Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 188 of 222
Found at i:60096579 original size:30 final size:30
Alignment explanation
Indices: 60096542--60096622 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
60096532 AAATTTTTAA
* * *
60096542 AAATTACATTTTGACCCCTAATTTTTTC-T
1 AAATTACATTTCGGCCCCTAATATTTTCAT
*
60096571 AAATTTACATCTCGGCCCCTAATATTTTCAT
1 AAA-TTACATTTCGGCCCCTAATATTTTCAT
*
60096602 AAATTACATTTGGGCCCCTAA
1 AAATTACATTTCGGCCCCTAA
60096623 ACTTTCTCGA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 3 0.07
30 37 0.84
31 4 0.09
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (30 bp):
AAATTACATTTCGGCCCCTAATATTTTCAT
Found at i:60097222 original size:26 final size:26
Alignment explanation
Indices: 60097191--60097251 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
60097181 GAAGAAGAAG
60097191 AAGAAAAAGAAAG-GAA-AAAAAAAGA
1 AAGAAAAA-AAAGAGAAGAAAAAAAGA
* *
60097216 ACAGAAAAAAGAGAGAAGAAAAAGAGA
1 A-AGAAAAAAAAGAGAAGAAAAAAAGA
60097243 AAGAAAAAA
1 AAGAAAAAA
60097252 TATCTTACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 4 0.13
26 18 0.58
27 9 0.29
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (26 bp):
AAGAAAAAAAAGAGAAGAAAAAAAGA
Found at i:60097223 original size:13 final size:12
Alignment explanation
Indices: 60097188--60097251 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 12
60097178 CCCGAAGAAG
60097188 AAGAAGAAAAAGA
1 AAGAA-AAAAAGA
60097201 AAGGAAAAAAAAAGA
1 AA-G--AAAAAAAGA
60097216 ACAGAAAAAAGAGA
1 A-AGAAAAAA-AGA
*
60097230 GAAGAAAAAGAGA
1 -AAGAAAAAAAGA
60097243 AAGAAAAAA
1 AAGAAAAAA
60097252 TATCTTACAC
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
12 8 0.19
13 11 0.26
14 11 0.26
15 10 0.23
16 3 0.07
ACGTcount: A:0.77, C:0.02, G:0.22, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAGA
Found at i:60097224 original size:27 final size:26
Alignment explanation
Indices: 60097194--60097251 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
60097184 GAAGAAGAAG
60097194 AAAAAGAAAGGAA-AAAAAAAGAACAGA
1 AAAAAGAAA-GAAGAAAAAAAGAA-AGA
* *
60097221 AAAAAGAGAGAAGAAAAAGAGAAAGA
1 AAAAAGAAAGAAGAAAAAAAGAAAGA
60097247 AAAAA
1 AAAAA
60097252 TATCTTACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.78, C:0.02, G:0.21, T:0.00
Consensus pattern (26 bp):
AAAAAGAAAGAAGAAAAAAAGAAAGA
Found at i:60097238 original size:15 final size:14
Alignment explanation
Indices: 60097182--60097251 Score: 58
Period size: 15 Copynumber: 5.1 Consensus size: 14
60097172 TTCGGCCCCG
60097182 AAGAAGAAGAAGAAA
1 AAGAAGAAGAA-AAA
*
60097197 AAGAA-AGGAAAAA
1 AAGAAGAAGAAAAA
*
60097210 AA-AAGAACAGAAAA
1 AAGAAGAAGA-AAAA
60097224 AAGAGAGAAGAAAAA
1 AAGA-AGAAGAAAAA
*
60097239 GAG-A-AAGAAAAA
1 AAGAAGAAGAAAAA
60097251 A
1 A
60097252 TATCTTACAC
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
12 10 0.22
13 8 0.18
14 10 0.22
15 12 0.27
16 5 0.11
ACGTcount: A:0.76, C:0.01, G:0.23, T:0.00
Consensus pattern (14 bp):
AAGAAGAAGAAAAA
Found at i:60097947 original size:20 final size:20
Alignment explanation
Indices: 60097905--60097948 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
60097895 GAAAATGTTC
* *
60097905 AAAATTTCTCGTGTTTTAAT
1 AAAAATTCTCGTGTTTGAAT
*
60097925 AAAAATTCTCGTGTTTGATT
1 AAAAATTCTCGTGTTTGAAT
60097945 AAAA
1 AAAA
60097949 TCCCGATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.43
Consensus pattern (20 bp):
AAAAATTCTCGTGTTTGAAT
Found at i:60098257 original size:17 final size:18
Alignment explanation
Indices: 60098221--60098533 Score: 144
Period size: 18 Copynumber: 16.7 Consensus size: 18
60098211 TAAAAATAAT
60098221 AATTTTCGTGTTTTCAAA
1 AATTTTCGTGTTTTCAAA
60098239 AATTTCTCGTG-TTTCAAAAA
1 AATTT-TCGTGTTTTC--AAA
*
60098259 AATTTTGACTTTTCGCGTTTT-AAA
1 AA---T---T-TTCGTGTTTTCAAA
*
60098283 AAATTTCGTGTTTTCAAAA
1 AATTTTCGTGTTTTC-AAA
* * *
60098302 AATTCTCATG-CTTCAAA
1 AATTTTCGTGTTTTCAAA
*
60098319 AATCTTCGTGTTTTC-AA
1 AATTTTCGTGTTTTCAAA
* *
60098336 AATTCTAGTG-TTTCAAAA
1 AATTTTCGTGTTTTC-AAA
60098354 AATTTTCGTGTTTTC-AA
1 AATTTTCGTGTTTTCAAA
*
60098371 AATTTCTCGTGTTTTCTAA
1 AATTT-TCGTGTTTTCAAA
** *
60098390 AATTCCCGT-TTTTCGAA
1 AATTTTCGTGTTTTCAAA
*
60098407 AATTTTCTTGTTTTCAAAA
1 AATTTTCGTGTTTTC-AAA
*
60098426 AATATTTCCGTG-TTTCATA
1 AAT-TTT-CGTGTTTTCAAA
* **
60098445 AATTTCCGTGTTTGAAAAAAA
1 AATTTTCGTGTTT---TCAAA
*
60098466 AATTCTC-T-TCTTTCAAAA
1 AATTTTCGTGT-TTTC-AAA
*
60098484 AAATTTCTGTGTTTTCAAA
1 AATTTTC-GTGTTTTCAAA
** *
60098503 AATTGACCGTG-TTTCATA
1 AATT-TTCGTGTTTTCAAA
60098521 AATTTTCGTGTTT
1 AATTTTCGTGTTT
60098534 AAAAAAAAAT
Statistics
Matches: 220, Mismatches: 41, Indels: 68
0.67 0.12 0.21
Matches are distributed among these distances:
16 4 0.02
17 56 0.25
18 68 0.31
19 45 0.20
20 21 0.10
21 11 0.05
23 1 0.00
24 5 0.02
26 5 0.02
27 4 0.02
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (18 bp):
AATTTTCGTGTTTTCAAA
Found at i:60098392 original size:36 final size:37
Alignment explanation
Indices: 60098275--60098457 Score: 163
Period size: 35 Copynumber: 5.1 Consensus size: 37
60098265 GACTTTTCGC
* *
60098275 GTTTT-AAAAAA-TTTCGTGTTTTCAAAAAATTCTCAT
1 GTTTTCAAAAAATTTTCGTGTTTTC-AAAATTTCTCGT
* * *
60098311 G-CTTC-AAAAATCTTCGTGTTTTCAAAA-TTCTAGT
1 GTTTTCAAAAAATTTTCGTGTTTTCAAAATTTCTCGT
60098345 G-TTTCAAAAAATTTTCGTGTTTTCAAAATTTCTCGT
1 GTTTTCAAAAAATTTTCGTGTTTTCAAAATTTCTCGT
* ** *
60098381 GTTTTC-TAAAATTCCCGT-TTTTCGAAAATTT-TCTT
1 GTTTTCAAAAAATTTTCGTGTTTTC-AAAATTTCTCGT
60098416 GTTTTCAAAAAATATTTCCGTG-TTTCATAAATTTC-CGT
1 GTTTTCAAAAAAT-TTT-CGTGTTTTCA-AAATTTCTCGT
60098454 GTTT
1 GTTT
60098458 GAAAAAAAAA
Statistics
Matches: 120, Mismatches: 15, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
34 9 0.08
35 46 0.38
36 40 0.33
37 6 0.05
38 19 0.16
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.46
Consensus pattern (37 bp):
GTTTTCAAAAAATTTTCGTGTTTTCAAAATTTCTCGT
Found at i:60098409 original size:53 final size:53
Alignment explanation
Indices: 60098294--60098425 Score: 144
Period size: 53 Copynumber: 2.5 Consensus size: 53
60098284 AATTTCGTGT
* * * * *
60098294 TTTCAAAAAATTCTCATG-CTTCAAAA-ATCTTCGTGTTTTCAAAATTCTAGTG
1 TTTCAAAAAATTTTCGTGTTTTCAAAATTTC-TCGTGTTTTCAAAATTCCAGTG
* *
60098346 TTTCAAAAAATTTTCGTGTTTTCAAAATTTCTCGTGTTTTCTAAAATTCCCGTT
1 TTTCAAAAAATTTTCGTGTTTTCAAAATTTCTCGTGTTTTC-AAAATTCCAGTG
* *
60098400 TTTC-GAAAATTTTCTTGTTTTCAAAA
1 TTTCAAAAAATTTTCGTGTTTTCAAAA
60098426 AATATTTCCG
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
52 16 0.24
53 37 0.54
54 15 0.22
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.45
Consensus pattern (53 bp):
TTTCAAAAAATTTTCGTGTTTTCAAAATTTCTCGTGTTTTCAAAATTCCAGTG
Found at i:60098679 original size:37 final size:35
Alignment explanation
Indices: 60098622--60098732 Score: 102
Period size: 35 Copynumber: 3.1 Consensus size: 35
60098612 TTTCAAAAAG
**
60098622 AAAATTC--GTGTTTTCAAAAAAAATCTCGTGTTTT
1 AAAATTCTTGTGTTTTTTAAAAAAAT-TCGTGTTTT
* *
60098656 AGAATTTTTTGTGTTTTTTAAAAAAAATTCGTGTTTCT
1 A-AAATTCTTGTGTTTTTT-AAAAAAATTCGTGTTT-T
* *
60098694 AAAATTCTTGT-ATTTTTAAAAAATTTCGTGTTTT
1 AAAATTCTTGTGTTTTTTAAAAAAATTCGTGTTTT
60098728 CAAAA
1 -AAAA
60098733 AAAGGAAAAG
Statistics
Matches: 63, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
34 2 0.03
35 23 0.37
36 5 0.08
37 23 0.37
38 10 0.16
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (35 bp):
AAAATTCTTGTGTTTTTTAAAAAAATTCGTGTTTT
Found at i:60098691 original size:20 final size:19
Alignment explanation
Indices: 60098593--60098735 Score: 73
Period size: 20 Copynumber: 7.6 Consensus size: 19
60098583 TAAACAAATT
**
60098593 TTTTTAAAAAATTTTCGTG
1 TTTTTAAAAAAAATTCGTG
**
60098612 TTTCAAAAAGAAAATTCGTG
1 TTTTTAAAA-AAAATTCGTG
*
60098632 TTTTCAAAAAAAATCTCGTG
1 TTTTTAAAAAAAAT-TCGTG
* *** *
60098652 -TTTT-AGAATTTTTTGTG
1 TTTTTAAAAAAAATTCGTG
60098669 TTTTTTAAAAAAAATTCGTG
1 -TTTTTAAAAAAAATTCGTG
* *
60098689 TTTCT----AAAATTCTTG
1 TTTTTAAAAAAAATTCGTG
* *
60098704 TATTTTTAAAAAATTTCGTG
1 T-TTTTAAAAAAAATTCGTG
*
60098724 TTTTCAAAAAAA
1 TTTTTAAAAAAA
60098736 GGAAAAGTTG
Statistics
Matches: 90, Mismatches: 24, Indels: 20
0.67 0.18 0.15
Matches are distributed among these distances:
15 10 0.11
16 3 0.03
17 4 0.04
18 4 0.04
19 32 0.36
20 37 0.41
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.45
Consensus pattern (19 bp):
TTTTTAAAAAAAATTCGTG
Found at i:60098722 original size:35 final size:37
Alignment explanation
Indices: 60098638--60098727 Score: 105
Period size: 37 Copynumber: 2.5 Consensus size: 37
60098628 CGTGTTTTCA
* * * *
60098638 AAAAAAATCTCGTGTTTTAGAATTTTTTGTGTTTTTT
1 AAAAAAATTTCGTGTTTTAGAAATTCTTGTGATTTTT
*
60098675 AAAAAAAATTCGTGTTTCTA-AAATTCTTGT-ATTTTT
1 AAAAAAATTTCGTGTTT-TAGAAATTCTTGTGATTTTT
60098711 -AAAAAATTTCGTGTTTT
1 AAAAAAATTTCGTGTTTT
60098728 CAAAAAAAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
34 1 0.02
35 15 0.33
36 5 0.11
37 23 0.50
38 2 0.04
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (37 bp):
AAAAAAATTTCGTGTTTTAGAAATTCTTGTGATTTTT
Found at i:60106872 original size:10 final size:9
Alignment explanation
Indices: 60106851--60106929 Score: 72
Period size: 9 Copynumber: 8.4 Consensus size: 9
60106841 TATTATGCCT
60106851 AAAAAAACA
1 AAAAAAACA
*
60106860 AAAAAATAGA
1 AAAAAA-ACA
*
60106870 AAAAAATA-G
1 AAAAAA-ACA
*
60106879 AAAGAAACA
1 AAAAAAACA
60106888 AAAAAAACAA
1 AAAAAAAC-A
60106898 AAAAAAACA
1 AAAAAAACA
60106907 AAAAACAA-A
1 AAAAA-AACA
60106916 CAAAAAAACA
1 -AAAAAAACA
60106926 AAAA
1 AAAA
60106930 TGGAAAAATC
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
8 1 0.02
9 31 0.53
10 27 0.46
ACGTcount: A:0.85, C:0.09, G:0.04, T:0.03
Consensus pattern (9 bp):
AAAAAAACA
Found at i:60106875 original size:19 final size:18
Alignment explanation
Indices: 60106851--60106929 Score: 77
Period size: 19 Copynumber: 4.3 Consensus size: 18
60106841 TATTATGCCT
* * *
60106851 AAAAAAACAAAAAAATAG
1 AAAAAAAAAAAAAAAAAC
* * *
60106869 AAAAAAATAGAAAGAAAC
1 AAAAAAAAAAAAAAAAAC
60106887 AAAAAAAACAAAAAAAAAC
1 AAAAAAAA-AAAAAAAAAC
*
60106906 AAAAAACAAACAAAAAAAC
1 AAAAAA-AAAAAAAAAAAC
60106925 AAAAA
1 AAAAA
60106930 TGGAAAAATC
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
18 20 0.40
19 28 0.56
20 2 0.04
ACGTcount: A:0.85, C:0.09, G:0.04, T:0.03
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAAAC
Found at i:60106903 original size:30 final size:29
Alignment explanation
Indices: 60106851--60106929 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
60106841 TATTATGCCT
* * *
60106851 AAAA-AAACAAAAAAATAGAAAAAAA-TA
1 AAAACAAACAAAAAAACAAAAAAAAACAA
* *
60106878 GAAAGAAACAAAAAAAACAAAAAAAAACAA
1 AAAACAAAC-AAAAAAACAAAAAAAAACAA
60106908 AAAACAAACAAAAAAACAAAAA
1 AAAACAAACAAAAAAACAAAAA
60106930 TGGAAAAATC
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
27 3 0.07
28 4 0.09
29 28 0.65
30 8 0.19
ACGTcount: A:0.85, C:0.09, G:0.04, T:0.03
Consensus pattern (29 bp):
AAAACAAACAAAAAAACAAAAAAAAACAA
Found at i:60106937 original size:1 final size:1
Alignment explanation
Indices: 60106851--60106929 Score: 50
Period size: 1 Copynumber: 79.0 Consensus size: 1
60106841 TATTATGCCT
* * * * * * * * * *
60106851 AAAAAAACAAAAAAATAGAAAAAAATAGAAAGAAACAAAAAAAACAAAAAAAAACAAAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
60106916 CAAAAAAACAAAAA
1 AAAAAAAAAAAAAA
60106930 TGGAAAAATC
Statistics
Matches: 54, Mismatches: 24, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.85, C:0.09, G:0.04, T:0.03
Consensus pattern (1 bp):
A
Found at i:60108016 original size:79 final size:78
Alignment explanation
Indices: 60107796--60108815 Score: 1016
Period size: 78 Copynumber: 13.0 Consensus size: 78
60107786 AAGAAATATT
* * * *
60107796 TTTTAATTTTTTTTTTTCAAAAATCAACTCATAATGCGAAAGATGAGTTGAGCCTCGGGTCACAT
1 TTTTAAATTTCTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACAT
60107861 GCCGAGGTATTTC
66 GCCGAGGTATTTC
*
60107874 TTTTAAATTTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACAT
1 TTTTAAATTTCTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACAT
60107939 GCCGAGGTATTTC
66 GCCGAGGTATTTC
60107952 TTTTAAATTTCTTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
1 TTTTAAATTTCTTTTTTC-AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
60108017 TGCCGAGGTATTTC
65 TGCCGAGGTATTTC
*
60108031 TTTTAAATTTCTTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGGGTTGAGCCTCGGGTCAC
1 TTTTAAATTTCTTTTTTC--AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
60108096 --GCTGAGGTA----
64 ATGCCGAGGTATTTC
* * *
60108105 TTTTCAATTTCTATTTTTTCAAAAAAATCAAATCAACTCATAATACGAGAGGTGAGTTGACCCTC
1 TTTTAAATTTC--TTTTTTC-----AA--AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC
* *
60108170 TGGTAACATGCCGAGGTATTTC
57 GGGTCACATGCCGAGGTATTTC
* * * * *
60108192 TTTTAAATTTCTACTTTTCAAAAATCAACTCATATTGCGAAAAGTGAGTTGAGCCTCAGGTCACA
1 TTTTAAATTTCT-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
**
60108257 CACCGAGGTA--TC
65 TGCCGAGGTATTTC
* * * * * *
60108269 -TTT-AATTTATGTTTTTCAAAAATCAACTCATAATGCGAGAAGTGTGTTGAACCTTGGGCCGCA
1 TTTTAAATTTCT-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG--TCA
*
60108332 CAT--TGAGGTA-TT-
63 CATGCCGAGGTATTTC
* * *
60108344 TTTCAAATTTTGTTTTTTTCAAAGATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
1 TTTTAAA-TTT-CTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
60108409 ATGCCGAGGTATTTC
64 ATGCCGAGGTATTTC
*
60108424 TTTTAAATTTCTTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGGGTTGAGCCTCGGGTCAC
1 TTTTAAATTTCTTTTTTC--AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
60108489 --GCTGAGGTA----
64 ATGCCGAGGTATTTC
* * *
60108498 TTTTCAATTTCTATTTTTTCAAAAAAATCAAATCAACTCATAATACGAGAGGTGAGTTGACCCTC
1 TTTTAAATTTC--TTTTTTC-----AA--AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC
* *
60108563 CGGTAACATGCCGAGGTATTTC
57 GGGTCACATGCCGAGGTATTTC
* * * * *
60108585 TTTTAAATTTCTACTTTTCAAAAATCAACTCATATTGCGAAAAGTGAGTTGAGCCTCAGGTCACA
1 TTTTAAATTTCT-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
**
60108650 CACCGAGGTA--TC
65 TGCCGAGGTATTTC
* * * * * *
60108662 -TTT-AATTTATGTTTTTCAAAAATCAACTCATAATGCGAGAAGTGTGTTGAACCTTGGGCCGCA
1 TTTTAAATTTCT-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG--TCA
*
60108725 CAT--TGAGGTA-TT-
63 CATGCCGAGGTATTTC
* * * * * *
60108737 TTTCAAATTTTGTTTTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCAGGCCAC
1 TTTTAAA-TTT-CTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
60108802 ATGCCGAGCTATTT
64 ATGCCGAGGTATTT
60108816 TTTATTTTTG
Statistics
Matches: 796, Mismatches: 93, Indels: 105
0.80 0.09 0.11
Matches are distributed among these distances:
74 20 0.03
75 104 0.13
76 36 0.05
77 16 0.02
78 213 0.27
79 185 0.23
80 94 0.12
81 80 0.10
83 16 0.02
85 2 0.00
86 10 0.01
87 20 0.03
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (78 bp):
TTTTAAATTTCTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACAT
GCCGAGGTATTTC
Found at i:60108649 original size:240 final size:231
Alignment explanation
Indices: 60107796--60108819 Score: 1004
Period size: 240 Copynumber: 4.4 Consensus size: 231
60107786 AAGAAATATT
* * *
60107796 TTTTAATTT-TTTTTTTTC--AAAAATCAACTCATAATGCGAAAGATGAGTTGAGCCTCGGGTCA
1 TTTTAATTTCTATTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
60107858 CATGCCGAGGTATTTCTTTTAAATTTAT-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGT
66 CATGCCGAGGTA-TT-TTTTAAATTTCTATTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGT
60107922 TGAGCCTCGGGTCACATGCCGAGGTATTTCTTTTAAATTTCT-TTTTTCAAAAAATCAACTCATA
129 TGAGCCTCGGGTCACATGCCGAGGTATTTCTTTTAAATTTCTATTTTTC-AAAAATCAACTCATA
*
60107986 ATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTA
193 ATGCGAGAAGTGAGTTGAGCCTCGGGTCAC--GCCGAGGTA
*
60108027 TTTCTTTTAAATTTC--TTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGGGTTGAGCCTCG
1 ----TTTT-AATTTCTATTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCG
* * *
60108090 GGTCAC--GCTGAGGTA--TTTTCAATTTCTATTTTTTCAAAAAAATCAAATCAACTCATAATAC
61 GGTCACATGCCGAGGTATTTTTTAAATTTCTA-TTTTTC-----AA--AAATCAACTCATAATGC
* * * *
60108151 GAGAGGTGAGTTGACCCTCTGGTAACATGCCGAGGTATTTCTTTTAAATTTCTACTTTTCAAAAA
118 GAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTCTTTTAAATTTCTATTTTTCAAAAA
* * * *
60108216 TCAACTCATATTGCGAAAAGTGAGTTGAGCCTCAGGTCACACACCGAGGTA
183 TCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGT--CACGCCGAGGTA
* * * *
60108267 TCTTTAA-TT-TATGTTTTTC--AAAAATCAACTCATAATGCGAGAAGTGTGTTGAACCTTGGGC
1 T-TTTAATTTCTAT-TTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG-
* * * * * *
60108328 CGCACAT--TGAGGTATTTTTCAAATTTTGTTTTTTTCAAAGATCAACTCATAATGCGAGAGGTG
63 -TCACATGCCGAGGTATTTTTTAAA-TTTCTATTTTTCAAAAATCAACTCATAATGCGAGAGGTG
60108391 AGTTGAGCCTCGGGTCACATGCCGAGGTATTTCTTTTAAATTTCT-TTTTTCAAAAAAATCAACT
126 AGTTGAGCCTCGGGTCACATGCCGAGGTATTTCTTTTAAATTTCTATTTTTC--AAAAATCAACT
* * *
60108455 CATAATGCGAGAGGTGGGTTGAGCCTCGGGTCACGCTGAGGTA
189 CATAATGCGAGAAGTGAGTTGAGCCTCGGGTCACGCCGAGGTA
* *
60108498 TTTTCAATTTCTATTTTTTCAAAAAAATCAAATCAACTCATAATACGAGAGGTGAGTTGACCCTC
1 TTTT-AATTTCTATTTTTTC---AAAA--AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC
* * * * * *
60108563 CGGTAACATGCCGAGGTATTTCTTTTAAATTTCTACTTTTCAAAAATCAACTCATATTGCGAAAA
60 GGGTCACATGCCGAGGTA-TT-TTTTAAATTTCTATTTTTCAAAAATCAACTCATAATGCGAGAG
* ** * *
60108628 GTGAGTTGAGCCTCAGGTCACACACCGAGGTA--TC-TTT-AATTTATGTTTTTCAAAAATCAAC
123 GTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTCTTTTAAATTTCTATTTTTCAAAAATCAAC
* * *
60108689 TCATAATGCGAGAAGTGTGTTGAACCTTGGG-C-CGCACATTGAGGTA
188 TCATAATGCGAGAAGTGAGTTGAGCCTCGGGTCACGC-C---GAGGTA
* * * *
60108735 TTTTTCAAATTT-TGTTTTTTTC--AAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCAG
1 -TTTT--AATTTCT-ATTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGG
* *
60108797 GCCACATGCCGAGCTATTTTTTA
62 GTCACATGCCGAGGTATTTTTTA
60108820 TTTTTGTTTT
Statistics
Matches: 665, Mismatches: 73, Indels: 107
0.79 0.09 0.13
Matches are distributed among these distances:
230 8 0.01
231 30 0.05
232 120 0.18
233 49 0.07
234 5 0.01
235 95 0.14
236 15 0.02
237 82 0.12
238 9 0.01
239 62 0.09
240 176 0.26
241 11 0.02
242 3 0.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (231 bp):
TTTTAATTTCTATTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
CATGCCGAGGTATTTTTTAAATTTCTATTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTG
AGCCTCGGGTCACATGCCGAGGTATTTCTTTTAAATTTCTATTTTTCAAAAATCAACTCATAATG
CGAGAAGTGAGTTGAGCCTCGGGTCACGCCGAGGTA
Found at i:60108842 original size:393 final size:393
Alignment explanation
Indices: 60107809--60108815 Score: 1720
Period size: 393 Copynumber: 2.6 Consensus size: 393
60107799 TAATTTTTTT
* * **
60107809 TTTTCAAAAATCAACTCATAATGCG-AAAGATGAGTTGAGCCTCGGGTCACATGCCGAGGTATTT
1 TTTTCAAAAATCAACTCATATTGCGAAAAG-TGAGTTGAGCCTCAGGTCACACACCGAGGTA--T
* * * * *
60107873 CTTTTAAATTTAT-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG--TC
63 C-TTT-AATTTATGTTTTTCAAAAATCAACTCATAATGCGAGAAGTGTGTTGAACCTTGGGCCGC
* * * *
60107935 ACATGCCGAGGTATTTCTTTTAAA-TTT-CTTTTTTCAAAAAATCAACTCATAATGCGAGAGGTG
126 ACAT--TGAGGTA-TT-TTTCAAATTTTGTTTTTTTC-AAAGATCAACTCATAATGCGAGAGGTG
60107998 AGTTGAGCCTCGGGTCACATGCCGAGGTATTTCTTTTAAATTTCTTTTTTCAAAAAAATCAACTC
186 AGTTGAGCCTCGGGTCACATGCCGAGGTATTTCTTTTAAATTTCTTTTTTCAAAAAAATCAACTC
60108063 ATAATGCGAGAGGTGGGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTCTATTTTTTCAAA
251 ATAATGCGAGAGGTGGGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTCTATTTTTTCAAA
*
60108128 AAAATCAAATCAACTCATAATACGAGAGGTGAGTTGACCCTCTGGTAACATGCCGAGGTATTTCT
316 AAAATCAAATCAACTCATAATACGAGAGGTGAGTTGACCCTCCGGTAACATGCCGAGGTATTTCT
60108193 TTTAAATTTCTAC
381 TTTAAATTTCTAC
60108206 TTTTCAAAAATCAACTCATATTGCGAAAAGTGAGTTGAGCCTCAGGTCACACACCGAGGTATCTT
1 TTTTCAAAAATCAACTCATATTGCGAAAAGTGAGTTGAGCCTCAGGTCACACACCGAGGTATCTT
60108271 TAATTTATGTTTTTCAAAAATCAACTCATAATGCGAGAAGTGTGTTGAACCTTGGGCCGCACATT
66 TAATTTATGTTTTTCAAAAATCAACTCATAATGCGAGAAGTGTGTTGAACCTTGGGCCGCACATT
60108336 GAGGTATTTTTCAAATTTTGTTTTTTTCAAAGATCAACTCATAATGCGAGAGGTGAGTTGAGCCT
131 GAGGTATTTTTCAAATTTTGTTTTTTTCAAAGATCAACTCATAATGCGAGAGGTGAGTTGAGCCT
60108401 CGGGTCACATGCCGAGGTATTTCTTTTAAATTTCTTTTTTCAAAAAAATCAACTCATAATGCGAG
196 CGGGTCACATGCCGAGGTATTTCTTTTAAATTTCTTTTTTCAAAAAAATCAACTCATAATGCGAG
60108466 AGGTGGGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTCTATTTTTTCAAAAAAATCAAAT
261 AGGTGGGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTCTATTTTTTCAAAAAAATCAAAT
60108531 CAACTCATAATACGAGAGGTGAGTTGACCCTCCGGTAACATGCCGAGGTATTTCTTTTAAATTTC
326 CAACTCATAATACGAGAGGTGAGTTGACCCTCCGGTAACATGCCGAGGTATTTCTTTTAAATTTC
60108596 TAC
391 TAC
60108599 TTTTCAAAAATCAACTCATATTGCGAAAAGTGAGTTGAGCCTCAGGTCACACACCGAGGTATCTT
1 TTTTCAAAAATCAACTCATATTGCGAAAAGTGAGTTGAGCCTCAGGTCACACACCGAGGTATCTT
60108664 TAATTTATGTTTTTCAAAAATCAACTCATAATGCGAGAAGTGTGTTGAACCTTGGGCCGCACATT
66 TAATTTATGTTTTTCAAAAATCAACTCATAATGCGAGAAGTGTGTTGAACCTTGGGCCGCACATT
*
60108729 GAGGTATTTTTCAAATTTTGTTTTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCT
131 GAGGTATTTTTCAAATTTTGTTTTTTTCAAAGATCAACTCATAATGCGAGAGGTGAGTTGAGCCT
* * *
60108794 CAGGCCACATGCCGAGCTATTT
196 CGGGTCACATGCCGAGGTATTT
60108816 TTTATTTTTG
Statistics
Matches: 586, Mismatches: 18, Indels: 16
0.95 0.03 0.03
Matches are distributed among these distances:
392 6 0.01
393 458 0.78
394 59 0.10
395 2 0.00
396 5 0.01
397 52 0.09
398 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (393 bp):
TTTTCAAAAATCAACTCATATTGCGAAAAGTGAGTTGAGCCTCAGGTCACACACCGAGGTATCTT
TAATTTATGTTTTTCAAAAATCAACTCATAATGCGAGAAGTGTGTTGAACCTTGGGCCGCACATT
GAGGTATTTTTCAAATTTTGTTTTTTTCAAAGATCAACTCATAATGCGAGAGGTGAGTTGAGCCT
CGGGTCACATGCCGAGGTATTTCTTTTAAATTTCTTTTTTCAAAAAAATCAACTCATAATGCGAG
AGGTGGGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTCTATTTTTTCAAAAAAATCAAAT
CAACTCATAATACGAGAGGTGAGTTGACCCTCCGGTAACATGCCGAGGTATTTCTTTTAAATTTC
TAC
Found at i:60109047 original size:29 final size:30
Alignment explanation
Indices: 60108990--60109048 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
60108980 ACAAAAAATA
*
60108990 AAAAATTACATTTTAGTCCCTAAACTTTTT
1 AAAAATTACATTTTAGACCCTAAACTTTTT
* * *
60109020 AAAAATTATATTTT-GACCCTTAATTTTTT
1 AAAAATTACATTTTAGACCCTAAACTTTTT
60109049 TTCTAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.47
Consensus pattern (30 bp):
AAAAATTACATTTTAGACCCTAAACTTTTT
Found at i:60109692 original size:12 final size:13
Alignment explanation
Indices: 60109663--60109730 Score: 69
Period size: 12 Copynumber: 5.7 Consensus size: 13
60109653 CCCGAAGAAG
*
60109663 AAGAAAAAA-AGG
1 AAGAAAAAAGAGA
60109675 AA-AAAAAAGA-A
1 AAGAAAAAAGAGA
60109686 AAGAAAAAAGAGA
1 AAGAAAAAAGAGA
60109699 GAAG-AAAAAGAGA
1 -AAGAAAAAAGAGA
60109712 AAG--AAAA-AGA
1 AAGAAAAAAGAGA
60109722 AAGAAAAAA
1 AAGAAAAAA
60109731 TATCTTACAC
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
10 6 0.12
11 12 0.24
12 18 0.37
13 10 0.20
14 3 0.06
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAGAGA
Found at i:60109693 original size:14 final size:14
Alignment explanation
Indices: 60109669--60109728 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
60109659 GAAGAAGAAA
60109669 AAAAGGAAAAAAAAG
1 AAAA-GAAAAAAAAG
*
60109684 AAAAGAAAAAAGAG
1 AAAAGAAAAAAAAG
* *
60109698 AGAAG-AAAAAGAG
1 AAAAGAAAAAAAAG
60109711 -AAAGAAAAAGAAAG
1 AAAAGAAAAA-AAAG
60109725 AAAA
1 AAAA
60109729 AATATCTTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
12 3 0.08
13 12 0.32
14 16 0.42
15 7 0.18
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAAG
Found at i:60109720 original size:25 final size:23
Alignment explanation
Indices: 60109657--60109730 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 23
60109647 TTCGGCCCCG
*
60109657 AAGAAGAAGAAAAAAAG-GAAAAAA
1 AAGAA-AAGAAAAAGAGAG-AAAAA
60109681 AAGAAAAGAAAAAAGAGAGAAGAAA
1 AAGAAAAG-AAAAAGAGAGAA-AAA
*
60109706 AAGAGAAAGAAAAAGAAAGAAAAA
1 AAGA-AAAGAAAAAGAGAGAAAAA
60109730 A
1 A
60109731 TATCTTACAC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
23 3 0.07
24 18 0.41
25 19 0.43
26 4 0.09
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (23 bp):
AAGAAAAGAAAAAGAGAGAAAAA
Found at i:60109725 original size:36 final size:36
Alignment explanation
Indices: 60109657--60109730 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
60109647 TTCGGCCCCG
60109657 AAGAAGAAGAAAAAAAGGAAAAAAAAGAAAAGAAAA
1 AAGAAGAAGAAAAAAAGGAAAAAAAAGAAAAGAAAA
*
60109693 AAGAGAGAAGAAAAAGA-GAAAGAAAAAG-AAAGAAAA
1 AAGA-AGAAGAAAAAAAGGAAA-AAAAAGAAAAGAAAA
60109729 AA
1 AA
60109731 TATCTTACAC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
36 18 0.51
37 17 0.49
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (36 bp):
AAGAAGAAGAAAAAAAGGAAAAAAAAGAAAAGAAAA
Found at i:60110411 original size:20 final size:21
Alignment explanation
Indices: 60110381--60110424 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
60110371 GAAAATGTTC
60110381 AAAATTCCTCGTGTTTTAATA
1 AAAATTCCTCGTGTTTTAATA
*
60110402 AAAATT-CTCGTGTTTTATTA
1 AAAATTCCTCGTGTTTTAATA
60110422 AAA
1 AAA
60110425 TCCCGGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.43
Consensus pattern (21 bp):
AAAATTCCTCGTGTTTTAATA
Found at i:60110715 original size:15 final size:15
Alignment explanation
Indices: 60110697--60110747 Score: 66
Period size: 15 Copynumber: 3.1 Consensus size: 15
60110687 AAAAAATAAT
60110697 AATTTTCGTGTTTCA
1 AATTTTCGTGTTTCA
60110712 AATTTTCGTGTTTTCAAA
1 AATTTTCGTG-TTTC--A
60110730 AATTTCTCGTGTTTCA
1 AATTT-TCGTGTTTCA
60110746 AA
1 AA
60110748 AAAATATGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 10 0.31
16 7 0.22
18 10 0.31
19 5 0.16
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (15 bp):
AATTTTCGTGTTTCA
Found at i:60110741 original size:19 final size:17
Alignment explanation
Indices: 60110697--60111060 Score: 159
Period size: 18 Copynumber: 20.1 Consensus size: 17
60110687 AAAAAATAAT
60110697 AATTTTCGTGTTTC--A
1 AATTTTCGTGTTTCAAA
60110712 AATTTTCGTGTTTTCAAA
1 AATTTTCGTG-TTTCAAA
60110730 AATTTCTCGTGTTTCAAA
1 AATTT-TCGTGTTTCAAA
** * *
60110748 AA-AAT-ATG-TTC-GA
1 AATTTTCGTGTTTCAAA
*
60110761 ATTTTTGCGT-TTTCAAA
1 AATTTT-CGTGTTTCAAA
*
60110778 AAATTTCGTGTTTTCAAA
1 AATTTTCGTG-TTTCAAA
60110796 AATTTCTCGTGTTTCAAAAAA
1 AATTT-TCGTGTTTC---AAA
60110817 ATTTTGACTTTTCGTGTTTTCAAA
1 A-----A-TTTTCGTG-TTTCAAA
* * *
60110841 AATTCTCATGCTTCAAA
1 AATTTTCGTGTTTCAAA
*
60110858 AATCTTCGTGTTTTC-AA
1 AATTTTCGTG-TTTCAAA
* * *
60110875 AATTCTAGTATTTCAAAA
1 AATTTTCGTGTTTC-AAA
*
60110893 AATTTTCGTGTTTTCGAA
1 AATTTTCGTG-TTTCAAA
** * *
60110911 AATTCCCGTTTTTCGAA
1 AATTTTCGTGTTTCAAA
*
60110928 AATTTTCTTGTTTTCAAAA
1 AATTTTCGTG-TTTC-AAA
*
60110947 AATATTTCCGTGTTTCATA
1 AAT-TTT-CGTGTTTCAAA
* *
60110966 AATTTCCGTGTTTGAAAAAAA
1 AATTTTCGTGTTT----CAAA
* *
60110987 AATTCTCGTCTTTCAAAAA
1 AATTTTCGTGTTTC--AAA
60111006 AATTTTCGTGTTTTCAAA
1 AATTTTCGTG-TTTCAAA
** *
60111024 AATTGACAGTGTTTCATA
1 AATTTTC-GTGTTTCAAA
60111042 AATTTTCGTGTTTCAAA
1 AATTTTCGTGTTTCAAA
60111059 AA
1 AA
60111061 AAAAATCTTC
Statistics
Matches: 259, Mismatches: 52, Indels: 74
0.67 0.14 0.19
Matches are distributed among these distances:
13 2 0.01
14 4 0.02
15 12 0.05
16 16 0.06
17 57 0.22
18 82 0.32
19 39 0.15
20 11 0.04
21 19 0.07
24 4 0.02
26 6 0.02
27 7 0.03
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (17 bp):
AATTTTCGTGTTTCAAA
Found at i:60110792 original size:66 final size:62
Alignment explanation
Indices: 60110697--60110876 Score: 206
Period size: 66 Copynumber: 2.9 Consensus size: 62
60110687 AAAAAATAAT
* *
60110697 AATTTTCGTG-TTTC-AAATTTTCGTGTTTTCAAAAATTTCTCGTGTTTCAAAAAAATATGTTCG
1 AATTTTCGCGTTTTCAAAAATTTCGTGTTTTCAAAAATTTCTCGTGTTTCAAAAAAAT-T-TT-G
*
60110760 AATTTTTGCGTTTTCAAAAAATTTCGTGTTTTCAAAAATTTCTCGTGTTTCAAAAAAATTTTG
1 AATTTTCGCGTTTTC-AAAAATTTCGTGTTTTCAAAAATTTCTCGTGTTTCAAAAAAATTTTG
* * * * *
60110823 ACTTTTCGTGTTTTCAAAAATTCTCATG-CTTCAAAAATCT-TCGTGTTTTCAAAA
1 AATTTTCGCGTTTTCAAAAATT-TCGTGTTTTCAAAAATTTCTCGTG-TTTCAAAA
60110877 TTCTAGTATT
Statistics
Matches: 103, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
61 5 0.05
62 25 0.24
63 25 0.24
64 6 0.06
65 1 0.01
66 41 0.40
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (62 bp):
AATTTTCGCGTTTTCAAAAATTTCGTGTTTTCAAAAATTTCTCGTGTTTCAAAAAAATTTTG
Found at i:60110873 original size:35 final size:35
Alignment explanation
Indices: 60110825--60111060 Score: 154
Period size: 35 Copynumber: 6.5 Consensus size: 35
60110815 AAATTTTGAC
**
60110825 TTTTCGTGTTTTCAAAAATTCTCATGCTTCAAAAA
1 TTTTCGTGTTTTCAAAAATTCTCATATTTCAAAAA
*
60110860 TCTTCGTGTTTTC-AAAATTCT-AGTATTTCAAAAAA
1 TTTTCGTGTTTTCAAAAATTCTCA-TATTTC-AAAAA
* * * * *
60110895 TTTTCGTGTTTTCGAAAATTCCCGTTTTTCGAAAA
1 TTTTCGTGTTTTCAAAAATTCTCATATTTCAAAAA
* * * * *
60110930 TTTTCTTGTTTTCAAAAAATATTTCCGTGTTTCATAAA
1 TTTTCGTGTTTTC-AAAAAT-TCT-CATATTTCAAAAA
* ** * *
60110968 TTTCCGTGTTTGAAAAAAAAATTCTCGTCTTTCAAAAAAA
1 TTTTCGTGTTT---TCAAAAATTCTCATATTTC--AAAAA
** * *
60111008 TTTTCGTGTTTTCAAAAATTGACAGTGTTTCATAAA
1 TTTTCGTGTTTTCAAAAATTCTCA-TATTTCAAAAA
60111044 TTTTCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
60111061 AAAAATCTTC
Statistics
Matches: 158, Mismatches: 30, Indels: 26
0.74 0.14 0.12
Matches are distributed among these distances:
33 1 0.01
34 12 0.08
35 54 0.34
36 29 0.18
37 9 0.06
38 31 0.20
39 2 0.01
40 20 0.13
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (35 bp):
TTTTCGTGTTTTCAAAAATTCTCATATTTCAAAAA
Found at i:60111063 original size:38 final size:37
Alignment explanation
Indices: 60110927--60111077 Score: 121
Period size: 38 Copynumber: 3.9 Consensus size: 37
60110917 CGTTTTTCGA
* *
60110927 AAATTTTCTTGTTTTCAAAAAATATTTCCGTGTTTCAT
1 AAATTTTCGTGTTTTCAAAAAAAATTT-CGTGTTTCAT
* ** * *
60110965 AAATTTCCGTGTTTGAAAAAAAAATTCTCGTCTTTCAAAA
1 AAATTTTCGTGTTTTCAAAAAAAATT-TCGTGTTTC--AT
*
60111005 AAATTTTCGTGTTTTC---AAAAATTGACAGTGTTTCAT
1 AAATTTTCGTGTTTTCAAAAAAAATT-TC-GTGTTTCAT
60111041 AAATTTTCGTG-TTTCAAAAAAAAAATCTTCGTGTTTC
1 AAATTTTCGTGTTTTC--AAAAAAAAT-TTCGTGTTTC
60111078 GTTTTTTATC
Statistics
Matches: 88, Mismatches: 15, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
35 4 0.05
36 12 0.14
37 8 0.09
38 34 0.39
39 8 0.09
40 21 0.24
41 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (37 bp):
AAATTTTCGTGTTTTCAAAAAAAATTTCGTGTTTCAT
Found at i:60111178 original size:19 final size:19
Alignment explanation
Indices: 60111133--60111179 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
60111123 AAAATTTTCA
*
60111133 TGTTTCAAAAAGAAAATTTG
1 TGTTTC-AAAAGAAAATTCG
60111153 TGTTTTCAAAA-AAAATCTCG
1 TG-TTTCAAAAGAAAAT-TCG
60111173 TGTTTCA
1 TGTTTCA
60111180 GAATTTTCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 10 0.42
20 10 0.42
21 4 0.17
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (19 bp):
TGTTTCAAAAGAAAATTCG
Found at i:60115892 original size:23 final size:23
Alignment explanation
Indices: 60115861--60115911 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
60115851 ACCTACTTTC
* *
60115861 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
*
60115884 TTACAGTAGTGATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
60115907 TTACA
1 TTACA
60115912 TGAACATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:60119868 original size:93 final size:93
Alignment explanation
Indices: 60119755--60119940 Score: 336
Period size: 93 Copynumber: 2.0 Consensus size: 93
60119745 CACTCATGAC
*
60119755 TTTCAAAAGAAGGTATATATGCTTAGCAAATACATTAAAATGGTAATTTGAAAAGCTAGTATTCA
1 TTTCAAAAGAAGGTATATATGCTTAGCAAATACAATAAAATGGTAATTTGAAAAGCTAGTATTCA
60119820 AGATTCAATACATAGAATATTAGATATT
66 AGATTCAATACATAGAATATTAGATATT
* * *
60119848 TTTCAAAAGAATGTATATATGCTTAGCAAATACAATCAAATGGTCATTTGAAAAGCTAGTATTCA
1 TTTCAAAAGAAGGTATATATGCTTAGCAAATACAATAAAATGGTAATTTGAAAAGCTAGTATTCA
60119913 AGATTCAATACATAGAATATTAGATATT
66 AGATTCAATACATAGAATATTAGATATT
60119941 ATGTGATGTT
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 89 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (93 bp):
TTTCAAAAGAAGGTATATATGCTTAGCAAATACAATAAAATGGTAATTTGAAAAGCTAGTATTCA
AGATTCAATACATAGAATATTAGATATT
Found at i:60127591 original size:6 final size:6
Alignment explanation
Indices: 60127580--60127607 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
60127570 AGTATCATAG
60127580 ATTTAT ATTTAT ATTTAT ATTTAT ATTT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTT
60127608 TTAACGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTAT
Found at i:60134185 original size:21 final size:21
Alignment explanation
Indices: 60134161--60134204 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
60134151 GAATCTTTAG
*
60134161 TATTTATTGTATCATTT-TATT
1 TATTTAAT-TATCATTTCTATT
*
60134182 TATTTAATTATCCTTTCTATT
1 TATTTAATTATCATTTCTATT
60134203 TA
1 TA
60134205 ATTAGGTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTTAATTATCATTTCTATT
Found at i:60134676 original size:27 final size:27
Alignment explanation
Indices: 60134646--60134700 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
60134636 AATTTTGAAT
60134646 TCTAAAAATATGTCTTGATTTATTTTC
1 TCTAAAAATATGTCTTGATTTATTTTC
60134673 TCTAAAAATATGTCTTGATTTATTTTC
1 TCTAAAAATATGTCTTGATTTATTTTC
60134700 T
1 T
60134701 TATATTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.07, T:0.53
Consensus pattern (27 bp):
TCTAAAAATATGTCTTGATTTATTTTC
Found at i:60138003 original size:3 final size:3
Alignment explanation
Indices: 60137995--60138023 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
60137985 AAATCAATGT
60137995 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
60138024 TAAATCGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:60142466 original size:39 final size:37
Alignment explanation
Indices: 60142423--60142506 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
60142413 TAAGTGAAAG
* *
60142423 TTATAAAAATTATTAAATTTTATTAAAAATAAAAAAAAA
1 TTATAAAAATGATAAAATTTTA-T-AAAATAAAAAAAAA
* ***
60142462 TTATAAAAATGGTAAAATTTTATAAAATTCTAAAAAA
1 TTATAAAAATGATAAAATTTTATAAAATAAAAAAAAA
60142499 TTATAAAA
1 TTATAAAA
60142507 TTTTATAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 19 0.49
38 1 0.03
39 19 0.49
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (37 bp):
TTATAAAAATGATAAAATTTTATAAAATAAAAAAAAA
Found at i:60142469 original size:9 final size:9
Alignment explanation
Indices: 60142393--60142556 Score: 57
Period size: 10 Copynumber: 17.3 Consensus size: 9
60142383 ATGGACAAAT
*
60142393 AAAATGATA
1 AAAATTATA
60142402 AAAA--ATA
1 AAAATTATA
* *
60142409 AAAATAAGTG
1 AAAATTA-TA
*
60142419 AAAGTTATA
1 AAAATTATA
60142428 AAAATTATTA
1 AAAATTA-TA
**
60142438 AATTTTATTA
1 AAAATTA-TA
* *
60142448 AAAATAAAAA
1 AAAAT-TATA
60142458 AAAATTATA
1 AAAATTATA
**
60142467 AAAATGGT-
1 AAAATTATA
*
60142475 AAAATTTTA
1 AAAATTATA
*
60142484 TAAAATTCTAA
1 -AAAATTAT-A
60142495 AAAATTATA
1 AAAATTATA
*
60142504 AAATTTTATAAA
1 AAA-ATTAT--A
60142516 GAAAATTATA
1 -AAAATTATA
*
60142526 AAAAATATA
1 AAAATTATA
*
60142535 AAGAAATAT-
1 AA-AATTATA
60142544 AAAATTCATA
1 AAAATT-ATA
60142554 AAA
1 AAA
60142557 GAATTATCAT
Statistics
Matches: 117, Mismatches: 23, Indels: 29
0.69 0.14 0.17
Matches are distributed among these distances:
7 7 0.06
8 9 0.08
9 38 0.32
10 53 0.45
11 2 0.02
12 5 0.04
13 3 0.03
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.30
Consensus pattern (9 bp):
AAAATTATA
Found at i:60142469 original size:10 final size:10
Alignment explanation
Indices: 60142423--60142547 Score: 64
Period size: 10 Copynumber: 12.8 Consensus size: 10
60142413 TAAGTGAAAG
60142423 TTAT-AAAAA
1 TTATAAAAAA
* **
60142432 TTATTAAATT
1 TTATAAAAAA
*
60142442 TTATTAAAAA
1 TTATAAAAAA
* *
60142452 TAAAAAAAAA
1 TTATAAAAAA
60142462 TTAT-AAAAA
1 TTATAAAAAA
**
60142471 TGGT--AAAA
1 TTATAAAAAA
* *
60142479 TTTTATAAAA
1 TTATAAAAAA
*
60142489 TTCTAAAAAA
1 TTATAAAAAA
**
60142499 TTATAAAATT
1 TTATAAAAAA
60142509 TTATAAAGAAAA
1 TTAT-AA-AAAA
60142521 TTATAAAAAA
1 TTATAAAAAA
60142531 -TATAAAGAAA
1 TTATAAA-AAA
60142541 -TATAAAA
1 TTATAAAA
60142548 TTCATAAAAG
Statistics
Matches: 90, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
8 6 0.07
9 18 0.20
10 56 0.62
11 4 0.04
12 6 0.07
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:60142478 original size:18 final size:19
Alignment explanation
Indices: 60142456--60142506 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
60142446 TAAAAATAAA
*
60142456 AAAAAATTATAAAAATGGT
1 AAAAAATTATAAAAATGCT
** *
60142475 AAAATTTTAT-AAAATTCT
1 AAAAAATTATAAAAATGCT
60142493 AAAAAATTATAAAA
1 AAAAAATTATAAAA
60142507 TTTTATAAAG
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (19 bp):
AAAAAATTATAAAAATGCT
Found at i:60142488 original size:28 final size:29
Alignment explanation
Indices: 60142456--60142529 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 29
60142446 TAAAAATAAA
*
60142456 AAAAAATTATAAAAATGGTAAAATTTTAT
1 AAAAAATTATAAAAATGATAAAATTTTAT
* *
60142485 --AAAATTCTAAAAAATTATAAAATTTTAT
1 AAAAAATTAT-AAAAATGATAAAATTTTAT
60142513 AAAGAAAATTATAAAAA
1 -AA-AAAATTATAAAAA
60142530 ATATAAAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
27 7 0.19
28 17 0.47
31 5 0.14
32 7 0.19
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (29 bp):
AAAAAATTATAAAAATGATAAAATTTTAT
Found at i:60142536 original size:21 final size:22
Alignment explanation
Indices: 60142495--60142548 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
60142485 AAAATTCTAA
**
60142495 AAAATTATAAAATTTTATAAAG
1 AAAATTATAAAATAATATAAAG
60142517 AAAATTATAAAA-AATATAAAG
1 AAAATTATAAAATAATATAAAG
60142538 -AAA-TATAAAAT
1 AAAATTATAAAAT
60142549 TCATAAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 7 0.24
20 3 0.10
21 7 0.24
22 12 0.41
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (22 bp):
AAAATTATAAAATAATATAAAG
Found at i:60142765 original size:29 final size:29
Alignment explanation
Indices: 60142733--60142860 Score: 116
Period size: 29 Copynumber: 4.4 Consensus size: 29
60142723 TTTTTGATGC
*
60142733 ATTTTATAATTATTT-ATGATTTTTATAAA
1 ATTTTATAATTATTTAATAATTTTTAT-AA
* * *
60142762 ATTTTACAATTTTTTTATAATTTTTTATAA
1 ATTTTATAATTATTTAATAA-TTTTTATAA
* * * *
60142792 ACTTTATAATTTTTTCATAATTTTTATTA
1 ATTTTATAATTATTTAATAATTTTTATAA
* *
60142821 TTTTTATTAA-AATTTAATAATTTTTATAA
1 ATTTTA-TAATTATTTAATAATTTTTATAA
*
60142850 TTTTTATAATT
1 ATTTTATAATT
60142861 TTTTTGCTAC
Statistics
Matches: 81, Mismatches: 14, Indels: 8
0.79 0.14 0.08
Matches are distributed among these distances:
28 3 0.04
29 46 0.57
30 25 0.31
31 7 0.09
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (29 bp):
ATTTTATAATTATTTAATAATTTTTATAA
Found at i:60142785 original size:9 final size:9
Alignment explanation
Indices: 60142734--60142863 Score: 107
Period size: 9 Copynumber: 13.4 Consensus size: 9
60142724 TTTTGATGCA
60142734 TTTTATAAT
1 TTTTATAAT
*
60142743 TATTTATGAT
1 T-TTTATAAT
*
60142753 TTTTATAAAA
1 TTTTAT-AAT
*
60142763 TTTTACAATTT
1 TTTTATAA--T
60142774 TTTTATAATT
1 TTTTATAA-T
*
60142784 TTTTATAAA
1 TTTTATAAT
*
60142793 CTTTATAATT
1 TTTTATAA-T
60142803 TTTTCATAAT
1 TTTT-ATAAT
*
60142813 TTTTATTAT
1 TTTTATAAT
*
60142822 TTTTATTAAAA
1 TTTTA-T-AAT
*
60142833 TTTAATAAT
1 TTTTATAAT
60142842 TTTTATAAT
1 TTTTATAAT
60142851 TTTTATAAT
1 TTTTATAAT
60142860 TTTT
1 TTTT
60142864 TTGCTACACG
Statistics
Matches: 97, Mismatches: 16, Indels: 16
0.75 0.12 0.12
Matches are distributed among these distances:
9 47 0.48
10 34 0.35
11 16 0.16
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:60142797 original size:19 final size:19
Alignment explanation
Indices: 60142733--60142864 Score: 97
Period size: 19 Copynumber: 6.8 Consensus size: 19
60142723 TTTTTGATGC
* *
60142733 ATTTTATAATTATTTATGA
1 ATTTTATAATTTTTTATAA
* ** *
60142752 TTTTTATAAAATTTTACAA
1 ATTTTATAATTTTTTATAA
*
60142771 TTTTTTTATAATTTTTTATAA
1 --ATTTTATAATTTTTTATAA
*
60142792 ACTTTATAATTTTTTCATAA
1 ATTTTATAATTTTTT-ATAA
* *
60142812 TTTTTATTA-TTTTTATTAAA
1 ATTTTATAATTTTTTA-T-AA
*
60142832 ATTTAATAA-TTTTTATAA
1 ATTTTATAATTTTTTATAA
*
60142850 TTTTTATAATTTTTT
1 ATTTTATAATTTTTT
60142865 TGCTACACGT
Statistics
Matches: 88, Mismatches: 19, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
18 10 0.11
19 38 0.43
20 24 0.27
21 16 0.18
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (19 bp):
ATTTTATAATTTTTTATAA
Found at i:60142814 original size:11 final size:10
Alignment explanation
Indices: 60142734--60142864 Score: 94
Period size: 10 Copynumber: 13.4 Consensus size: 10
60142724 TTTTGATGCA
60142734 TTTTATAATT
1 TTTTATAATT
* *
60142744 ATTTATGA-T
1 TTTTATAATT
**
60142753 TTTTATAAAA
1 TTTTATAATT
*
60142763 TTTTACAATTT
1 TTTTATAA-TT
60142774 TTTTATAATT
1 TTTTATAATT
*
60142784 TTTTATAA-A
1 TTTTATAATT
*
60142793 CTTTATAATT
1 TTTTATAATT
60142803 TTTTCATAA-T
1 TTTT-ATAATT
*
60142813 TTTTATTA-T
1 TTTTATAATT
**
60142822 TTTTATTAAAA
1 TTTTA-TAATT
*
60142833 TTTAATAA-T
1 TTTTATAATT
60142842 TTTTATAA-T
1 TTTTATAATT
60142851 TTTTATAATT
1 TTTTATAATT
60142861 TTTT
1 TTTT
60142865 TGCTACACGT
Statistics
Matches: 95, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
9 39 0.41
10 41 0.43
11 15 0.16
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTTATAATT
Found at i:60143523 original size:20 final size:21
Alignment explanation
Indices: 60143484--60143523 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
60143474 AGTTTTAAAA
60143484 TCACCCTATATTTTCTGCCTT
1 TCACCCTATATTTTCTGCCTT
*
60143505 TCACCCTATTTTTTC-GCCT
1 TCACCCTATATTTTCTGCCT
60143524 GAATGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.12, C:0.35, G:0.05, T:0.47
Consensus pattern (21 bp):
TCACCCTATATTTTCTGCCTT
Found at i:60153579 original size:27 final size:28
Alignment explanation
Indices: 60153549--60153607 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
60153539 ACACACTCGG
**
60153549 AATAATAT-AAATCCTCCTTAACACACA
1 AATAATATCAAATCCTCCCAAACACACA
* *
60153576 AAT-ATATCATATCCTCCCAAACACACC
1 AATAATATCAAATCCTCCCAAACACACA
60153603 AATAA
1 AATAA
60153608 GGCATTAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 4 0.15
27 21 0.81
28 1 0.04
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (28 bp):
AATAATATCAAATCCTCCCAAACACACA
Found at i:60153880 original size:29 final size:29
Alignment explanation
Indices: 60153843--60153899 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
60153833 CATATAATTC
60153843 AATATTCACACATATTCTTACTTAATTTT
1 AATATTCACACATATTCTTACTTAATTTT
60153872 AATATTCACACATATTCTTACTTAATTT
1 AATATTCACACATATTCTTACTTAATTT
60153900 CAAATGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (29 bp):
AATATTCACACATATTCTTACTTAATTTT
Found at i:60153928 original size:24 final size:23
Alignment explanation
Indices: 60153884--60153930 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
60153874 TATTCACACA
60153884 TATTCTTACTTAATTTCAAATGT
1 TATTCTTACTTAATTTCAAATGT
*
60153907 TATTACTTACCTTACTTT-AAATGT
1 TATT-CTTA-CTTAATTTCAAATGT
60153931 CCCATGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
25 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.51
Consensus pattern (23 bp):
TATTCTTACTTAATTTCAAATGT
Found at i:60154207 original size:22 final size:24
Alignment explanation
Indices: 60154166--60154209 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
60154156 TAACTAAGCT
*
60154166 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTATAACTTAATTCA
60154190 TACTTA-TTTTAT-ACTTAATT
1 TACTTACTTTTATAACTTAATT
60154210 TCTTGCCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 5 0.26
24 6 0.32
ACGTcount: A:0.30, C:0.16, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTATAACTTAATTCA
Found at i:60156810 original size:52 final size:52
Alignment explanation
Indices: 60156731--60156895 Score: 216
Period size: 46 Copynumber: 3.2 Consensus size: 52
60156721 TACTTCTGAT
* *
60156731 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGA-AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGA
** *
60156784 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGA
60156836 C------AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGA
*
60156882 CAAAGTGATAAGTG
1 C-AAGTGAAAAGTG
60156896 GCTACACTTA
Statistics
Matches: 96, Mismatches: 9, Indels: 14
0.81 0.08 0.12
Matches are distributed among these distances:
46 43 0.45
52 41 0.43
53 12 0.12
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.27
Consensus pattern (52 bp):
CAAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGA
Found at i:60156903 original size:37 final size:37
Alignment explanation
Indices: 60156859--60156967 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
60156849 GATAGCTTTA
60156859 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
60156896 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
60156933 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
60156968 ATCATACGTA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:60157662 original size:5 final size:5
Alignment explanation
Indices: 60157643--60157719 Score: 138
Period size: 5 Copynumber: 15.4 Consensus size: 5
60157633 TTAGTTTATT
60157643 TAATA T-ATAA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAAT-A TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
60157693 TAATA TAATA TAATA TAATA TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TA
60157720 TAAAACATAA
Statistics
Matches: 70, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
4 2 0.03
5 66 0.94
6 2 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:60160630 original size:5 final size:5
Alignment explanation
Indices: 60160620--60160688 Score: 138
Period size: 5 Copynumber: 13.8 Consensus size: 5
60160610 TCCTTCATCA
60160620 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
60160670 CATAT CATAT CATAT CATA
1 CATAT CATAT CATAT CATA
60160689 AATATTAGAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 64 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (5 bp):
CATAT
Found at i:60171577 original size:27 final size:28
Alignment explanation
Indices: 60171538--60171594 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
60171528 ATATCATTTG
* *
60171538 ACAAGTTTAAGTACT-AAATTAGATAAAA
1 ACAAGTTTAAGTA-TGAAATAAGAAAAAA
60171566 ACAAG-TTAAGTATGAAATAAGAAAAAA
1 ACAAGTTTAAGTATGAAATAAGAAAAAA
60171593 AC
1 AC
60171595 TAAATTAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 1 0.04
27 20 0.77
28 5 0.19
ACGTcount: A:0.58, C:0.07, G:0.12, T:0.23
Consensus pattern (28 bp):
ACAAGTTTAAGTATGAAATAAGAAAAAA
Found at i:60189594 original size:27 final size:27
Alignment explanation
Indices: 60189553--60189697 Score: 136
Period size: 27 Copynumber: 5.4 Consensus size: 27
60189543 AACACGCTAG
* *
60189553 GAAATGAATGCCTTTGTGGCAATTTAT
1 GAAAGGAATGCCTTTGTGGCAATATAT
* *
60189580 GAAAGGAATGACTTTGTGACAATATAT
1 GAAAGGAATGCCTTTGTGGCAATATAT
* *
60189607 GGAAGGAATGTCTTTGTGGCAATATAT
1 GAAAGGAATGCCTTTGTGGCAATATAT
* * *
60189634 G-AATGAATGCCTTCGTGGCAGACTCTA-
1 GAAAGGAATGCCTTTGTGGCA-A-TATAT
* *
60189661 -AAGGGAATGCCTTTGTGGCAA-ACTCT
1 GAAAGGAATGCCTTTGTGGCAATA-TAT
60189687 GAAAGGAATGC
1 GAAAGGAATGC
60189698 ATTAACAGTG
Statistics
Matches: 95, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
25 1 0.01
26 17 0.18
27 74 0.78
28 3 0.03
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (27 bp):
GAAAGGAATGCCTTTGTGGCAATATAT
Found at i:60192049 original size:14 final size:14
Alignment explanation
Indices: 60192030--60192057 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
60192020 CGCATACATA
60192030 TCAAAATATCAATC
1 TCAAAATATCAATC
60192044 TCAAAATATCAATC
1 TCAAAATATCAATC
60192058 ATCATATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (14 bp):
TCAAAATATCAATC
Found at i:60192316 original size:47 final size:48
Alignment explanation
Indices: 60192197--60192341 Score: 166
Period size: 47 Copynumber: 2.9 Consensus size: 48
60192187 CTCGTCCATT
* *
60192197 TGAAACACAATTTGTGGACAAACCACCACTGATTTGCAGATAAACTGCAAC
1 TGAAACAC--TTTGTGGACAAGCCACCAC-GATATGCAGATAAACTGCAAC
* * *
60192248 TGATAACACTTTGTGGACAAGCCACCAC-ATATGTAGATATACTGCCAC
1 TGA-AACACTTTGTGGACAAGCCACCACGATATGCAGATAAACTGCAAC
* **
60192296 TGAAACACTTTGTGGACAAGCCACCACTGATTTATAGATAAACTGC
1 TGAAACACTTTGTGGACAAGCCACCAC-GATATGCAGATAAACTGC
60192342 CACATACTTC
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
47 24 0.29
48 19 0.23
49 14 0.17
50 18 0.22
51 3 0.04
52 5 0.06
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (48 bp):
TGAAACACTTTGTGGACAAGCCACCACGATATGCAGATAAACTGCAAC
Found at i:60194427 original size:20 final size:21
Alignment explanation
Indices: 60194402--60194485 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
60194392 TGATCAGTAT
*
60194402 ACGACACA-TAAGTGCCTGAA
1 ACGACACACGAAGTGCCTGAA
* *
60194422 ACGACACACGAGGTGCCTGAT
1 ACGACACACGAAGTGCCTGAA
*
60194443 ACGACACACGAGGTGCCTGATA
1 ACGACACACGAAGTGCCTGA-A
* **
60194465 TATGACACAAAAAGTGCCTGA
1 -ACGACACACGAAGTGCCTGA
60194486 TCGGCAAAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 8 0.15
21 29 0.55
23 16 0.30
ACGTcount: A:0.36, C:0.25, G:0.24, T:0.15
Consensus pattern (21 bp):
ACGACACACGAAGTGCCTGAA
Found at i:60194473 original size:23 final size:21
Alignment explanation
Indices: 60194400--60194464 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
60194390 CCTGATCAGT
* *
60194400 ATACGACACA-TAAGTGCCTG
1 ATACGACACACGAGGTGCCTG
*
60194420 AAACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
60194441 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
60194462 ATA
1 ATA
60194465 TATGACACAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 9 0.22
21 31 0.77
ACGTcount: A:0.34, C:0.26, G:0.25, T:0.15
Consensus pattern (21 bp):
ATACGACACACGAGGTGCCTG
Found at i:60195766 original size:4 final size:4
Alignment explanation
Indices: 60195757--60195783 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
60195747 ATTTGTCAAC
60195757 TTAT TTAT TTAT TTAT TTAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTA
60195784 AAATATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:60195805 original size:11 final size:11
Alignment explanation
Indices: 60195789--60195830 Score: 57
Period size: 11 Copynumber: 3.5 Consensus size: 11
60195779 ATTTAAAATA
60195789 TAATAATAATT
1 TAATAATAATT
60195800 TAATAATACTAATT
1 TAAT-A-A-TAATT
60195814 TAATAATAATT
1 TAATAATAATT
60195825 TAATAA
1 TAATAA
60195831 CATTTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 15 0.54
12 2 0.07
13 2 0.07
14 9 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (11 bp):
TAATAATAATT
Found at i:60195807 original size:14 final size:14
Alignment explanation
Indices: 60195788--60195823 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
60195778 TATTTAAAAT
60195788 ATAATAATAATTTA
1 ATAATAATAATTTA
*
60195802 ATAATACTAATTTA
1 ATAATAATAATTTA
60195816 ATAATAAT
1 ATAATAAT
60195824 TTAATAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
ATAATAATAATTTA
Found at i:60197448 original size:12 final size:12
Alignment explanation
Indices: 60197431--60197458 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
60197421 CTTCTCGAAG
60197431 AATCAACTCTTT
1 AATCAACTCTTT
60197443 AATCAACTCTTT
1 AATCAACTCTTT
60197455 AATC
1 AATC
60197459 TCAAAAGTAG
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:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (12 bp):
AATCAACTCTTT
Found at i:60201892 original size:21 final size:21
Alignment explanation
Indices: 60201868--60201915 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
60201858 CGGCACATAA
60201868 GTGCCTGAAACGACACACGAG
1 GTGCCTGAAACGACACACGAG
* *
60201889 GTGCTTGATACGACACACGAG
1 GTGCCTGAAACGACACACGAG
60201910 GTGCCT
1 GTGCCT
60201916 AATATACGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.17
Consensus pattern (21 bp):
GTGCCTGAAACGACACACGAG
Found at i:60203118 original size:3 final size:3
Alignment explanation
Indices: 60203110--60203162 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
60203100 TATTCCTAGT
* *
60203110 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
60203158 GAA TA
1 TAA TA
60203163 TATTTTAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:60203305 original size:14 final size:14
Alignment explanation
Indices: 60203286--60203331 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
60203276 TATTTAAAAT
60203286 ATAATAATAATTTA
1 ATAATAATAATTTA
*
60203300 ATAATACTAATTTA
1 ATAATAATAATTTA
60203314 ATAATAATAATTTA
1 ATAATAATAATTTA
60203328 ATAA
1 ATAA
60203332 AATTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATAATAATTTA
Found at i:60204519 original size:32 final size:32
Alignment explanation
Indices: 60204483--60204546 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
60204473 GTTACAACAA
*
60204483 AGTAAGTACTCCGAGGA-TCGTACCTTAGGGAT
1 AGTAAGTACTCCGAGGAGT-GTACCTAAGGGAT
*
60204515 AGTAAGTACTCTGAGGAGTGTACCTAAGGGAT
1 AGTAAGTACTCCGAGGAGTGTACCTAAGGGAT
60204547 TGCAATTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (32 bp):
AGTAAGTACTCCGAGGAGTGTACCTAAGGGAT
Found at i:60212071 original size:50 final size:50
Alignment explanation
Indices: 60211997--60212183 Score: 178
Period size: 50 Copynumber: 3.6 Consensus size: 50
60211987 TCTTGTACTA
* * ** *
60211997 CCAATGCCATTTCCCAGATATGGTCTTACATGGGAGTTCCCTTATCGGTG
1 CCAATGCCATGTCCCAGAAATGGTCTTACATGGGACCTCCCATATCGGTG
* * * *
60212047 CCCATGCCATGTCCGAGAAATGGTCTTACGA-GGGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGAAATGGTCTTAC-ATGGGACCTCCCATATCGGTG
* * * *
60212097 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATG
1 CCAATGCCATGTCCCAGAAATGGTCTTACATGGGACCTCCCAT-A--TC---GGTG
*
60212153 CCAATGCCATGTCCCAGACATGGTCTTACAT
1 CCAATGCCATGTCCCAGAAATGGTCTTACAT
60212184 AGGATCTCTT
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
49 1 0.01
50 76 0.67
51 1 0.01
53 2 0.02
56 33 0.29
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGAAATGGTCTTACATGGGACCTCCCATATCGGTG
Found at i:60221828 original size:33 final size:33
Alignment explanation
Indices: 60221791--60221886 Score: 111
Period size: 33 Copynumber: 2.9 Consensus size: 33
60221781 GATATTCTAG
* * * *
60221791 TGGGATAGTAAACATAAAATAGAGATAGTCCGT
1 TGGGACAGTAAACACAAAACAGAGATAGTCCGC
* *
60221824 TGGGACGGTAAACACAGAACAGAGATAGTCCGC
1 TGGGACAGTAAACACAAAACAGAGATAGTCCGC
* * *
60221857 TAGGACAGTAAACACAGAACAAAGATAGTC
1 TGGGACAGTAAACACAAAACAGAGATAGTC
60221887 TATCAGGACA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.43, C:0.16, G:0.25, T:0.17
Consensus pattern (33 bp):
TGGGACAGTAAACACAAAACAGAGATAGTCCGC
Found at i:60222504 original size:56 final size:55
Alignment explanation
Indices: 60222352--60222504 Score: 131
Period size: 56 Copynumber: 2.8 Consensus size: 55
60222342 CGGGATAGAA
* *
60222352 ATAA-TTTTTTTCATATACTTGTTTATTGAATGATTA-ATTATCGAGGTGAGTAT
1 ATAATTTTTTTTCATATGCTTGTTTATTGAATGATTAGAATATCGAGGTGAGTAT
* * * * *
60222405 ATCATTTTCGTATGAATTGATTTGC-TG-TGATTGAA-G-TT-GAATATTGAGGTGAGTAT
1 ATAATTTT--T-T---TTCATATGCTTGTTTATTGAATGATTAGAATATCGAGGTGAGTAT
60222461 ATAATTTTTTTTCATATGCTTGTTTATTGAATGATTAGTAATAT
1 ATAATTTTTTTTCATATGCTTGTTTATTGAATGATTAG-AATAT
60222505 GATTTAATTA
Statistics
Matches: 75, Mismatches: 11, Indels: 25
0.68 0.10 0.23
Matches are distributed among these distances:
50 7 0.09
51 2 0.03
52 7 0.09
53 5 0.07
54 6 0.08
55 1 0.01
56 30 0.40
57 2 0.03
58 7 0.09
59 2 0.03
60 6 0.08
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.48
Consensus pattern (55 bp):
ATAATTTTTTTTCATATGCTTGTTTATTGAATGATTAGAATATCGAGGTGAGTAT
Found at i:60223884 original size:17 final size:15
Alignment explanation
Indices: 60223854--60223887 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
60223844 CTCCCAGACT
60223854 TAATAAAATAATAAA
1 TAATAAAATAATAAA
60223869 TAATAAAACTTAATAAA
1 TAATAAAA--TAATAAA
60223886 TA
1 TA
60223888 CAATATTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
17 9 0.53
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
TAATAAAATAATAAA
Found at i:60236300 original size:17 final size:18
Alignment explanation
Indices: 60236278--60236313 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
60236268 ACTTTATGTC
60236278 TTAAAA-AATATAATATA
1 TTAAAATAATATAATATA
60236295 TTAAAATTAATATAATATA
1 TTAAAA-TAATATAATATA
60236314 AGCCATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAAAATAATATAATATA
Found at i:60260927 original size:59 final size:59
Alignment explanation
Indices: 60260835--60260952 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
60260825 AAATACAGAC
60260835 TTGATTTTAATTGAAAACATGATCGATTGAGGCAAAAACATTATAAGCATGAATCAAAT
1 TTGATTTTAATTGAAAACATGATCGATTGAGGCAAAAACATTATAAGCATGAATCAAAT
*
60260894 TTGATTTTAATTGAAAACATGATCGATTGAGGCACAAACATTATAAGCATGAATCAAAT
1 TTGATTTTAATTGAAAACATGATCGATTGAGGCAAAAACATTATAAGCATGAATCAAAT
60260953 AAATATTATT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (59 bp):
TTGATTTTAATTGAAAACATGATCGATTGAGGCAAAAACATTATAAGCATGAATCAAAT
Found at i:60264268 original size:19 final size:19
Alignment explanation
Indices: 60264243--60264288 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
60264233 AATGGTTAAA
60264243 AATAAAAA-TAAATAAAAGT
1 AATAAAAATTAAATAAAA-T
* *
60264262 TATAAAAATTTAATAAAAT
1 AATAAAAATTAAATAAAAT
60264281 AATAAAAA
1 AATAAAAA
60264289 ATATTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AATAAAAATTAAATAAAAT
Found at i:60264269 original size:20 final size:19
Alignment explanation
Indices: 60264246--60264291 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
60264236 GGTTAAAAAT
*
60264246 AAAAATAAATAAAAGTTATA
1 AAAAATAAATAAAA-TAATA
* *
60264266 AAAATTTAATAAAATAATA
1 AAAAATAAATAAAATAATA
60264285 AAAAATA
1 AAAAATA
60264292 TTTAAATTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAATAAATAAAATAATA
Found at i:60264302 original size:29 final size:29
Alignment explanation
Indices: 60264247--60264326 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 29
60264237 GTTAAAAATA
* * *
60264247 AAAATAA-ATAAAAGTTATAAAAATTTAAT
1 AAAATAAGAAAAAAATTAT-AAATTTTAAT
* *
60264276 AAAATAATAAAAAATATT-TAAATTTTATT
1 AAAATAAGAAAAAA-ATTATAAATTTTAAT
*
60264305 AAAATTAGAAAAAAATTATAAA
1 AAAATAAGAAAAAAATTATAAA
60264327 AATTGTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 3 0.07
29 31 0.74
30 6 0.14
31 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAATAAGAAAAAAATTATAAATTTTAAT
Found at i:60264323 original size:20 final size:19
Alignment explanation
Indices: 60264304--60264370 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 19
60264294 TAAATTTTAT
60264304 TAAAATTAGAAAAAAATTA
1 TAAAATTAGAAAAAAATTA
60264323 TAAAAATT-GTAAAAATAA-TA
1 T-AAAATTAG-AAAAA-AATTA
60264343 TAGAAATATAGAAAAAAATTA
1 TA-AAAT-TAGAAAAAAATTA
60264364 TAAAATT
1 TAAAATT
60264371 TTATAAAGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
19 4 0.10
20 24 0.59
21 12 0.29
22 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (19 bp):
TAAAATTAGAAAAAAATTA
Found at i:60266659 original size:20 final size:20
Alignment explanation
Indices: 60266634--60266683 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
60266624 AGGAAGATGA
60266634 TACTTAATTCA-TCTTTTATT
1 TACTTAATT-ATTCTTTTATT
*
60266654 TACTTAGTTATTCTTTTATT
1 TACTTAATTATTCTTTTATT
*
60266674 TACTAAATTA
1 TACTTAATTA
60266684 CTACTTTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.28, C:0.12, G:0.02, T:0.58
Consensus pattern (20 bp):
TACTTAATTATTCTTTTATT
Found at i:60267260 original size:10 final size:10
Alignment explanation
Indices: 60267247--60267328 Score: 80
Period size: 10 Copynumber: 8.4 Consensus size: 10
60267237 TTTTGATACA
60267247 TTTTATAATT
1 TTTTATAATT
*
60267257 TTTTATGA-T
1 TTTTATAATT
**
60267266 TTTTATAAAA
1 TTTTATAATT
*
60267276 TTTTACAATT
1 TTTTATAATT
60267286 TTTTATATATT
1 TTTTATA-ATT
**
60267297 TTTTACGA-T
1 TTTTATAATT
60267306 TTTTATAA-T
1 TTTTATAATT
60267315 TTTTATAATT
1 TTTTATAATT
60267325 TTTT
1 TTTT
60267329 TCTGTTTTTA
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
9 24 0.41
10 26 0.45
11 8 0.14
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (10 bp):
TTTTATAATT
Found at i:60267268 original size:29 final size:27
Alignment explanation
Indices: 60267236--60267327 Score: 87
Period size: 29 Copynumber: 3.2 Consensus size: 27
60267226 TTAAAGTGCC
60267236 TTTTTGATACATTTTATAATTTTTTATGA
1 TTTTT-ATACATTTTATAATTTTTTAT-A
* *
60267265 TTTTTATAAAATTTTACAATTTTTTATA
1 TTTTTAT-ACATTTTATAATTTTTTATA
*
60267293 TATTTTTTACGATTTTTATAA-TTTTTATAA
1 T-TTTTATAC-A-TTTTATAATTTTTTAT-A
60267323 TTTTT
1 TTTTT
60267328 TTCTGTTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
28 5 0.09
29 39 0.74
30 9 0.17
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.64
Consensus pattern (27 bp):
TTTTTATACATTTTATAATTTTTTATA
Found at i:60267328 original size:29 final size:29
Alignment explanation
Indices: 60267247--60267346 Score: 82
Period size: 29 Copynumber: 3.4 Consensus size: 29
60267237 TTTTGATACA
* * * *
60267247 TTTTATAATTTTTTATGATTTTTATA-AAA
1 TTTTATAA-TTTTTATAATTTTTTTACGAT
*
60267276 TTTTACAATTTTT-TATATATTTTTTACGAT
1 TTTTATAATTTTTATA-AT-TTTTTTACGAT
60267306 TTTTATAATTTTTATAATTTTTTT-CTG-T
1 TTTTATAATTTTTATAATTTTTTTAC-GAT
60267334 TTTTATATATTTT
1 TTTTATA-ATTTT
60267347 GAATTAAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
27 1 0.02
28 16 0.27
29 25 0.42
30 15 0.25
31 2 0.03
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (29 bp):
TTTTATAATTTTTATAATTTTTTTACGAT
Found at i:60267611 original size:86 final size:86
Alignment explanation
Indices: 60267511--60267687 Score: 230
Period size: 86 Copynumber: 2.1 Consensus size: 86
60267501 CCTAATGGTC
* * ** *
60267511 TTTTTTATGTATTTTGACAGTTCAAGTACCCAATTAAGTGCAAAAAAAA-GGGGTTTAACTGCTT
1 TTTTTTATGCATTTTGAAAGTTCAAGTACCCAATTAAGTGCAAAAAAAAGGGGGGCTAACTGCTG
* *
60267575 TTTTTGAAAAAGTTTGAGAAT
66 TTTTAGAAAAAATTTGAGAAT
* * * *
60267596 TTTTTTGATGCATTTTGAAAGTTTAAGTACCTAATTGAGTGCAAAAAAAAGGGGGGCTAATTGCT
1 TTTTTT-ATGCATTTTGAAAGTTCAAGTACCCAATTAAGTGCAAAAAAAAGGGGGGCTAACTGCT
*
60267661 GTTTTAGAAAAAATTTGAGAGT
65 GTTTTAGAAAAAATTTGAGAAT
60267683 TTTTT
1 TTTTT
60267688 ACGCCCTTAA
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
85 6 0.08
86 38 0.49
87 34 0.44
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (86 bp):
TTTTTTATGCATTTTGAAAGTTCAAGTACCCAATTAAGTGCAAAAAAAAGGGGGGCTAACTGCTG
TTTTAGAAAAAATTTGAGAAT
Found at i:60268663 original size:31 final size:30
Alignment explanation
Indices: 60268624--60268686 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
60268614 ACTGATTAAT
60268624 TGAATAAAATTCATACATAATAATACATGG
1 TGAATAAAATTCATACATAATAATACATGG
* * *
60268654 TGAAGTAAAATTTATACGTAATAATATATGG
1 TGAA-TAAAATTCATACATAATAATACATGG
60268685 TG
1 TG
60268687 GAACTCAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.33
Consensus pattern (30 bp):
TGAATAAAATTCATACATAATAATACATGG
Found at i:60268704 original size:34 final size:31
Alignment explanation
Indices: 60268624--60268711 Score: 83
Period size: 31 Copynumber: 2.8 Consensus size: 31
60268614 ACTGATTAAT
60268624 TGAA-TAAAAT-TCATACATAATAATACATGG
1 TGAACTAAAATCT-ATACATAATAATACATGG
* * * *
60268654 TGAAGTAAAATTTATACGTAATAATATATGG
1 TGAACTAAAATCTATACATAATAATACATGG
60268685 TGGAACTCAAAGATCTATACAT-ATAAT
1 T-GAACT-AAA-ATCTATACATAATAAT
60268712 TTACAAGATG
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
30 4 0.08
31 23 0.48
32 5 0.10
33 8 0.17
34 8 0.17
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (31 bp):
TGAACTAAAATCTATACATAATAATACATGG
Found at i:60270187 original size:14 final size:14
Alignment explanation
Indices: 60270170--60270196 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
60270160 GAGTATGGTA
60270170 AAATATTTAAAAAT
1 AAATATTTAAAAAT
60270184 AAATATTTAAAAA
1 AAATATTTAAAAA
60270197 GGTACTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATTTAAAAAT
Found at i:60271994 original size:44 final size:43
Alignment explanation
Indices: 60271945--60272076 Score: 192
Period size: 44 Copynumber: 3.0 Consensus size: 43
60271935 ACTAATGTAA
** *
60271945 TATTTGATAGTACAAAATTAGTTGAAAATTTTAGAAGAGCTAAT
1 TATTTG-TAGTACAAAATTAGTTGAAAGCTCTAGAAGAGCTAAT
*
60271989 TATTTGCTAGTTCAAAATTAGTTGAAAGCTCTAGAAGAGCTAAT
1 TATTTG-TAGTACAAAATTAGTTGAAAGCTCTAGAAGAGCTAAT
*
60272033 TATTTTGTAGTATAAAATTAGTTGAAAGCTCTAGAAGAGCTAAT
1 TA-TTTGTAGTACAAAATTAGTTGAAAGCTCTAGAAGAGCTAAT
60272077 ATATCAATAT
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
44 76 0.95
45 4 0.05
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (43 bp):
TATTTGTAGTACAAAATTAGTTGAAAGCTCTAGAAGAGCTAAT
Found at i:60275073 original size:27 final size:27
Alignment explanation
Indices: 60275025--60275320 Score: 260
Period size: 27 Copynumber: 11.0 Consensus size: 27
60275015 AAATCCATAA
**
60275025 CAGTCATTTTATCTCCTA--GGGGTATAA
1 CAGTCATTTTA-C-CCTATGGGGGTATTT
60275052 CAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * *
60275079 CAGTCATTCTACCCCATTGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
*
60275106 CGGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * * *
60275133 C-GATTATTTTACCTTAT-AGGGTGTTT
1 CAG-TCATTTTACCCTATGGGGGTATTT
* * *
60275159 CGGTCATTCTACCCTATAGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * * *
60275186 CAGTCATTCTATCTTATAGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * *
60275213 C-GATCATTCTACCTTATGCGGGTATTT
1 CAG-TCATTTTACCCTATGGGGGTATTT
* * *
60275240 CGGTCATTTTACCCTATGGAGGTGTTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* *
60275267 CAGTCATTCTACCCTATAGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * * *
60275294 CGGTTATTTTATCCTATGGAGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
60275321 TGGTCATAAC
Statistics
Matches: 222, Mismatches: 40, Indels: 14
0.80 0.14 0.05
Matches are distributed among these distances:
25 4 0.02
26 22 0.10
27 195 0.88
28 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (27 bp):
CAGTCATTTTACCCTATGGGGGTATTT
Found at i:60275129 original size:81 final size:81
Alignment explanation
Indices: 60275055--60275327 Score: 325
Period size: 81 Copynumber: 3.4 Consensus size: 81
60275045 GGTATAACAG
* * * *
60275055 TCATTTTACCCTATGGGGGTATTTCAGTCATTCTACCCCATTGGGGTATTTCGGTCATTTTACCC
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCCTATTGGGGTATTTCAGTCATTCTACCC
*
60275120 TATGGGGGTATTTCGA
66 TATAGGGGTATTTCGA
* * * * * * *
60275136 TTATTTTACCTTAT-AGGGTGTTTCGGTCATTCTACCCTATAGGGGTATTTCAGTCATTCTATCT
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCCTATTGGGGTATTTCAGTCATTCTACCC
60275200 TATAGGGGTATTTCGA
66 TATAGGGGTATTTCGA
* * * * *
60275216 TCATTCTACCTTATGCGGGTATTTCGGTCATTTTACCCTA-TGGAGGTGTTTCAGTCATTCTACC
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCCTATTGG-GGTATTTCAGTCATTCTACC
*
60275280 CTATAGGGGTATTTCGG
65 CTATAGGGGTATTTCGA
* * * *
60275297 TTATTTTATCCTATGGAGGTATTTTGGTCAT
1 TCATTTTACCCTATGGGGGTATTTCGGTCAT
60275328 AACAATGTAA
Statistics
Matches: 161, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
80 70 0.43
81 91 0.57
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.42
Consensus pattern (81 bp):
TCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCCTATTGGGGTATTTCAGTCATTCTACCC
TATAGGGGTATTTCGA
Found at i:60275187 original size:107 final size:108
Alignment explanation
Indices: 60275052--60275294 Score: 344
Period size: 107 Copynumber: 2.3 Consensus size: 108
60275042 AGGGGTATAA
* * * * *
60275052 CAGTCATTTTACCCTATGGGGGTATTTCAGTCATTCTACCCCATTGGGGTATTTCGGTCATTTTA
1 CAGTCATTCTACCCTATAGGGGTATTTCAGTCATTCTACCCCATAGGGGTATTTCGATCATTCTA
* * *
60275117 CCCTATGGGGGTATTTCGATTATTTTACCTTATAG-GGTGTTT
66 CCCTATGCGGGTATTTCGATCATTTTACCCTATAGAGGTGTTT
* * **
60275159 CGGTCATTCTACCCTATAGGGGTATTTCAGTCATTCTATCTTATAGGGGTATTTCGATCATTCTA
1 CAGTCATTCTACCCTATAGGGGTATTTCAGTCATTCTACCCCATAGGGGTATTTCGATCATTCTA
* * *
60275224 CCTTATGCGGGTATTTCGGTCATTTTACCCTATGGAGGTGTTT
66 CCCTATGCGGGTATTTCGATCATTTTACCCTATAGAGGTGTTT
60275267 CAGTCATTCTACCCTATAGGGGTATTTC
1 CAGTCATTCTACCCTATAGGGGTATTTC
60275295 GGTTATTTTA
Statistics
Matches: 119, Mismatches: 16, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
107 85 0.71
108 34 0.29
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.41
Consensus pattern (108 bp):
CAGTCATTCTACCCTATAGGGGTATTTCAGTCATTCTACCCCATAGGGGTATTTCGATCATTCTA
CCCTATGCGGGTATTTCGATCATTTTACCCTATAGAGGTGTTT
Found at i:60275327 original size:54 final size:53
Alignment explanation
Indices: 60275027--60275327 Score: 291
Period size: 54 Copynumber: 5.6 Consensus size: 53
60275017 ATCCATAACA
** * * * *
60275027 GTCATTTTATCTCCTA-GGGGTATAACAGTCATTTTACCCTATGGGGGTATTTCA
1 GTCATTTTA-C-CCTATGGGGTATTTCGGTCATTCTACCCTATAGGGGTATTTCG
* * * *
60275081 GTCATTCTACCCCATTGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTA-TGGGGTATTTCGGTCATTCTACCCTATAGGGGTATTTCG
* * * * * *
60275135 ATTATTTTACCTTATAGGGTGTTTCGGTCATTCTACCCTATAGGGGTATTTCA
1 GTCATTTTACCCTATGGGGTATTTCGGTCATTCTACCCTATAGGGGTATTTCG
* * * * *
60275188 GTCATTCTATCTTATAGGGGTATTTCGATCATTCTACCTTAT-GCGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTCGGTCATTCTACCCTATAG-GGGTATTTCG
* *
60275242 GTCATTTTACCCTATGGAGGTGTTTCAGTCATTCTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGG-GGTATTTCGGTCATTCTACCCTATAGGGGTATTTCG
* * *
60275296 GTTATTTTATCCTATGGAGGTATTTTGGTCAT
1 GTCATTTTACCCTATGG-GGTATTTCGGTCAT
60275328 AACAATGTAA
Statistics
Matches: 204, Mismatches: 37, Indels: 12
0.81 0.15 0.05
Matches are distributed among these distances:
52 3 0.01
53 49 0.24
54 151 0.74
55 1 0.00
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (53 bp):
GTCATTTTACCCTATGGGGTATTTCGGTCATTCTACCCTATAGGGGTATTTCG
Found at i:60280002 original size:29 final size:29
Alignment explanation
Indices: 60279910--60280029 Score: 170
Period size: 30 Copynumber: 4.0 Consensus size: 29
60279900 CATATTTATG
* *
60279910 GAAAATCAAAGATATGGGTATCAAATAAT
1 GAAAGTCAAAGATATGGGTATCAAATATT
60279939 GAAAAGTCAAAGATATGGGTATCAAATATT
1 G-AAAGTCAAAGATATGGGTATCAAATATT
60279969 GGAAAGTCAAAGATAT-GGTATCAAATATT
1 -GAAAGTCAAAGATATGGGTATCAAATATT
*
60279998 AGAAAGTCAAAGATATGGGTATCGAGATATT
1 -GAAAGTCAAAGATATGGGTATC-AAATATT
60280029 G
1 G
60280030 GCATAATAAA
Statistics
Matches: 83, Mismatches: 4, Indels: 7
0.88 0.04 0.07
Matches are distributed among these distances:
29 29 0.35
30 47 0.57
31 7 0.08
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.26
Consensus pattern (29 bp):
GAAAGTCAAAGATATGGGTATCAAATATT
Found at i:60280006 original size:59 final size:61
Alignment explanation
Indices: 60279908--60280030 Score: 189
Period size: 59 Copynumber: 2.0 Consensus size: 61
60279898 TCCATATTTA
60279908 TGGAAAATCAAAGATATGGGTATCAAATAATGAAAAGTCAAAGATATGGGTATC-AAATAT
1 TGGAAAATCAAAGATATGGGTATCAAATAATGAAAAGTCAAAGATATGGGTATCGAAATAT
* * *
60279968 TGGAAAGTCAAAGATAT-GGTATCAAAT-ATTAGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAATCAAAGATATGGGTATCAAATAATGA-AAAGTCAAAGATATGGGTATCGAAATAT
60280028 TGG
1 TGG
60280031 CATAATAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
58 3 0.05
59 31 0.53
60 24 0.41
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.26
Consensus pattern (61 bp):
TGGAAAATCAAAGATATGGGTATCAAATAATGAAAAGTCAAAGATATGGGTATCGAAATAT
Found at i:60284626 original size:15 final size:15
Alignment explanation
Indices: 60284606--60284713 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
60284596 TTTATGGAAA
60284606 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
60284621 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
60284635 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
60284651 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
60284665 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
60284681 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
60284695 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
60284711 ATC
1 ATC
60284714 GAGATATTGG
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 13 0.19
15 43 0.62
16 13 0.19
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:60284635 original size:30 final size:30
Alignment explanation
Indices: 60284599--60284713 Score: 203
Period size: 30 Copynumber: 3.8 Consensus size: 30
60284589 ATCCATATTT
*
60284599 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
60284629 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
60284659 TTGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
60284689 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
60284714 GAGATATTGG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 83 1.00
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:60289762 original size:42 final size:42
Alignment explanation
Indices: 60289715--60289813 Score: 137
Period size: 42 Copynumber: 2.4 Consensus size: 42
60289705 TTCAGTATAG
* * * *
60289715 CTGATGATGCACTTATGTGCCAGTATATTTGCATCGATTTC-T
1 CTGATGATGCACTTATGTGCCAATATAATTACATCGA-TACAT
*
60289757 CTGATGATGCACTTATGTGCCAATATAATTACTTCGATACAT
1 CTGATGATGCACTTATGTGCCAATATAATTACATCGATACAT
60289799 CTGATGATGCACTTA
1 CTGATGATGCACTTA
60289814 CGTGGAAGTA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 2 0.04
42 49 0.96
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.37
Consensus pattern (42 bp):
CTGATGATGCACTTATGTGCCAATATAATTACATCGATACAT
Found at i:60295189 original size:24 final size:23
Alignment explanation
Indices: 60295155--60295201 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
60295145 TTTACGTTCT
60295155 GGAAAGCTAAAAGAAAAAGAAAAA
1 GGAAAGCTAAAAG-AAAAGAAAAA
*
60295179 GGAAAGTTAAAAGAAAAGAAAAA
1 GGAAAGCTAAAAGAAAAGAAAAA
60295202 TTAAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.21, T:0.06
Consensus pattern (23 bp):
GGAAAGCTAAAAGAAAAGAAAAA
Found at i:60295196 original size:17 final size:18
Alignment explanation
Indices: 60295169--60295207 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
60295159 AGCTAAAAGA
* *
60295169 AAAAGAAAAAGGAAAGTT
1 AAAAGAAAAAGAAAAATT
60295187 AAAAG-AAAAGAAAAATT
1 AAAAGAAAAAGAAAAATT
60295204 AAAA
1 AAAA
60295208 TTATAGGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.10
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAATT
Found at i:60298496 original size:5 final size:5
Alignment explanation
Indices: 60298486--60298591 Score: 212
Period size: 5 Copynumber: 21.2 Consensus size: 5
60298476 GATTGTCTAT
60298486 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
60298536 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
60298586 ATATA A
1 ATATA A
60298592 GCACGAGTTT
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 101 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:60298750 original size:17 final size:16
Alignment explanation
Indices: 60298728--60298759 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
60298718 AATAGTTGTG
60298728 ATAATTATACATTTAAC
1 ATAATTATA-ATTTAAC
60298745 ATAATTATAATTTAA
1 ATAATTATAATTTAA
60298760 TAGAAGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATTATAATTTAAC
Found at i:60298781 original size:43 final size:44
Alignment explanation
Indices: 60298710--60298813 Score: 111
Period size: 44 Copynumber: 2.3 Consensus size: 44
60298700 TTTAAAAAGT
* * * * *
60298710 TGAAATAAAATAGTTGTGATAATTATACATTTA-ACATAATTATAA
1 TGAAAT-AAA-AGTTATGGTAATAATACATTTACAAATAATTAGAA
** *
60298755 TTTAATAGAAGTTATGGTAATAATACATTTACAAATAATTAGAA
1 TGAAATAAAAGTTATGGTAATAATACATTTACAAATAATTAGAA
60298799 TGAAATAAAAGTTAT
1 TGAAATAAAAGTTAT
60298814 TCCAATTTTA
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
43 19 0.40
44 24 0.51
45 4 0.09
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.37
Consensus pattern (44 bp):
TGAAATAAAAGTTATGGTAATAATACATTTACAAATAATTAGAA
Found at i:60300337 original size:11 final size:11
Alignment explanation
Indices: 60300321--60300350 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
60300311 TTTTTTAAAT
60300321 AAAAATAATAA
1 AAAAATAATAA
60300332 AAAAATAATAA
1 AAAAATAATAA
60300343 AAAAATAA
1 AAAAATAA
60300351 GATACTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAATAATAA
Found at i:60300492 original size:16 final size:17
Alignment explanation
Indices: 60300471--60300512 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
60300461 TTTAAAAAAA
60300471 TATAAAATTTAG-ATTT
1 TATAAAATTTAGAATTT
*
60300487 TATAAATATTTTGAATTT
1 TATAAA-ATTTAGAATTT
60300505 TA-AAAATT
1 TATAAAATT
60300513 ATTTTGAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 9 0.39
17 8 0.35
18 6 0.26
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
TATAAAATTTAGAATTT
Found at i:60300545 original size:20 final size:20
Alignment explanation
Indices: 60300484--60300538 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
60300474 AAAATTTAGA
*
60300484 TTTTATAAA-TATTTTGAA-
1 TTTTAAAAATTATTTTGAAC
60300502 TTTTAAAAATTATTTTGAAC
1 TTTTAAAAATTATTTTGAAC
*
60300522 TTTTGAAAATTATTTTG
1 TTTTAAAAATTATTTTG
60300539 TGTTTTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.24
19 9 0.27
20 16 0.48
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (20 bp):
TTTTAAAAATTATTTTGAAC
Found at i:60322358 original size:27 final size:27
Alignment explanation
Indices: 60322314--60322367 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
60322304 CCATAATCCT
*
60322314 CGTGTTTACTATCCTGTTAGAATATTC
1 CGTGTTTAATATCCTGTTAGAATATTC
* * *
60322341 CGTGTTTAATGTCTTGTTAGACTATTC
1 CGTGTTTAATATCCTGTTAGAATATTC
60322368 TACGATGCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (27 bp):
CGTGTTTAATATCCTGTTAGAATATTC
Found at i:60326684 original size:48 final size:48
Alignment explanation
Indices: 60326615--60326712 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
60326605 TTACATAGTT
60326615 TTTTTTCCTTTACTTTTTAGATTATGAGAAGCTCGATCGGGTTGGAAG
1 TTTTTTCCTTTACTTTTTAGATTATGAGAAGCTCGATCGGGTTGGAAG
60326663 TTTTTTCCTTTACTTTTTAGATTATGAGAAGCTCGATCGGGTTGGAAG
1 TTTTTTCCTTTACTTTTTAGATTATGAGAAGCTCGATCGGGTTGGAAG
60326711 TT
1 TT
60326713 CGTCGAAGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.20, C:0.12, G:0.22, T:0.45
Consensus pattern (48 bp):
TTTTTTCCTTTACTTTTTAGATTATGAGAAGCTCGATCGGGTTGGAAG
Found at i:60332975 original size:6 final size:6
Alignment explanation
Indices: 60332964--60333004 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
60332954 AGGATTTCTA
*
60332964 ATTATC ATTATC ATTATC ATTATC ATTATC ATTATT ATTAT
1 ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC ATTAT
60333005 ATTTACACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54
Consensus pattern (6 bp):
ATTATC
Found at i:60336792 original size:45 final size:45
Alignment explanation
Indices: 60336741--60336831 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
60336731 GAATTAAGAT
60336741 AGGTGAATCAGCCTTCTAGTAAGCCTTATAGTTTTGCACATTATG
1 AGGTGAATCAGCCTTCTAGTAAGCCTTATAGTTTTGCACATTATG
60336786 AGGTGAATCAGCCTTCTAGTAAGCCTTATAGTTTTGCACATTATG
1 AGGTGAATCAGCCTTCTAGTAAGCCTTATAGTTTTGCACATTATG
60336831 A
1 A
60336832 CTATATAAGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (45 bp):
AGGTGAATCAGCCTTCTAGTAAGCCTTATAGTTTTGCACATTATG
Found at i:60339412 original size:36 final size:36
Alignment explanation
Indices: 60339372--60339449 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
60339362 ACAAAGACTA
* * *
60339372 TCACATGGCATGAATAACATACCCACATATTTACTG
1 TCACATGGCATGAACAACACACCCACATATTCACTG
* *
60339408 TCACATGGCATGAACAACACACCCTCATATTCACTT
1 TCACATGGCATGAACAACACACCCACATATTCACTG
60339444 TCACAT
1 TCACAT
60339450 CATTCATCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.29, G:0.09, T:0.27
Consensus pattern (36 bp):
TCACATGGCATGAACAACACACCCACATATTCACTG
Found at i:60340190 original size:20 final size:21
Alignment explanation
Indices: 60340153--60340192 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
60340143 TTTTGGGTTT
60340153 TAACTAAAACATTCAATTTTCA
1 TAACTAAAACA-TCAATTTTCA
60340175 TAACTAAAAC-TCAATTTT
1 TAACTAAAACATCAATTTT
60340193 AAAGTCAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (21 bp):
TAACTAAAACATCAATTTTCA
Found at i:60341912 original size:24 final size:24
Alignment explanation
Indices: 60341862--60341914 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
60341852 TTTCTAGAAG
* * *
60341862 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGAATTTATTAGCACAATAT
*
60341886 ATTTAGAATTTATTAGCACAATTT
1 ATTTAGAATTTATTAGCACAATAT
60341910 ATTTA
1 ATTTA
60341915 ACCTACTAAT
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:0.38, C:0.04, G:0.08, T:0.51
Consensus pattern (24 bp):
ATTTAGAATTTATTAGCACAATAT
Found at i:60343859 original size:24 final size:24
Alignment explanation
Indices: 60343831--60343882 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
60343821 TTTTTAGAAG
*
60343831 ATTTAATATTTATTAGTATAATAT
1 ATTTAATATTTATTAGCATAATAT
*
60343855 ATTTAATATTTATTAGCATAATTT
1 ATTTAATATTTATTAGCATAATAT
60343879 ATTT
1 ATTT
60343883 GACCTACGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (24 bp):
ATTTAATATTTATTAGCATAATAT
Found at i:60343917 original size:26 final size:26
Alignment explanation
Indices: 60343887--60343939 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
60343877 TTATTTGACC
*
60343887 TACGAATTTAGCTTATAAATAATCTT
1 TACGAATTTAACTTATAAATAATCTT
*
60343913 TACGAATTTAACTTATAAATAGTCTT
1 TACGAATTTAACTTATAAATAATCTT
60343939 T
1 T
60343940 TTTTTATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (26 bp):
TACGAATTTAACTTATAAATAATCTT
Found at i:60351865 original size:13 final size:13
Alignment explanation
Indices: 60351847--60351872 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60351837 TTTGATTCAT
60351847 ATTAGCCTTGGGC
1 ATTAGCCTTGGGC
60351860 ATTAGCCTTGGGC
1 ATTAGCCTTGGGC
60351873 TCTTCGGCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.31, T:0.31
Consensus pattern (13 bp):
ATTAGCCTTGGGC
Found at i:60358921 original size:33 final size:29
Alignment explanation
Indices: 60358883--60358957 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 29
60358873 CAACTATAAG
60358883 TGCCGAATGCACATATTCACTTATACCCACCTA
1 TGCCGAATGCACATA-T-A--TATACCCACCTA
*
60358916 TGCCGAATGCATACATATATATATCCACCTA
1 TGCCGAATGC--ACATATATATACCCACCTA
60358947 TGCCGAATGCA
1 TGCCGAATGCA
60358958 TACATATACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
29 1 0.03
31 21 0.54
33 11 0.28
34 1 0.03
35 5 0.13
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (29 bp):
TGCCGAATGCACATATATATACCCACCTA
Found at i:60358947 original size:31 final size:31
Alignment explanation
Indices: 60358904--60358965 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
60358894 CATATTCACT
60358904 TATACCCACCTATGCCGAATGCATACATATA
1 TATACCCACCTATGCCGAATGCATACATATA
*
60358935 TATATCCACCTATGCCGAATGCATACATATA
1 TATACCCACCTATGCCGAATGCATACATATA
60358966 CACACTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.27
Consensus pattern (31 bp):
TATACCCACCTATGCCGAATGCATACATATA
Found at i:60359222 original size:41 final size:41
Alignment explanation
Indices: 60359151--60359348 Score: 193
Period size: 41 Copynumber: 4.8 Consensus size: 41
60359141 TTTAAACAGA
* * * * *
60359151 TTCACTGGCACTTCA-CCTGATAGACTTATAGTCTAATTCCG
1 TTCACCGGCACTT-AGCCTGCTAGGCGTATAGTCTAATTCAG
* * * *
60359192 TTTACCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCGTATAGTCTAATTCAG
** * * * *
60359233 TTCACTTGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCGTATAGTCTAATTCAG
* * *
60359274 TTCACCGGCACTAAGCCTGCT-GGACGTATAGTCCAATTCAA
1 TTCACCGGCACTTAGCCTGCTAGG-CGTATAGTCTAATTCAG
*
60359315 TTCACCGGCACTTAGCCTGCTAGACGTATAGTCT
1 TTCACCGGCACTTAGCCTGCTAGGCGTATAGTCT
60359349 GAACAATTTC
Statistics
Matches: 129, Mismatches: 25, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
40 3 0.02
41 125 0.97
42 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGGCGTATAGTCTAATTCAG
Found at i:60359281 original size:82 final size:82
Alignment explanation
Indices: 60359150--60359345 Score: 218
Period size: 82 Copynumber: 2.4 Consensus size: 82
60359140 ATTTAAACAG
* * * * *
60359150 ATTCACTGGCACTTCA-CCTGATAGACTTATAGTCTAATTCCGTTTACCGGCACTTAGCCTGCTA
1 ATTCACTGGCACTT-AGCCTGCTAGACTTATAGCCTAATTCAGTTCACCGGCACTAAGCCTGCT-
*
60359214 GG-CCTATAG-CCTGATTCA
64 GGACCTATAGTCC-AATTCA
* * * * *
60359232 GTTCACTTGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTAAGCCTGCTGG
1 ATTCACTGGCACTTAGCCTGCTAGACTTATAGCCTAATTCAGTTCACCGGCACTAAGCCTGCTGG
*
60359297 ACGTATAGTCCAATTCA
66 ACCTATAGTCCAATTCA
* *
60359314 ATTCACCGGCACTTAGCCTGCTAGACGTATAG
1 ATTCACTGGCACTTAGCCTGCTAGACTTATAG
60359346 TCTGAACAAT
Statistics
Matches: 93, Mismatches: 18, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
81 3 0.03
82 88 0.95
83 2 0.02
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (82 bp):
ATTCACTGGCACTTAGCCTGCTAGACTTATAGCCTAATTCAGTTCACCGGCACTAAGCCTGCTGG
ACCTATAGTCCAATTCA
Done.