 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.34
Consensus pattern (147 bp):
CAGTGGTACTTTCATGATTCAAGTAACAAATAAGCATATTCAATATAGAAATTCAATCAATATAT
GCCACAATTCAACCAAATAAATTTGCATATTCAATACTCAAATATCATACTTTTACACCATTTCA
ATTGATGATTAAACTAG
Found at i:28013587 original size:21 final size:21
Alignment explanation
Indices: 28013561--28013775 Score: 177
Period size: 21 Copynumber: 10.3 Consensus size: 21
28013551 GTGTTTTACT
*
28013561 TTCTGTTCAGCTCTAATGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * * *
28013582 TTCTGTTTAACTCATATGAGT
1 TTCTGTTCAGCTCTTATGAGC
* *
28013603 TTCCGTTCAGCTCTTTTGAGC
1 TTCTGTTCAGCTCTTATGAGC
*
28013624 TTCTGTTCAACTCTTATGAG-
1 TTCTGTTCAGCTCTTATGAGC
* *
28013644 TTTTCATTCAGCTCTTATGAGC
1 TTCT-GTTCAGCTCTTATGAGC
* * *
28013666 TTCCGTTCAACTCTTATGAGT
1 TTCTGTTCAGCTCTTATGAGC
28013687 TTCTGTTCAGCTCTT-TCGAGC
1 TTCTGTTCAGCTCTTAT-GAGC
* * * * *
28013708 TTCTGTTAAACCCTTATGGGT
1 TTCTGTTCAGCTCTTATGAGC
* * *
28013729 TTTTGTTTAGCTCTCATGAGC
1 TTCTGTTCAGCTCTTATGAGC
* *
28013750 TTCTGTTTAGCT-TT-TGATC
1 TTCTGTTCAGCTCTTATGAGC
28013769 TTCTGTT
1 TTCTGTT
28013776 AACGATGTAC
Statistics
Matches: 150, Mismatches: 40, Indels: 10
0.75 0.20 0.05
Matches are distributed among these distances:
19 11 0.07
20 5 0.03
21 131 0.87
22 3 0.02
ACGTcount: A:0.16, C:0.21, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTATGAGC
Found at i:28013612 original size:42 final size:42
Alignment explanation
Indices: 28013560--28013756 Score: 245
Period size: 42 Copynumber: 4.7 Consensus size: 42
28013550 TGTGTTTTAC
* * *
28013560 TTTCTGTTCAGCTCTAATGAGCTTCTGTTTAACTCATATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACTCTTATGAG
* *
28013602 TTTCCGTTCAGCTCTTTTGAGCTTCTGTTCAACTCTTATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACTCTTATGAG
* *
28013644 TTT-TCATTCAGCTCTTATGAGCTTCCGTTCAACTCTTATGAG
1 TTTCT-GTTCAGCTCTTATGAGCTTCTGTTCAACTCTTATGAG
* * *
28013686 TTTCTGTTCAGCTCTT-TCGAGCTTCTGTTAAACCCTTATGGG
1 TTTCTGTTCAGCTCTTAT-GAGCTTCTGTTCAACTCTTATGAG
* * *
28013728 TTTTTGTTTAGCTCTCATGAGCTTCTGTT
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTT
28013757 TAGCTTTTGA
Statistics
Matches: 134, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.01
42 131 0.98
43 2 0.01
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (42 bp):
TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACTCTTATGAG
Found at i:28017181 original size:24 final size:21
Alignment explanation
Indices: 28017153--28017199 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 21
28017143 GAATAATATT
28017153 TATTTTATATAAAAATTATAAATA
1 TATTTT-TA-AAAAATTA-AAATA
28017177 TA-TTTTAAAAAATTAAAATA
1 TATTTTTAAAAAATTAAAATA
28017197 TAT
1 TAT
28017200 ATTAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
20 7 0.32
21 8 0.36
22 2 0.09
23 3 0.14
24 2 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATTTTTAAAAAATTAAAATA
Found at i:28017187 original size:20 final size:19
Alignment explanation
Indices: 28017158--28017205 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
28017148 ATATTTATTT
28017158 TATA-TAAAAATTATAAATA
1 TATATTAAAAATTA-AAATA
*
28017177 TATTTTAAAAAATTAAAATA
1 TATATT-AAAAATTAAAATA
28017197 TATATTAAA
1 TATATTAAA
28017206 TTAAGTCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 6 0.24
20 11 0.44
21 8 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TATATTAAAAATTAAAATA
Found at i:28017189 original size:21 final size:20
Alignment explanation
Indices: 28017163--28017205 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
28017153 TATTTTATAT
*
28017163 AAAAATTATAAATATATTTTA
1 AAAAATTA-AAATATATATTA
28017184 AAAAATTAAAATATATATTA
1 AAAAATTAAAATATATATTA
28017204 AA
1 AA
28017206 TTAAGTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAATTAAAATATATATTA
Found at i:28018358 original size:42 final size:42
Alignment explanation
Indices: 28018305--28018391 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
28018295 TGATATATAG
28018305 TTAGAATATGTTTTTAAATGATGTTTGGAATTGATGATTGAA
1 TTAGAATATGTTTTTAAATGATGTTTGGAATTGATGATTGAA
*
28018347 TTAGAATATGTTTTTAAATGATGTTTGGAATTTATGATTGAA
1 TTAGAATATGTTTTTAAATGATGTTTGGAATTGATGATTGAA
28018389 TTA
1 TTA
28018392 AATTATGATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (42 bp):
TTAGAATATGTTTTTAAATGATGTTTGGAATTGATGATTGAA
Found at i:28021982 original size:49 final size:49
Alignment explanation
Indices: 28021928--28022023 Score: 192
Period size: 49 Copynumber: 2.0 Consensus size: 49
28021918 ACTCCCCAAA
28021928 GGAGGAACATGAAGAAGCAGTGTTTCAGATTCTGAGATACTTGAAGAAT
1 GGAGGAACATGAAGAAGCAGTGTTTCAGATTCTGAGATACTTGAAGAAT
28021977 GGAGGAACATGAAGAAGCAGTGTTTCAGATTCTGAGATACTTGAAGA
1 GGAGGAACATGAAGAAGCAGTGTTTCAGATTCTGAGATACTTGAAGA
28022024 GTTCACCTGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.36, C:0.10, G:0.29, T:0.24
Consensus pattern (49 bp):
GGAGGAACATGAAGAAGCAGTGTTTCAGATTCTGAGATACTTGAAGAAT
Found at i:28022626 original size:19 final size:19
Alignment explanation
Indices: 28022602--28022642 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
28022592 TATTTTAAAG
28022602 TTATTTAGGTAGATAAATC
1 TTATTTAGGTAGATAAATC
*
28022621 TTATTTAGGTAGATAACTC
1 TTATTTAGGTAGATAAATC
28022640 TTA
1 TTA
28022643 GAATAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (19 bp):
TTATTTAGGTAGATAAATC
Found at i:28027969 original size:14 final size:14
Alignment explanation
Indices: 28027950--28027989 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
28027940 TTGTTTGCCA
28027950 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
28027964 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
28027978 GGAAAATGTTTT
1 GTAAAATGTTTT
28027990 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:28027998 original size:20 final size:20
Alignment explanation
Indices: 28027973--28028012 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28027963 CGTAAAATGA
*
28027973 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
28027993 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
28028013 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:28028002 original size:34 final size:35
Alignment explanation
Indices: 28027958--28028024 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
28027948 CAGTAAAATG
*
28027958 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
28027992 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
28028025 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:28028028 original size:14 final size:15
Alignment explanation
Indices: 28027952--28028028 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
28027942 GTTTGCCAGT
* *
28027952 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
28027966 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
28027980 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
28028000 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
28028015 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
28028029 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:28029087 original size:11 final size:11
Alignment explanation
Indices: 28029071--28029104 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
28029061 GCAGGAATTA
28029071 GTACAATATAT
1 GTACAATATAT
*
28029082 GTACAATATAA
1 GTACAATATAT
28029093 GTACAATATAT
1 GTACAATATAT
28029104 G
1 G
28029105 AGAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (11 bp):
GTACAATATAT
Found at i:28029999 original size:16 final size:16
Alignment explanation
Indices: 28029978--28030011 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
28029968 GGACGGAGAG
*
28029978 GAAATGAGGAGGAAAT
1 GAAATGAGAAGGAAAT
28029994 GAAATGAGAAGGAAAT
1 GAAATGAGAAGGAAAT
28030010 GA
1 GA
28030012 GAGGTTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.35, T:0.12
Consensus pattern (16 bp):
GAAATGAGAAGGAAAT
Found at i:28033587 original size:20 final size:18
Alignment explanation
Indices: 28033537--28033588 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
28033527 CTACAAGATA
28033537 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
28033554 AATATTAAGA-TAATCATTTT
1 AATATTAA-ATTAAT-A-TTT
28033574 AATATTAAATTAATA
1 AATATTAAATTAATA
28033589 AAATACTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:28048391 original size:19 final size:19
Alignment explanation
Indices: 28048363--28048404 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
28048353 TGAGAGCTAA
*
28048363 GAGAGTTGAGAGAGAGGAT
1 GAGAGATGAGAGAGAGGAT
* *
28048382 GAGAGATGAGAGGGATGAT
1 GAGAGATGAGAGAGAGGAT
28048401 GAGA
1 GAGA
28048405 TGAGGGATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.48, T:0.14
Consensus pattern (19 bp):
GAGAGATGAGAGAGAGGAT
Found at i:28048394 original size:15 final size:16
Alignment explanation
Indices: 28048369--28048433 Score: 77
Period size: 14 Copynumber: 4.3 Consensus size: 16
28048359 CTAAGAGAGT
28048369 TGAGA-GAGAGGATGA
1 TGAGATGAGAGGATGA
28048384 -GAGATGAGAGGGATGA
1 TGAGATGAGA-GGATGA
28048400 TGAGATGAG-GGATGA
1 TGAGATGAGAGGATGA
*
28048415 TG-GATGA-TGGATGA
1 TGAGATGAGAGGATGA
28048429 TGAGA
1 TGAGA
28048434 AATGAACTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
14 17 0.38
15 14 0.31
16 6 0.13
17 8 0.18
ACGTcount: A:0.35, C:0.00, G:0.46, T:0.18
Consensus pattern (16 bp):
TGAGATGAGAGGATGA
Found at i:28048419 original size:7 final size:7
Alignment explanation
Indices: 28048394--28048430 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
28048384 GAGATGAGAG
28048394 GGATGAT
1 GGATGAT
*
28048401 GAGATGAG
1 G-GATGAT
28048409 GGATGAT
1 GGATGAT
28048416 GGATGAT
1 GGATGAT
28048423 GGATGAT
1 GGATGAT
28048430 G
1 G
28048431 AGAAATGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.30, C:0.00, G:0.46, T:0.24
Consensus pattern (7 bp):
GGATGAT
Found at i:28050613 original size:23 final size:22
Alignment explanation
Indices: 28050582--28050629 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
28050572 TTGCAAAGAT
*
28050582 TAAATCCTAATTA-CTAAATAAA
1 TAAATCCTAAATACCTAAA-AAA
28050604 TAAATTCCTAAATACCTAAAAAA
1 TAAA-TCCTAAATACCTAAAAAA
28050627 TAA
1 TAA
28050630 TTAAATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 14 0.61
24 5 0.22
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAATCCTAAATACCTAAAAAA
Found at i:28052347 original size:20 final size:20
Alignment explanation
Indices: 28052322--28052359 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28052312 ACCCCCTTTA
28052322 TTAACATAAA-AATTTAAAAT
1 TTAACA-AAATAATTTAAAAT
28052342 TTAACAAAATAATTTAAA
1 TTAACAAAATAATTTAAA
28052360 CTAGAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAACAAAATAATTTAAAAT
Found at i:28058966 original size:15 final size:16
Alignment explanation
Indices: 28058941--28059005 Score: 68
Period size: 14 Copynumber: 4.3 Consensus size: 16
28058931 CTAAGAGAGT
28058941 TGAGA-GAGAGGATGA
1 TGAGATGAGAGGATGA
*
28058956 -GAGATGAGAGGGATAA
1 TGAGATGAGA-GGATGA
28058972 TGAGATGAG-GGATGA
1 TGAGATGAGAGGATGA
*
28058987 TG-GATGA-TGGATGA
1 TGAGATGAGAGGATGA
28059001 TGAGA
1 TGAGA
28059006 AATGAGCTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
14 17 0.40
15 13 0.30
16 5 0.12
17 8 0.19
ACGTcount: A:0.37, C:0.00, G:0.45, T:0.18
Consensus pattern (16 bp):
TGAGATGAGAGGATGA
Found at i:28061511 original size:2 final size:2
Alignment explanation
Indices: 28061504--28061529 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28061494 TCATGGTCTT
28061504 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
28061530 AGTTTACCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28063786 original size:11 final size:12
Alignment explanation
Indices: 28063758--28063785 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28063748 TCCCTATTGC
28063758 AAAAAGAAAAAA
1 AAAAAGAAAAAA
28063770 AAAAAGAAAAAA
1 AAAAAGAAAAAA
28063782 AAAA
1 AAAA
28063786 GTGAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:28072415 original size:31 final size:31
Alignment explanation
Indices: 28072372--28072448 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
28072362 AATCTTTGTA
* * *
28072372 ATTTT-GTAATTTAACTTTTAATGTA-TTTTT
1 ATTTTAGTAATTTAAATTTT-AGGTAGTTCTT
*
28072402 ATTTTAGTTATTTAAATTTTAGGTAGTTCTT
1 ATTTTAGTAATTTAAATTTTAGGTAGTTCTT
*
28072433 ATTTTAGTCATTTAAA
1 ATTTTAGTAATTTAAA
28072449 AAATATTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
30 9 0.22
31 31 0.77
ACGTcount: A:0.29, C:0.04, G:0.09, T:0.58
Consensus pattern (31 bp):
ATTTTAGTAATTTAAATTTTAGGTAGTTCTT
Found at i:28075180 original size:21 final size:21
Alignment explanation
Indices: 28075156--28075220 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
28075146 AACAAAAACC
28075156 CATAAGGGTTTAATAGAAGCT
1 CATAAGGGTTTAATAGAAGCT
* * * *
28075177 CATAAGAGCTTAAT-GAAAACC
1 CATAAGGGTTTAATAG-AAGCT
* *
28075198 CATAAGGGTTAAACAGAAGCT
1 CATAAGGGTTTAATAGAAGCT
28075219 CA
1 CA
28075221 AAAGAGCTGA
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.22
Consensus pattern (21 bp):
CATAAGGGTTTAATAGAAGCT
Found at i:28075196 original size:42 final size:42
Alignment explanation
Indices: 28075146--28075261 Score: 151
Period size: 42 Copynumber: 2.8 Consensus size: 42
28075136 ATAAGTGCTA
* * *
28075146 AACAAAAACCCATAAGGGTTTAATAGAAGCTCATAAGAGCTT
1 AACAAAAACCCATAAGGGTTTAACAGAAGCTCAAAAGAGCTG
** *
28075188 AATGAAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTG
1 AACAAAAACCCATAAGGGTTTAACAGAAGCTCAAAAGAGCTG
* * *
28075230 AACAAAAACTCATATGAGTTTAACAGAAGCTC
1 AACAAAAACCCATAAGGGTTTAACAGAAGCTC
28075262 GTGCGAGCTA
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (42 bp):
AACAAAAACCCATAAGGGTTTAACAGAAGCTCAAAAGAGCTG
Found at i:28082859 original size:42 final size:42
Alignment explanation
Indices: 28082812--28082967 Score: 136
Period size: 42 Copynumber: 3.7 Consensus size: 42
28082802 GCCCGAAGGC
* *
28082812 TGAACGGAAGCACATAAGTGCTAAACAGAAACCCATAAGGGT
1 TGAACGGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* * *
28082854 TGAACGGAAGCTCATAAGAGCTTAA-TGAAAACCTATAAGGGT
1 TGAACGGAAGCTCATAAGAGCTAAACAG-AAACCCATAAGGGT
* * * * * * *
28082896 TAAACAGAAGCTCAAAAGAGCTGAACAGAAACTCATATGAGT
1 TGAACGGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* * * * *
28082938 TTAACAGAAGCTCGTGAGAACTAAAC-GAAA
1 TGAACGGAAGCTCATAAGAGCTAAACAGAAA
28082968 AGTAAACACC
Statistics
Matches: 92, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
41 5 0.05
42 86 0.93
43 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (42 bp):
TGAACGGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
Done.