Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold457
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: 607290
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 1 of 3
Found at i:3951 original size:15 final size:15
Alignment explanation
Indices: 3933--3962 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3923 CCAAATTGAG
3933 GAAGCTCAAAATGAA
1 GAAGCTCAAAATGAA
*
3948 GAAGCTCCAAATGAA
1 GAAGCTCAAAATGAA
3963 ATTGATGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.17, G:0.20, T:0.13
Consensus pattern (15 bp):
GAAGCTCAAAATGAA
Found at i:3958 original size:16 final size:16
Alignment explanation
Indices: 3922--3962 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
3912 GATAAAAATG
* *
3922 TCCAAATTGAGGAAGC
1 TCCAAAATGAAGAAGC
3938 T-CAAAATGAAGAAGC
1 TCCAAAATGAAGAAGC
3953 TCC-AAATGAA
1 TCCAAAATGAA
3963 ATTGATGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (16 bp):
TCCAAAATGAAGAAGC
Found at i:7936 original size:49 final size:48
Alignment explanation
Indices: 7881--7985 Score: 165
Period size: 49 Copynumber: 2.1 Consensus size: 48
7871 TTTTATGTGT
* *
7881 GTGAATTACTTTATTAAGGGGGAGATTTTTTAATAAAAGTGGAGAATGC
1 GTGAATTAC-TAATTAAGGGGGAGATTTTTTAATAAAAGGGGAGAATGC
*
7930 GTGAATTTGCTAATTAAGGGGGAGATTTTTTAATAAAAGGGGAGAATGC
1 GTGAA-TTACTAATTAAGGGGGAGATTTTTTAATAAAAGGGGAGAATGC
7979 GTGAATT
1 GTGAATT
7986 TGCTAAAATA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
48 2 0.04
49 47 0.90
50 3 0.06
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (48 bp):
GTGAATTACTAATTAAGGGGGAGATTTTTTAATAAAAGGGGAGAATGC
Found at i:7986 original size:49 final size:49
Alignment explanation
Indices: 7893--7991 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
7883 GAATTACTTT
*
7893 ATTAAGGGGGAGATTTTTTAATAAAAGTGGAGAATGCGTGAATTTGCTA
1 ATTAAGGGGGAGATTTTTTAATAAAAGGGGAGAATGCGTGAATTTGCTA
7942 ATTAAGGGGGAGATTTTTTAATAAAAGGGGAGAATGCGTGAATTTGCTA
1 ATTAAGGGGGAGATTTTTTAATAAAAGGGGAGAATGCGTGAATTTGCTA
7991 A
1 A
7992 AATAACCTTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.31
Consensus pattern (49 bp):
ATTAAGGGGGAGATTTTTTAATAAAAGGGGAGAATGCGTGAATTTGCTA
Found at i:11370 original size:17 final size:17
Alignment explanation
Indices: 11348--11380 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
11338 ATTAATAAAT
11348 AAATAAATAAT-TAATTA
1 AAATAAA-AATATAATTA
11365 AAATAAAAATATAATT
1 AAATAAAAATATAATT
11381 GCATCTCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATAAAAATATAATTA
Found at i:11370 original size:21 final size:19
Alignment explanation
Indices: 11333--11380 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
11323 TATTTCGAAT
11333 TAAAT-ATTAATAAATAAA
1 TAAATAATTAATAAATAAA
11351 TAAATAATTAATTAAAATAAA
1 TAAATAATTAA-T-AAATAAA
11372 -AATATAATT
1 TAA-ATAATT
11381 GCATCTCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 5 0.19
19 5 0.19
20 3 0.12
21 13 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAATAATTAATAAATAAA
Found at i:11419 original size:8 final size:8
Alignment explanation
Indices: 11398--11427 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
11388 TAAATTTAAA
11398 GCCCAAGT
1 GCCCAAGT
11406 GCCCCAAGT
1 G-CCCAAGT
11415 GCCCAAGT
1 GCCCAAGT
11423 GCCCA
1 GCCCA
11428 TCTTTGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.23, C:0.43, G:0.23, T:0.10
Consensus pattern (8 bp):
GCCCAAGT
Found at i:23713 original size:3 final size:3
Alignment explanation
Indices: 23705--23729 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
23695 AGCTTCGGGT
23705 GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA G
23730 CATCTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:25010 original size:22 final size:21
Alignment explanation
Indices: 24975--25024 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
24965 TTTGTTGATG
*
24975 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
24995 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
25016 AATTTGAAG
1 ATTTTGAAG
25025 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:25021 original size:21 final size:22
Alignment explanation
Indices: 24982--25024 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
24972 ATGATTTTGA
* *
24982 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
25004 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
25025 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:25309 original size:18 final size:20
Alignment explanation
Indices: 25274--25310 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
25264 TTCACATCAA
*
25274 ACAAGTATAATTTGAATAAC
1 ACAAGTATAATTTAAATAAC
25294 ACAA-TATAA-TTAAATAA
1 ACAAGTATAATTTAAATAA
25311 TAAATTCATC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.44
19 5 0.31
20 4 0.25
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (20 bp):
ACAAGTATAATTTAAATAAC
Found at i:27219 original size:45 final size:45
Alignment explanation
Indices: 27155--27250 Score: 156
Period size: 45 Copynumber: 2.1 Consensus size: 45
27145 TCTCACCTTC
27155 TTGCTCATAAGTCAACTCTCTCAGATGTTTTCTTTCGATTTGAGT
1 TTGCTCATAAGTCAACTCTCTCAGATGTTTTCTTTCGATTTGAGT
* * *
27200 TTGCTCATAAGTCAACTCTCTCGGATGTTTTCTTTTGGTTTGAGT
1 TTGCTCATAAGTCAACTCTCTCAGATGTTTTCTTTCGATTTGAGT
*
27245 TGGCTC
1 TTGCTC
27251 TTATTCATCA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.45
Consensus pattern (45 bp):
TTGCTCATAAGTCAACTCTCTCAGATGTTTTCTTTCGATTTGAGT
Found at i:33021 original size:30 final size:29
Alignment explanation
Indices: 32980--33076 Score: 106
Period size: 29 Copynumber: 3.2 Consensus size: 29
32970 GTTTAAGTTT
*
32980 GGTTACAGGTGTGGAAAC-GAGTTCAAACATA
1 GGTT-CAGGTGTAGAAACAG-GTTCAAACA-A
*
33011 GGTTCAGGTGTAGAAACAGGTTCAGACAA
1 GGTTCAGGTGTAGAAACAGGTTCAAACAA
* * *
33040 GGTTCAAGTGTAGAAACAGGTTTAGACACA
1 GGTTCAGGTGTAGAAACAGGTTCAAACA-A
33070 GGTTCAG
1 GGTTCAG
33077 ACACAAGTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
29 27 0.46
30 27 0.46
31 5 0.08
ACGTcount: A:0.34, C:0.13, G:0.30, T:0.23
Consensus pattern (29 bp):
GGTTCAGGTGTAGAAACAGGTTCAAACAA
Found at i:33051 original size:29 final size:30
Alignment explanation
Indices: 33000--33075 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 30
32990 GTGGAAACGA
* * *
33000 GTTCAAACATAGGTTCAGGTGTAGAAACAG
1 GTTCAGACACAGGTTCAAGTGTAGAAACAG
33030 GTTCAGACA-AGGTTCAAGTGTAGAAACAG
1 GTTCAGACACAGGTTCAAGTGTAGAAACAG
*
33059 GTTTAGACACAGGTTCA
1 GTTCAGACACAGGTTCA
33076 GACACAAGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
29 27 0.64
30 15 0.36
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (30 bp):
GTTCAGACACAGGTTCAAGTGTAGAAACAG
Found at i:33854 original size:32 final size:32
Alignment explanation
Indices: 33813--33889 Score: 145
Period size: 32 Copynumber: 2.4 Consensus size: 32
33803 ACACGAGTGC
33813 AATAGAACACGAACATGAACATGATAAATTGA
1 AATAGAACACGAACATGAACATGATAAATTGA
33845 AATAGAACACGAACATGAACATGATAAATTGA
1 AATAGAACACGAACATGAACATGATAAATTGA
*
33877 AATAGAATACGAA
1 AATAGAACACGAA
33890 TATAATATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.55, C:0.12, G:0.16, T:0.18
Consensus pattern (32 bp):
AATAGAACACGAACATGAACATGATAAATTGA
Found at i:34553 original size:4 final size:4
Alignment explanation
Indices: 34517--34581 Score: 55
Period size: 4 Copynumber: 16.2 Consensus size: 4
34507 AGACATAAAT
* * *
34517 TTTC TTT- TTT- TTCTC TTTT TTTC -TCC TTCC TTTC TTTCC TTTTC TTTC
1 TTTC TTTC TTTC TT-TC TTTC TTTC TTTC TTTC TTTC TTT-C -TTTC TTTC
34565 TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC T
34582 CAACTGTCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
3 7 0.13
4 38 0.73
5 4 0.08
6 3 0.06
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:46327 original size:16 final size:16
Alignment explanation
Indices: 46308--46342 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
46298 AACATTAAAC
* *
46308 CAATGTGCACAACCAT
1 CAATATGCAAAACCAT
46324 CAATATGCAAAACCAT
1 CAATATGCAAAACCAT
46340 CAA
1 CAA
46343 ATCATAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.29, G:0.09, T:0.17
Consensus pattern (16 bp):
CAATATGCAAAACCAT
Found at i:48595 original size:18 final size:18
Alignment explanation
Indices: 48572--48611 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
48562 CTTTGTTCTT
*
48572 GATATACTTGAGGATGAA
1 GATATACTTGAAGATGAA
* *
48590 GATATATTTGAAGATGAT
1 GATATACTTGAAGATGAA
48608 GATA
1 GATA
48612 CTTTTAACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.33
Consensus pattern (18 bp):
GATATACTTGAAGATGAA
Found at i:53514 original size:16 final size:16
Alignment explanation
Indices: 53493--53553 Score: 97
Period size: 16 Copynumber: 3.9 Consensus size: 16
53483 GCCAAGGAAA
53493 TATATCGATACATTAG
1 TATATCGATACATTAG
53509 TATATCGATACATTAG
1 TATATCGATACATTAG
*
53525 TATATCGATACATT-C
1 TATATCGATACATTAG
*
53540 TGTATCGATACATT
1 TATATCGATACATT
53554 TCTCATTATA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
15 13 0.30
16 30 0.70
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.39
Consensus pattern (16 bp):
TATATCGATACATTAG
Found at i:63525 original size:24 final size:21
Alignment explanation
Indices: 63446--63531 Score: 70
Period size: 21 Copynumber: 3.9 Consensus size: 21
63436 CAAAATGATG
63446 AAAAAATCAAAAGAAAAA--GCA
1 AAAAAAT-AAAA-AAAAAGGGCA
*
63467 AAAAAATAAAAAAAAAGTGCA
1 AAAAAATAAAAAAAAAGGGCA
63488 AAAGAAA-AATAAAAAAAGGGATCA
1 AAA-AAATAA-AAAAAAAGGG--CA
63512 ACAAAAATAAAAAAATAAGG
1 A-AAAAATAAAAAAA-AAGG
63532 ACATGAATGC
Statistics
Matches: 55, Mismatches: 1, Indels: 14
0.79 0.01 0.20
Matches are distributed among these distances:
19 5 0.09
20 4 0.07
21 15 0.27
22 12 0.22
24 11 0.20
25 8 0.15
ACGTcount: A:0.74, C:0.06, G:0.12, T:0.08
Consensus pattern (21 bp):
AAAAAATAAAAAAAAAGGGCA
Found at i:64777 original size:32 final size:31
Alignment explanation
Indices: 64718--65365 Score: 649
Period size: 32 Copynumber: 20.5 Consensus size: 31
64708 AAATCTTTTT
* * * * *
64718 CCTTCTCAAAGCCTACAGAAATTGGTGGTAAC
1 CCTTCT-AAAGCCCACACAAGTCGGTGGCAAC
64750 TCCTTCTAAAGCCCACACAAGTCGGTGGCAAC
1 -CCTTCTAAAGCCCACACAAGTCGGTGGCAAC
* *
64782 CCTTCTCAAAGCTCACACAAGTCGATGGCAAC
1 CCTTCT-AAAGCCCACACAAGTCGGTGGCAAC
* * *
64814 CCCTCTCAAAGCCCACAGAAGTTGGTGGC-AC
1 CCTTCT-AAAGCCCACACAAGTCGGTGGCAAC
* * * *
64845 CCTCTTTAAAGCCCACATAAGTCAGTGGTAAC
1 CCT-TCTAAAGCCCACACAAGTCGGTGGCAAC
* * * *
64877 CCTCTTTAAAGCTCACACAAGTCGATAGCAAC
1 CCT-TCTAAAGCCCACACAAGTCGGTGGCAAC
* * *
64909 CCCTCTAAAGCCCACACAAGTCAGTGGCATC
1 CCTTCTAAAGCCCACACAAGTCGGTGGCAAC
*
64940 CCTTCTCAAAGCCCACACAAGTTGGTGGC-AC
1 CCTTCT-AAAGCCCACACAAGTCGGTGGCAAC
*
64971 CCTCTCTAAAGCCCACACAAGTTGGTGGC-AC
1 CCT-TCTAAAGCCCACACAAGTCGGTGGCAAC
* * *
65002 CCTCTCTAAAGCCTACATAAGTCGGTGGTAAC
1 CCT-TCTAAAGCCCACACAAGTCGGTGGCAAC
*
65034 CCTTTCTAAAGCCCACACAAGTCGGTGGTAAC
1 CC-TTCTAAAGCCCACACAAGTCGGTGGCAAC
* *
65066 CCTTTTCAAAGCCCACACAAGTTGGTGGC-AC
1 CCTTCT-AAAGCCCACACAAGTCGGTGGCAAC
65097 CCTCTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CCT-TCTAAAGCCCACACAAGTCGGTGGCAAC
* * * * *
65129 CATTTTTAAAGTCCACATAAGTCGATGGCAAC
1 C-CTTCTAAAGCCCACACAAGTCGGTGGCAAC
* **
65161 CCCTCTAAAGCCCACACAAGTTAGTGGCAAC
1 CCTTCTAAAGCCCACACAAGTCGGTGGCAAC
* *
65192 CTCTTTTAAAGCCCATACAAGTCGGTGGCAACC
1 C-CTTCTAAAGCCCACACAAGTCGGTGGCAA-C
* *
65225 CCTTATAAAGTCCACACAAGTCGGTGGCAAC
1 CCTTCTAAAGCCCACACAAGTCGGTGGCAAC
* *
65256 TCTTTTCAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTCT-AAAGCCCACACAAGTCGGTGGCAAC
* * * * * *
65288 CCCTCTCAATGCCCACATAAATTGGTAGCAAC
1 CCTTCT-AAAGCCCACACAAGTCGGTGGCAAC
65320 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CC-T-TCTAAAGCCCACACAAGTCGGTGGCAAC
65353 CCTTCT-AAGCCCA
1 CCTTCTAAAGCCCA
65366 ATGTTATTGG
Statistics
Matches: 515, Mismatches: 84, Indels: 35
0.81 0.13 0.06
Matches are distributed among these distances:
30 7 0.01
31 168 0.33
32 305 0.59
33 32 0.06
34 3 0.01
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (31 bp):
CCTTCTAAAGCCCACACAAGTCGGTGGCAAC
Found at i:64878 original size:63 final size:64
Alignment explanation
Indices: 64757--65355 Score: 583
Period size: 63 Copynumber: 9.4 Consensus size: 64
64747 AACTCCTTCT
* * *
64757 AAAGCCCACACAAGTCGGTGGCAACCCT-TCTCAAAGCTCACACAAGTCGATGGCAACCCCTCTC
1 AAAGCCCACACAAGTCGGTGGCAACCCTCT-TTAAAGCCCACACAAGTCGGTGGCAACCCCTCTC
* * * * * *
64821 AAAGCCCACAGAAGTTGGTGGC-ACCCTCTTTAAAGCCCACATAAGTCAGTGGTAA-CCCTCTTT
1 AAAGCCCACACAAGTCGGTGGCAACCCTCTTTAAAGCCCACACAAGTCGGTGGCAACCCCTC-TC
* * * * * * *
64884 AAAGCTCACACAAGTCGATAGCAACCC-CTCTAAAGCCCACACAAGTCAGTGGCATCCCTTCTC
1 AAAGCCCACACAAGTCGGTGGCAACCCTCTTTAAAGCCCACACAAGTCGGTGGCAACCCCTCTC
* * *
64947 AAAGCCCACACAAGTTGGTGGC-ACCCTCTCTAAAGCCCACACAAGTTGGTGGC-A-CCCTCTC
1 AAAGCCCACACAAGTCGGTGGCAACCCTCTTTAAAGCCCACACAAGTCGGTGGCAACCCCTCTC
* * * * * *
65008 TAAAGCCTACATAAGTCGGTGGTAACCCT-TTCTAAAGCCCACACAAGTCGGTGGTAACCCTTTT
1 -AAAGCCCACACAAGTCGGTGGCAACCCTCTT-TAAAGCCCACACAAGTCGGTGGCAACCCCTCT
65072 C
64 C
* * ** * *
65073 AAAGCCCACACAAGTTGGTGGC-ACCCTCTCTAAAGCCCACACAAGTCGGTGGCAACCATTTTT
1 AAAGCCCACACAAGTCGGTGGCAACCCTCTTTAAAGCCCACACAAGTCGGTGGCAACCCCTCTC
* * * * ** * * *
65136 AAAGTCCACATAAGTCGATGGCAACCC-CTCTAAAGCCCACACAAGTTAGTGGCAACCTCTTTT
1 AAAGCCCACACAAGTCGGTGGCAACCCTCTTTAAAGCCCACACAAGTCGGTGGCAACCCCTCTC
* * * * *
65199 AAAGCCCATACAAGTCGGTGGCAACCC-CTTATAAAGTCCACACAAGTCGGTGGCAACTCTTTTC
1 AAAGCCCACACAAGTCGGTGGCAACCCTCTT-TAAAGCCCACACAAGTCGGTGGCAACCCCTCTC
* * * * * * *
65263 AAAGCCCACACAAGTCGGTGGCAACCC-CTCTCAATGCCCACATAAATTGGTAGCAACCCTTCTC
1 AAAGCCCACACAAGTCGGTGGCAACCCTCT-TTAAAGCCCACACAAGTCGGTGGCAACCCCTCTC
65327 TAAAGCCCACACAAGTCGGTGGCAACCCT
1 -AAAGCCCACACAAGTCGGTGGCAACCCT
65356 TCTAAGCCCA
Statistics
Matches: 444, Mismatches: 75, Indels: 30
0.81 0.14 0.05
Matches are distributed among these distances:
61 6 0.01
62 28 0.06
63 246 0.55
64 131 0.30
65 33 0.07
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (64 bp):
AAAGCCCACACAAGTCGGTGGCAACCCTCTTTAAAGCCCACACAAGTCGGTGGCAACCCCTCTC
Found at i:65505 original size:52 final size:52
Alignment explanation
Indices: 65428--65949 Score: 305
Period size: 52 Copynumber: 9.8 Consensus size: 52
65418 AAGTCCGATA
65428 TCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATTTTTAAGCCCAATG
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATTTTTAAGCCCAATG
* * * * * * *
65480 TCGTTGGCTTTGAATTAGCACATTGGCATTCTTTTCATCCTTATCATATTTAAGTCCAATA
1 TCGCTGGCCTTGAATCAGCATATTGGCA--CCTTT-A-CC--AT--T-TTTAAGCCCAATG
** * * * * ** *
65541 TCATTGGCCTTGAATCAGCACATTGGAACCTTT---TTTTTTAAGTCTGATA
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATTTTTAAGCCCAATG
* * *
65590 TCGCTAGCCTTGAATCAACATATTGGCACCTTTACTATTTTTAAGCCCAATG
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATTTTTAAGCCCAATG
* * * *
65642 TCGTTGGCCCTAAATCAGCATATTAGCACCTTTACCATTTTTAAGCCCAATG
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATTTTTAAGCCCAATG
* * * * * *
65694 TCGCTGGCCTTGAATTAGCATATTAGCATTTTTCTCATCCTTATCATCTTTAAGTCTAATG
1 TCGCTGGCCTTGAATCAGCATATTGGCA-----C-C-T--TTACCATTTTTAAGCCCAATG
* * *** ** * *
65755 TCGCTGGCCTTAAATCAGCACATAAACACCTTTTTC-TTTCTTATGCCCAATA
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATTT-TTAAGCCCAATG
** *** * *
65807 TCATTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGTCCAATG
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATTTTTAAGCCCAATG
* * * *** * * *
65859 TCGCTGGCCTTGAATTAGCACATTGGCACCGTTGTTATTGTTAAGTCCAATA
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATTTTTAAGCCCAATG
* * * * * *
65911 TCACTAGCCTTGAATCAACATATTAGCATCTTTATCATT
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATT
65950 CTTCTCATCT
Statistics
Matches: 362, Mismatches: 85, Indels: 46
0.73 0.17 0.09
Matches are distributed among these distances:
49 38 0.10
50 1 0.00
51 2 0.01
52 224 0.62
53 2 0.01
54 5 0.01
55 2 0.01
56 3 0.01
57 1 0.00
58 3 0.01
59 5 0.01
60 1 0.00
61 75 0.21
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (52 bp):
TCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATTTTTAAGCCCAATG
Found at i:65765 original size:214 final size:216
Alignment explanation
Indices: 65413--65964 Score: 585
Period size: 217 Copynumber: 2.6 Consensus size: 216
65403 AAATCTTCTT
* * * * *
65413 TCTTTAAGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATTTTTAAGCCCAA
1 TCTTTAAGCCCAATGTCGCTGGCCCTAAATCAGCATATTGGCACCTTTACCATTTTTAAGCCCAA
* * * * *
65478 TGTCGTTGGCTTTGAATTAGCACATTGGCATTCTTTTCATCCTTATCATATTTAAGTCCAATATC
66 TGTCGCTGGCCTTGAATTAGCATATTAGCATT-TTTTCATCCTTATCATCTTTAAGTCCAATATC
* * ** * ** *
65543 ATTGGCCTTGAATCAGCACATTGGA-ACC-TTTT-TTT-TTAAGTCTGATATCGCTAGCCTTGAA
130 ACTGGCCTTAAATCAGCACA-TAAACACCTTTTTCTTTCTTAAGCCCAATATCACTAGCCTTGAA
65604 TCAACATATTGGCACCTT--TACTA
194 TCAACATATTGGCACCTTCGT-C-A
* * *
65627 TTTTTAAGCCCAATGTCGTTGGCCCTAAATCAGCATATTAGCACCTTTACCATTTTTAAGCCCAA
1 TCTTTAAGCCCAATGTCGCTGGCCCTAAATCAGCATATTGGCACCTTTACCATTTTTAAGCCCAA
* *
65692 TGTCGCTGGCCTTGAATTAGCATATTAGCATTTTTCTCATCCTTATCATCTTTAAGTCTAATGTC
66 TGTCGCTGGCCTTGAATTAGCATATTAGCATTTTT-TCATCCTTATCATCTTTAAGTCCAATATC
* * * *
65757 GCTGGCCTTAAATCAGCACATAAACACCTTTTTCTTTCTTATGCCCAATATCATTGGCCTTGAAT
130 ACTGGCCTTAAATCAGCACATAAACACCTTTTTCTTTCTTAAGCCCAATATCACTAGCCTTGAAT
*
65822 CAGCATATTGGCACCTTCGTCA
195 CAACATATTGGCACCTTCGTCA
* * * * * * *** * *
65844 TCTTTAAGTCCAATGTCGCTGGCCTTGAATTAGCACATTGGCACCGTTGTTATTGTTAAGTCCAA
1 TCTTTAAGCCCAATGTCGCTGGCCCTAAATCAGCATATTGGCACCTTTACCATTTTTAAGCCCAA
* * * * * * * *
65909 TATCACTAGCCTTGAATCAACATATTAGCATCTTTATCATTCTTCTCATCTTTAAG
66 TGTCGCTGGCCTTGAATTAGCATATTAGCAT-TTTTTCATCCTTATCATCTTTAAG
65965 CCTGATACCG
Statistics
Matches: 280, Mismatches: 50, Indels: 13
0.82 0.15 0.04
Matches are distributed among these distances:
213 5 0.02
214 131 0.47
215 4 0.01
216 3 0.01
217 132 0.47
218 4 0.01
219 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (216 bp):
TCTTTAAGCCCAATGTCGCTGGCCCTAAATCAGCATATTGGCACCTTTACCATTTTTAAGCCCAA
TGTCGCTGGCCTTGAATTAGCATATTAGCATTTTTTCATCCTTATCATCTTTAAGTCCAATATCA
CTGGCCTTAAATCAGCACATAAACACCTTTTTCTTTCTTAAGCCCAATATCACTAGCCTTGAATC
AACATATTGGCACCTTCGTCA
Found at i:65827 original size:113 final size:110
Alignment explanation
Indices: 65358--65964 Score: 375
Period size: 113 Copynumber: 5.6 Consensus size: 110
65348 GCAACCCTTC
* * * * * * ** * *
65358 TAAGCCCAATGTTATTGGCCTTGAATCAACATATTGGCACTTGTCAAATCTTCT-TTCTTTAAGT
1 TAAGCCCAATATCACTGGCCTTGAATCAGCATATTAGCA-TTTTCTCATCTTATCATCTTTAAGT
* * * * * **
65422 CCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATTTT
65 CCAATGTCGCTGGCCTTAAATCAGCACATTAGCACCTTTTTC-TTTT
* ** * * * * * *
65469 TAAGCCCAATGTCGTTGGCTTTGAATTAGCACATTGGCATTCTTTTCATCCTTATCATATTTAAG
1 TAAGCCCAATATCACTGGCCTTGAATCAGCATATTAGCATT-TTCTCAT-CTTATCATCTTTAAG
* ** * * *
65534 TCCAATATCATTGGCCTTGAATCAGCACATTGGAACC-TTTT-TTTT
64 TCCAATGTCGCTGGCCTTAAATCAGCACATTAGCACCTTTTTCTTTT
* ** * * * * ** *
65579 TAAGTCTGATATCGCTAGCCTTGAATCAACATATTGGCACCTT-T-A-C-TAT--T-TTTAAGCC
1 TAAGCCCAATATCACTGGCCTTGAATCAGCATATTAGCATTTTCTCATCTTATCATCTTTAAGTC
* * * **
65637 CAATGTCGTTGGCCCTAAATCAGCATATTAGCACCTTTACCATTTT
66 CAATGTCGCTGGCCTTAAATCAGCACATTAGCACCTTTTTC-TTTT
* * *
65683 TAAGCCCAATGTCGCTGGCCTTGAATTAGCATATTAGCATTTTTCTCATCCTTATCATCTTTAAG
1 TAAGCCCAATATCACTGGCCTTGAATCAGCATATTAGCA-TTTTCTCAT-CTTATCATCTTTAAG
* * *
65748 TCTAATGTCGCTGGCCTTAAATCAGCACATAAACACCTTTTTCTTTCT
64 TCCAATGTCGCTGGCCTTAAATCAGCACATTAGCACCTTTTTCTTT-T
* * * **
65796 TATGCCCAATATCATTGGCCTTGAATCAGCATATTGGCA----C-C-T-TCGTCATCTTTAAGTC
1 TAAGCCCAATATCACTGGCCTTGAATCAGCATATTAGCATTTTCTCATCTTATCATCTTTAAGTC
* * * * * *
65854 CAATGTCGCTGGCCTTGAATTAGCACATTGGCACCGTTGTTATTGT
66 CAATGTCGCTGGCCTTAAATCAGCACATTAGCACC-TTTTTCTTTT
* * * * *
65900 TAAGTCCAATATCACTAGCCTTGAATCAACATATTAGCATCTTTATCATTCTTCTCATCTTTAAG
1 TAAGCCCAATATCACTGGCCTTGAATCAGCATATTAGCAT-TTTCTCA-TCTTATCATCTTTAAG
65965 CCTGATACCG
Statistics
Matches: 383, Mismatches: 87, Indels: 50
0.74 0.17 0.10
Matches are distributed among these distances:
101 35 0.09
102 3 0.01
104 115 0.30
105 9 0.02
106 2 0.01
107 3 0.01
108 2 0.01
109 3 0.01
110 39 0.10
111 36 0.09
112 11 0.03
113 125 0.33
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.37
Consensus pattern (110 bp):
TAAGCCCAATATCACTGGCCTTGAATCAGCATATTAGCATTTTCTCATCTTATCATCTTTAAGTC
CAATGTCGCTGGCCTTAAATCAGCACATTAGCACCTTTTTCTTTT
Found at i:70539 original size:19 final size:21
Alignment explanation
Indices: 70499--70537 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
70489 TCCCGTGTAA
70499 ATGTATCGATACAATTTTTTG
1 ATGTATCGATACAATTTTTTG
70520 ATGTATCGATAC-ATTTTT
1 ATGTATCGATACAATTTTT
70538 GAAAATATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (21 bp):
ATGTATCGATACAATTTTTTG
Found at i:70610 original size:13 final size:13
Alignment explanation
Indices: 70592--70617 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
70582 CAATTTTTTG
70592 TGTATCGATACAT
1 TGTATCGATACAT
70605 TGTATCGATACAT
1 TGTATCGATACAT
70618 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:70701 original size:20 final size:20
Alignment explanation
Indices: 70676--70728 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
70666 ACATCTTTTT
70676 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
70696 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
70716 CATGTATCGATAC
1 CATGTATCGATAC
70729 TTTGAATTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:73199 original size:13 final size:13
Alignment explanation
Indices: 73181--73219 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
73171 ATAATCACCC
*
73181 TGTATCGATACAG
1 TGTATCGATACAA
73194 TGTATCGATACAA
1 TGTATCGATACAA
73207 TGTATCGATACAA
1 TGTATCGATACAA
73220 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:73230 original size:20 final size:20
Alignment explanation
Indices: 73205--73283 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
73195 GTATCGATAC
73205 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
73225 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
73250 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
73270 CATGTATCGATACA
1 AATGTATCGATACA
73284 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:77153 original size:21 final size:21
Alignment explanation
Indices: 77124--77168 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
77114 AAGTTTTCAT
*
77124 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
77144 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
77166 TTT
1 TTT
77169 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:79405 original size:13 final size:13
Alignment explanation
Indices: 79387--79412 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
79377 CAATTTTTTG
79387 TGTATCGATACAT
1 TGTATCGATACAT
79400 TGTATCGATACAT
1 TGTATCGATACAT
79413 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:79477 original size:21 final size:21
Alignment explanation
Indices: 79451--79526 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
79441 CTGCCAAGAA
79451 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
79472 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
79492 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
79513 ATGTATCGATACAT
1 ATGTATCGATACAT
79527 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:79496 original size:20 final size:20
Alignment explanation
Indices: 79471--79544 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
79461 ACATCTTTTT
79471 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
79491 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
79512 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
79532 CATGTATCGATAC
1 CATGTATCGATAC
79545 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:79508 original size:41 final size:41
Alignment explanation
Indices: 79451--79544 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
79441 CTGCCAAGAA
79451 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
79492 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
79533 ATGTATCGATAC
1 ATGTATCGATAC
79545 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:81786 original size:16 final size:15
Alignment explanation
Indices: 81753--81801 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
81743 TAAAAAAGAC
81753 AAAAAATTAAAAAAT
1 AAAAAATTAAAAAAT
*
81768 AAAAAATT-TAAAAT
1 AAAAAATTAAAAAAT
** *
81782 TTAAAATTTAAAAAT
1 AAAAAATTAAAAAAT
81797 AAAAA
1 AAAAA
81802 TAATATAAGC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAAATTAAAAAAT
Found at i:81802 original size:14 final size:14
Alignment explanation
Indices: 81754--81802 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
81744 AAAAAAGACA
*
81754 AAAAATTAAAAAAT
1 AAAAATTTAAAAAT
*
81768 AAAAAATTTAAAATT
1 -AAAAATTTAAAAAT
*
81783 TAAAATTTAAAAAT
1 AAAAATTTAAAAAT
81797 AAAAAT
1 AAAAAT
81803 AATATAAGCA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAAATTTAAAAAT
Found at i:85390 original size:15 final size:15
Alignment explanation
Indices: 85370--85411 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
85360 CTGCGTTGAT
85370 TGCAATGGTTGTCAA
1 TGCAATGGTTGTCAA
85385 TGCAATGGTTGTCAA
1 TGCAATGGTTGTCAA
*
85400 TGTAATGGTTGT
1 TGCAATGGTTGT
85412 ACTGACATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.24, C:0.10, G:0.29, T:0.38
Consensus pattern (15 bp):
TGCAATGGTTGTCAA
Found at i:88313 original size:24 final size:25
Alignment explanation
Indices: 88283--88333 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
88273 TTCATATTAA
*
88283 ATAAATTTAATTAAAAAA-TAAAAC
1 ATAAATTCAATTAAAAAAGTAAAAC
*
88307 ATAAATTCAATTAAAAAAGTGAAAC
1 ATAAATTCAATTAAAAAAGTAAAAC
88332 AT
1 AT
88334 TTTTTATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (25 bp):
ATAAATTCAATTAAAAAAGTAAAAC
Found at i:89015 original size:14 final size:15
Alignment explanation
Indices: 88996--89024 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
88986 ATGTTTATTA
88996 TTTTAAAT-TATTTT
1 TTTTAAATATATTTT
89010 TTTTAAATATATTTT
1 TTTTAAATATATTTT
89025 AAGAGGTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTAAATATATTTT
Found at i:91882 original size:2 final size:2
Alignment explanation
Indices: 91875--91905 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
91865 TTGCAATGCT
91875 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
91906 TTTTATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:91928 original size:11 final size:11
Alignment explanation
Indices: 91912--91944 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
91902 CTCTTTTTAT
91912 AAAAAAA-AAA
1 AAAAAAAGAAA
*
91922 GAAAAAAGAAA
1 AAAAAAAGAAA
91933 AAAAAAAGAAA
1 AAAAAAAGAAA
91944 A
1 A
91945 GAACCCTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:91935 original size:16 final size:16
Alignment explanation
Indices: 91912--91947 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
91902 CTCTTTTTAT
91912 AAAAAAAAAAGAAAAAAG
1 AAAAAAAAAAG--AAAAG
91930 AAAAAAAAAAGAAAAG
1 AAAAAAAAAAGAAAAG
91946 AA
1 AA
91948 CCCTCTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
18 11 0.61
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAGAAAAG
Found at i:91994 original size:16 final size:16
Alignment explanation
Indices: 91973--92005 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
91963 ATCTGTGTAC
91973 TTAGTGTGAGATTGCG
1 TTAGTGTGAGATTGCG
91989 TTAGTGTGAGATTGCG
1 TTAGTGTGAGATTGCG
92005 T
1 T
92006 AAGTATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.36, T:0.39
Consensus pattern (16 bp):
TTAGTGTGAGATTGCG
Found at i:95977 original size:24 final size:23
Alignment explanation
Indices: 95927--95973 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
95917 ATTATGTACT
95927 TTAAAGAATTATTTTAAATTTATAC
1 TTAAA-AATTATTTT-AATTTATAC
95952 TTAAAAATTATTTGT-ATTTATA
1 TTAAAAATTATTT-TAATTTATA
95974 ACTTGAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 7 0.33
24 8 0.38
25 6 0.29
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (23 bp):
TTAAAAATTATTTTAATTTATAC
Found at i:96988 original size:2 final size:2
Alignment explanation
Indices: 96981--97025 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
96971 AGATGGAAAC
96981 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
97023 AT A
1 AT A
97026 AGATGATAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:97219 original size:15 final size:16
Alignment explanation
Indices: 97199--97231 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
97189 TATTTATTTA
97199 TTTAT-AATATAAAAT
1 TTTATAAATATAAAAT
*
97214 TTTATAAATTTAAAAT
1 TTTATAAATATAAAAT
97230 TT
1 TT
97232 AAATTCTACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTATAAATATAAAAT
Found at i:97720 original size:6 final size:6
Alignment explanation
Indices: 97709--97737 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
97699 AAAAATTAAT
97709 TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
97738 TATATAATAA
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:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:97746 original size:18 final size:17
Alignment explanation
Indices: 97699--97749 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
97689 AAATAGAATA
97699 AAAAAT-TAATTAAAAAT
1 AAAAATATAA-TAAAAAT
*
97716 AAAAATAAAAATAAAAAT
1 AAAAAT-ATAATAAAAAT
97734 AAAATATATAATAAAA
1 AAAA-ATATAATAAAA
97750 TTTTAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 6 0.21
18 19 0.66
19 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAATATAATAAAAAT
Found at i:98215 original size:31 final size:31
Alignment explanation
Indices: 98180--98243 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
98170 CAAAAGAGGT
*
98180 ATTAAATTATATATAAAGTAAGTTGTAATTA
1 ATTAAATTATATATAAAGTAAGTGGTAATTA
98211 ATTAAATTATATATAAAGTAAGTGGTAATTA
1 ATTAAATTATATATAAAGTAAGTGGTAATTA
98242 AT
1 AT
98244 AGATCGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (31 bp):
ATTAAATTATATATAAAGTAAGTGGTAATTA
Found at i:101210 original size:14 final size:14
Alignment explanation
Indices: 101193--101222 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
101183 TAATAATCTA
101193 ATATGTATAAATAT
1 ATATGTATAAATAT
*
101207 ATATGTATATATAT
1 ATATGTATAAATAT
101221 AT
1 AT
101223 CTGAAGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (14 bp):
ATATGTATAAATAT
Found at i:104595 original size:16 final size:17
Alignment explanation
Indices: 104574--104605 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
104564 CTGATTGACA
104574 ATTTAATTT-TATTTTC
1 ATTTAATTTCTATTTTC
104590 ATTTAATTTCTATTTT
1 ATTTAATTTCTATTTT
104606 GAACGAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTAATTTCTATTTTC
Found at i:107141 original size:32 final size:33
Alignment explanation
Indices: 107100--107162 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
107090 AGCCAAACTT
* **
107100 GTATCGATACACCAAGTA-TGTATCGATACAAG
1 GTATCGATACACAAAAAATTGTATCGATACAAG
107132 GTATCGATACACAAAAAATTGTATCGATACA
1 GTATCGATACACAAAAAATTGTATCGATACA
107163 TTGGCTTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.25
Consensus pattern (33 bp):
GTATCGATACACAAAAAATTGTATCGATACAAG
Found at i:117161 original size:6 final size:7
Alignment explanation
Indices: 117142--117167 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
117132 TATAGACAAG
117142 GCAAAAA
1 GCAAAAA
117149 GCAAAAA
1 GCAAAAA
117156 GCAAAAA
1 GCAAAAA
117163 GCAAA
1 GCAAA
117168 GTAATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.15, G:0.15, T:0.00
Consensus pattern (7 bp):
GCAAAAA
Found at i:126451 original size:2 final size:2
Alignment explanation
Indices: 126444--126473 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
126434 AATTAGAGTA
*
126444 TG TG TG TG TG TG TG TG TG TG TG TG TT TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
126474 CGTATTTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:129563 original size:2 final size:2
Alignment explanation
Indices: 129556--129593 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
129546 CATAGAACTT
129556 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
129594 CACATTTACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:135483 original size:28 final size:26
Alignment explanation
Indices: 135452--135525 Score: 69
Period size: 29 Copynumber: 2.7 Consensus size: 26
135442 TATTAACTAA
135452 TAATTTTTACTATTAATATTTTAAATAG
1 TAATTTTTA-TATTAATATTTT-AATAG
* *
135480 TAATATTTTAATAATAATA-TTTAATAT
1 TAAT-TTTT-ATATTAATATTTTAATAG
* *
135507 TAAATATTATATTAATATT
1 TAATTTTTATATTAATATT
135526 AAATACTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
25 8 0.21
26 4 0.11
27 7 0.18
28 7 0.18
29 11 0.29
30 1 0.03
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (26 bp):
TAATTTTTATATTAATATTTTAATAG
Found at i:135492 original size:14 final size:14
Alignment explanation
Indices: 135444--135505 Score: 65
Period size: 14 Copynumber: 4.4 Consensus size: 14
135434 CATGATTATA
135444 TTAACTAATAAT-TT
1 TTAA-TAATAATATT
* *
135458 TTACTATTAATATT
1 TTAATAATAATATT
*
135472 TTAAATAGTAATATT
1 TT-AATAATAATATT
135487 TTAATAATAATA-T
1 TTAATAATAATATT
135500 TTAATA
1 TTAATA
135506 TTAAATATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
13 13 0.32
14 16 0.39
15 12 0.29
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (14 bp):
TTAATAATAATATT
Found at i:135569 original size:20 final size:19
Alignment explanation
Indices: 135504--135593 Score: 67
Period size: 20 Copynumber: 4.7 Consensus size: 19
135494 TAATATTTAA
* * *
135504 TATTAAA-TATTATATTAA
1 TATTAAATTATTAAAATAT
*
135522 TATTAAA-TACTAAAATAT
1 TATTAAATTATTAAAATAT
*
135540 TATAATAATTATTAAAATAT
1 TATTA-AATTATTAAAATAT
* *
135560 TATTTAAATTAATATAATTAT
1 TA-TTAAATTATTA-AAATAT
*
135581 TATTAAAATATTA
1 TATTAAATTATTA
135594 TTTTTATAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
18 18 0.32
19 2 0.04
20 28 0.49
21 9 0.16
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (19 bp):
TATTAAATTATTAAAATAT
Found at i:135600 original size:17 final size:17
Alignment explanation
Indices: 135548--135600 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
135538 ATTATAATAA
135548 TTATTAAAATATTATTT
1 TTATTAAAATATTATTT
** * *
135565 AAATT--AATATAATTA
1 TTATTAAAATATTATTT
135580 TTATTAAAATATTATTT
1 TTATTAAAATATTATTT
135597 TTAT
1 TTAT
135601 AATTTTAAAT
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
15 11 0.42
17 15 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTAAAATATTATTT
Found at i:135815 original size:23 final size:23
Alignment explanation
Indices: 135772--135816 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
135762 ATTAATATTT
*
135772 TAAAATATTTTTAGAATTAAAAA
1 TAAAATATTTTTAGAAGTAAAAA
**
135795 TAAAATATTTTTATTAGTAAAA
1 TAAAATATTTTTAGAAGTAAAA
135817 TTATATTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
TAAAATATTTTTAGAAGTAAAAA
Found at i:136187 original size:16 final size:15
Alignment explanation
Indices: 136166--136196 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
136156 TTTTACTTTC
136166 AAATTAAAAAAATAAA
1 AAATT-AAAAAATAAA
136182 AAATTAAAAAATAAA
1 AAATTAAAAAATAAA
136197 TTATAATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AAATTAAAAAATAAA
Found at i:138292 original size:21 final size:21
Alignment explanation
Indices: 138266--138311 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
138256 AAATAATGGG
*
138266 GAATATTTAGAGAAAAATATA
1 GAATATTTAGAGAAAAATAAA
* *
138287 GAATATTTGGAGAAGAATAAA
1 GAATATTTAGAGAAAAATAAA
138308 GAAT
1 GAAT
138312 GAAAAGTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.26
Consensus pattern (21 bp):
GAATATTTAGAGAAAAATAAA
Found at i:143186 original size:20 final size:20
Alignment explanation
Indices: 143141--143186 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
143131 GTTAACAGCC
*
143141 CATGATTCATGCATTTTGAG
1 CATGTTTCATGCATTTTGAG
143161 CTATGTTTCATGCA-TTTGAAG
1 C-ATGTTTCATGCATTTTG-AG
143182 CATGT
1 CATGT
143187 CCAACACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (20 bp):
CATGTTTCATGCATTTTGAG
Found at i:156215 original size:12 final size:12
Alignment explanation
Indices: 156198--156233 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
156188 CATCCTCCGT
156198 AAAAAAAACAAA
1 AAAAAAAACAAA
156210 AAAAAAAACAAA
1 AAAAAAAACAAA
* *
156222 CAAACAAACAAA
1 AAAAAAAACAAA
156234 CAACAAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAACAAA
Found at i:156222 original size:4 final size:4
Alignment explanation
Indices: 156203--156240 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
156193 TCCGTAAAAA
* *
156203 AAAC AAAA AAAA AAAC AAAC AAAC AAAC AAAC -AAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
156241 AAGGGTCTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:157654 original size:52 final size:52
Alignment explanation
Indices: 157589--158039 Score: 539
Period size: 52 Copynumber: 8.9 Consensus size: 52
157579 ATTACCACCT
* * *
157589 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATCGGCGTCTTTG
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGACTTTG
*
157641 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACG-CTTTTG
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGAC-TTTG
* * * *
157693 TCATCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGC-AC-CT-
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGACTTTG
* *
157742 TCATCTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATCGGC-ATCTTTG
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGA-CTTTG
* ** *
157794 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGATGCCTTTG
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGACTTTG
* * * *
157846 TCATCTTTAAGTCCAATTTTGCTGGCCTTAAATCAGCACATTGGC-AC-TT-
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGACTTTG
* * * * *
157895 TCATCTTTAAGTACAATATTGCT-GCCTTGAATCAACATATCGGCGTCTTTG
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGACTTTG
* * * *
157946 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGC-AC-CT-
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGACTTTG
* *
157995 TCATCTTTAAGTCCAATATCACTGACCTTGAATCAGCATATTGGC
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
158040 ATCCGTAACA
Statistics
Matches: 340, Mismatches: 49, Indels: 23
0.83 0.12 0.06
Matches are distributed among these distances:
48 17 0.05
49 103 0.30
50 7 0.02
51 24 0.07
52 189 0.56
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (52 bp):
TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGACTTTG
Found at i:157676 original size:101 final size:101
Alignment explanation
Indices: 157544--158187 Score: 593
Period size: 101 Copynumber: 6.3 Consensus size: 101
157534 CACCCTTCAC
* ** * * *
157544 CTTTAAGTCCAATGTTACTGGCCTTGCATCAGCACATTACCACCTTCATCTTTAAGTCCAATATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCACTTTCATCTTTAAGTCCAATATC
*
157609 GCTGGCCTTGAATCAACATATCGGCGTCTTTGTCAT
66 GCTGGCCTTGAATCAGCATATCGGCGTCTTTGTCAT
* **
157645 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACGCTTTTGTCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT-A-GCACTT-TCATCTTTAAGTCCAAT
* * * * * *
157710 GTTGCTGGCCTTGAATCAGCACATTGGC-AC-CT-TCAT
63 ATCGCTGGCCTTGAATCAGCATATCGGCGTCTTTGTCAT
* * **
157746 CTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATCGGCATCTTTGTCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCA-C-TT-TCATCTTTAAGTCCAAT
* * ** *
157811 ATCGCTGGCCTTGAATTAGCATATTGATGCCTTTGTCAT
63 ATCGCTGGCCTTGAATCAGCATATCGGCGTCTTTGTCAT
* * * * * *
157850 CTTTAAGTCCAATTTTGCTGGCCTTAAATCAGCACATTGGCACTTTCATCTTTAAGTACAATATT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCACTTTCATCTTTAAGTCCAATATC
*
157915 GCT-GCCTTGAATCAACATATCGGCGTCTTTGTCAT
66 GCTGGCCTTGAATCAGCATATCGGCGTCTTTGTCAT
* *
157950 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTCATCTTTAAGTCCAATATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCACTTTCATCTTTAAGTCCAATATC
* * * * ** **
158015 ACTGACCTTGAATCAGCATATTGGCATCCGTAACATT
66 GCTGGCCTTGAATCAGCATATCGGCGTCTTTGTCA-T
* * * * * *
158052 CCTTAA-CCCAATGTCGTTGGCCTT-AACTCAGCACATTAGCATTCTTCTCATCTTCAAGTCTAA
1 CTTTAAGTCCAATATCGCTGGCCTTGAA-TCAGCACATTAGCA--CTT-TCATCTTTAAGTCCAA
* * * * * * * *
158115 TGTCGCTGACCGTGAATCAGCACATTGACATTCTTT-ACAT
62 TATCGCTGGCCTTGAATCAGCATATCGGC-GTCTTTGTCAT
* *
158155 CTTTAAGCCCAATATCACTGGTCC-TGAATCAGC
1 CTTTAAGTCCAATATCGCTGG-CCTTGAATCAGC
158188 GTATTGGTCC
Statistics
Matches: 448, Mismatches: 77, Indels: 33
0.80 0.14 0.06
Matches are distributed among these distances:
99 2 0.00
100 88 0.20
101 189 0.42
102 11 0.02
103 13 0.03
104 138 0.31
105 7 0.02
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.34
Consensus pattern (101 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCACTTTCATCTTTAAGTCCAATATC
GCTGGCCTTGAATCAGCATATCGGCGTCTTTGTCAT
Found at i:157822 original size:153 final size:151
Alignment explanation
Indices: 157544--158040 Score: 730
Period size: 153 Copynumber: 3.3 Consensus size: 151
157534 CACCCTTCAC
* **
157544 CTTTAAGTCCAATGTTACTGGCCTTGCATCAGCACATTACCACCTTCATCTTTAAGTCCAATATC
1 CTTTAAGTCCAATGTTACTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT-CAATATC
157609 GCTGGCCTTGAATCAACATATCGGCGTCTTTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
65 GCTGGCCTTGAATCAACATATCGGCGTCTTTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
*
157674 CAGCATATTGACGCTTTTGTCAT
130 CAGCATATTGA-GCATTTGTCAT
*
157697 CTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCTAATATC
1 CTTTAAGTCCAATGTTACTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTC-AATATC
* *
157762 GCTGGCCTTGAATCAGCATATCGGCATCTTTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
65 GCTGGCCTTGAATCAACATATCGGCGTCTTTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* *
157827 TAGCATATTGATGCCTTTGTCAT
130 CAGCATATTGA-GCATTTGTCAT
* * * * *
157850 CTTTAAGTCCAATTTTGCTGGCCTTAAATCAGCACATTGGCACTTTCATCTTTAAGTACAATATT
1 CTTTAAGTCCAATGTTACTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT-CAATATC
*
157915 GCT-GCCTTGAATCAACATATCGGCGTCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAAT
65 GCTGGCCTTGAATCAACATATCGGCGTCTTTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* **
157979 CAGCACATT-AGCACCT-TCAT
130 CAGCATATTGAGCATTTGTCAT
* * * *
157999 CTTTAAGTCCAATATCACTGACCTTGAATCAGCATATTGGCA
1 CTTTAAGTCCAATGTTACTGGCCTTGAATCAGCACATTGGCA
158041 TCCGTAACAT
Statistics
Matches: 315, Mismatches: 27, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
149 40 0.13
150 3 0.01
151 1 0.00
152 66 0.21
153 204 0.65
154 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (151 bp):
CTTTAAGTCCAATGTTACTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCAATATCG
CTGGCCTTGAATCAACATATCGGCGTCTTTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATC
AGCATATTGAGCATTTGTCAT
Found at i:158135 original size:52 final size:51
Alignment explanation
Indices: 157539--158187 Score: 533
Period size: 52 Copynumber: 12.7 Consensus size: 51
157529 GTTGTCACCC
* * ** * ** *
157539 TTCACCTTTAAGTCCAATGTTACTGGCCTTGCATCAGCACATTACCA--CC
1 TTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTCT
* * * *
157588 TTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATCGGC-GTCTT
1 TTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTC-T
*
157639 TGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACGC-TT-T
1 T-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTG--GCATTCT
* * *
157691 TGTCATCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCA--CC
1 T-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTCT
* * *
157741 TTCATCTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATCGGCA-TCTT
1 TTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTC-T
* * *
157792 TGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGATGCCTT-T
1 T-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTG--GCATTCT
* * * *
157845 GTCATCTTTAAGTCCAATTTTGCTGGCCTTAAATCAGCACATTGGCA--CT
1 TTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTCT
* * * * * *
157894 TTCATCTTTAAGTACAATATTGCT-GCCTTGAATCAACATATCGGC-GTCTT
1 TTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTC-T
* * *
157944 TGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCA--CC
1 T-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTCT
* * * *
157994 TTCATCTTTAAGTCCAATATCACTGACCTTGAATCAGCATATTGGCATCCGT
1 TTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTC-T
** * * * * *
158046 AACATTCCTTAA-CCCAATGTCGTTGGCCTT-AACTCAGCACATTAGCATTCT
1 TTCA-TCTTTAAGTCCAATATCGCTGGCCTTGAA-TCAGCACATTGGCATTCT
* * * * * *
158097 TCTCATCTTCAAGTCTAATGTCGCTGACCGTGAATCAGCACATTGACATTCT
1 T-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTCT
* *
158149 TTACATCTTTAAGCCCAATATCACTGGTCC-TGAATCAGC
1 TT-CATCTTTAAGTCCAATATCGCTGG-CCTTGAATCAGC
158188 GTATTGGTCC
Statistics
Matches: 485, Mismatches: 84, Indels: 59
0.77 0.13 0.09
Matches are distributed among these distances:
48 17 0.04
49 141 0.29
50 10 0.02
51 33 0.07
52 267 0.55
53 11 0.02
54 5 0.01
55 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (51 bp):
TTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTCT
Found at i:158135 original size:253 final size:255
Alignment explanation
Indices: 157641--158185 Score: 656
Period size: 253 Copynumber: 2.1 Consensus size: 255
157631 GGCGTCTTTG
* * *
157641 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACGCTTTTGTCATCTTTAAGTC
1 TCATCTTTAAGTACAATATCGCTGGCCTTGAATCAACATATCGACGCTTTTGTCATCTTTAAGTC
* * * * *
157706 CAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCTAATATCGCTGGCCTT
66 CAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTCATCTTTAAGTCCAATATCACTGACCTT
** ** * * * *
157771 GAATCAGCATATCGGCATCTTTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATT
131 GAATCAGCATATCGGCATCCGTAACATCCTTAAGCCCAATATCGCTGGCCTTGAATCAGCACATT
* * * * * * *
157836 GATGCCTTTGTCATCTTTAAGTCCAATTTTGCTGGCCTTAAATCAGCACATTGGCA-CTT
196 GATGCCTTTCTCATCTTCAAGTCCAATGTCGCTGACCGTAAATCAGCACATTGACATCTT
* *
157895 TCATCTTTAAGTACAATATTGCT-GCCTTGAATCAACATATCGGCG-TCTTTGTCATCTTTAAGT
1 TCATCTTTAAGTACAATATCGCTGGCCTTGAATCAACATATCGACGCT-TTTGTCATCTTTAAGT
157958 CCAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTCATCTTTAAGTCCAATATCACTGACCT
65 CCAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTCATCTTTAAGTCCAATATCACTGACCT
* * *
158023 TGAATCAGCATATTGGCATCCGTAACATTCCTTAA-CCCAATGTCGTTGGCCTT-AACTCAGCAC
130 TGAATCAGCATATCGGCATCCGTAACA-TCCTTAAGCCCAATATCGCTGGCCTTGAA-TCAGCAC
* * *
158086 ATT-A-GCATTCTTCTCATCTTCAAGTCTAATGTCGCTGACCGTGAATCAGCACATTGACATTCT
193 ATTGATGC-CT-TTCTCATCTTCAAGTCCAATGTCGCTGACCGTAAATCAGCACATTGACA-TCT
158149 T
255 T
** *
158150 TACATCTTTAAGCCCAATATCACTGGTCC-TGAATCA
1 T-CATCTTTAAGTACAATATCGCTGG-CCTTGAATCA
158186 GCGTATTGGT
Statistics
Matches: 246, Mismatches: 35, Indels: 17
0.83 0.12 0.06
Matches are distributed among these distances:
251 2 0.01
252 5 0.02
253 180 0.73
254 27 0.11
255 4 0.02
256 18 0.07
257 8 0.03
258 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.34
Consensus pattern (255 bp):
TCATCTTTAAGTACAATATCGCTGGCCTTGAATCAACATATCGACGCTTTTGTCATCTTTAAGTC
CAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTCATCTTTAAGTCCAATATCACTGACCTT
GAATCAGCATATCGGCATCCGTAACATCCTTAAGCCCAATATCGCTGGCCTTGAATCAGCACATT
GATGCCTTTCTCATCTTCAAGTCCAATGTCGCTGACCGTAAATCAGCACATTGACATCTT
Found at i:159866 original size:20 final size:20
Alignment explanation
Indices: 159821--159866 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
159811 GTTAACAGCC
*
159821 CATGATTCATGCATTTTGAG
1 CATGTTTCATGCATTTTGAG
159841 CTATGTTTCATGCA-TTTGAAG
1 C-ATGTTTCATGCATTTTG-AG
159862 CATGT
1 CATGT
159867 CCAGCACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (20 bp):
CATGTTTCATGCATTTTGAG
Found at i:164356 original size:16 final size:16
Alignment explanation
Indices: 164331--164363 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
164321 AGTCGACAAC
*
164331 CTGAATTCGAAATGAT
1 CTGAACTCGAAATGAT
164347 CTGAACTCGAAATGAT
1 CTGAACTCGAAATGAT
164363 C
1 C
164364 CAAATCCAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (16 bp):
CTGAACTCGAAATGAT
Found at i:172945 original size:16 final size:16
Alignment explanation
Indices: 172908--172959 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
172898 TATTCTATAT
172908 ATATTATAATGTTA-TAA
1 ATATT-TAAT-TTATTAA
*
172925 TTATTTAATTTATTAA
1 ATATTTAATTTATTAA
* *
172941 ATATTTATTTTATAAA
1 ATATTTAATTTATTAA
172957 ATA
1 ATA
172960 AATTATTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 3 0.10
16 23 0.77
17 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
ATATTTAATTTATTAA
Found at i:173004 original size:28 final size:28
Alignment explanation
Indices: 172940--173007 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
172930 TAATTTATTA
**
172940 AATATTTATTTTATAAAATAAATTATTAT
1 AATATTTATTTTATAAAAT-AATTAAAAT
*
172969 AATA-TTATTTTATAAAAT-TTTAAAAT
1 AATATTTATTTTATAAAATAATTAAAAT
172995 AATTATTTATTTT
1 AA-TATTTATTTT
173008 TTTCACTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 7 0.21
27 2 0.06
28 21 0.62
29 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
AATATTTATTTTATAAAATAATTAAAAT
Found at i:173042 original size:24 final size:25
Alignment explanation
Indices: 172989--173043 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
172979 TATAAAATTT
** * *
172989 TAAAATAATTATTTATTTTTTTCAC
1 TAAAATAATTATTTATAATTTTAAA
173014 T-AAATAATTATTT-TAATTTTAAA
1 TAAAATAATTATTTATAATTTTAAA
173037 TAAAATA
1 TAAAATA
173044 TTAAGTTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 7 0.28
24 17 0.68
25 1 0.04
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (25 bp):
TAAAATAATTATTTATAATTTTAAA
Found at i:174360 original size:49 final size:49
Alignment explanation
Indices: 174307--174400 Score: 188
Period size: 49 Copynumber: 1.9 Consensus size: 49
174297 CCAATCAAAG
174307 CATATATTGCTTTGACAATTAAAATAAACGTTTTAACAATAGTTATAAT
1 CATATATTGCTTTGACAATTAAAATAAACGTTTTAACAATAGTTATAAT
174356 CATATATTGCTTTGACAATTAAAATAAACGTTTTAACAATAGTTA
1 CATATATTGCTTTGACAATTAAAATAAACGTTTTAACAATAGTTA
174401 CAGCGCACCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38
Consensus pattern (49 bp):
CATATATTGCTTTGACAATTAAAATAAACGTTTTAACAATAGTTATAAT
Found at i:184656 original size:22 final size:23
Alignment explanation
Indices: 184627--184680 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
184617 CAAAGTTTAA
*
184627 TTTAAAAAAAATGAGTTTATCAT
1 TTTAAAATAAATGAGTTTATCAT
** * *
184650 TTTAAAATTCATGAGTTTGTTAT
1 TTTAAAATAAATGAGTTTATCAT
184673 TTTAAAAT
1 TTTAAAAT
184681 TCATTTAAGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (23 bp):
TTTAAAATAAATGAGTTTATCAT
Found at i:184680 original size:23 final size:23
Alignment explanation
Indices: 184637--184684 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
184627 TTTAAAAAAA
184637 ATGAGTTTATCATTTTAAAATTC
1 ATGAGTTTATCATTTTAAAATTC
* *
184660 ATGAGTTTGTTATTTTAAAATTC
1 ATGAGTTTATCATTTTAAAATTC
184683 AT
1 AT
184685 TTAAGCATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.50
Consensus pattern (23 bp):
ATGAGTTTATCATTTTAAAATTC
Found at i:186750 original size:21 final size:20
Alignment explanation
Indices: 186710--186751 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
186700 TTTACTAACT
186710 TTAAATAATTAAAATTTAATA
1 TTAAATAATTAAAA-TTAATA
186731 TTAATATATATTAAAA-TAATA
1 TTAA-ATA-ATTAAAATTAATA
186752 ATTTTAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 9 0.47
22 3 0.16
23 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TTAAATAATTAAAATTAATA
Found at i:187518 original size:16 final size:16
Alignment explanation
Indices: 187497--187530 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
187487 TGACTATTAG
187497 TATCATTAAATCAATA
1 TATCATTAAATCAATA
187513 TATCATTAAATCAATA
1 TATCATTAAATCAATA
187529 TA
1 TA
187531 CCTTACTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (16 bp):
TATCATTAAATCAATA
Found at i:189464 original size:94 final size:93
Alignment explanation
Indices: 189280--189465 Score: 209
Period size: 94 Copynumber: 2.0 Consensus size: 93
189270 TATTCATTGG
* * *
189280 GGATACTTCAACCCAATTCTTCTGAGGGAATACTCCACTCCTTTTTTAAACTTGTCAATTTAAAT
1 GGATACTCCAACCCAATTCTTATGAGGGAATACTCCACTCCTTTTTTAAACTTATCAATTTAAAT
*
189345 CTTATCTTTACTTAAATTGTCATCATCAA
66 CTTATCTTTACCTAAATTG-CATCATCAA
** *
189374 GGATACTCCAACCTTATTCTTATGA-GGAGATACTCCAAC-CCTATTTTTAAATTTATCACAATT
1 GGATACTCCAACCCAATTCTTATGAGGGA-ATACTCC-ACTCCT-TTTTTAAACTTAT--CAATT
* *
189437 TAAATCTTATTTTTGCCTAAA-TG-ATCATC
61 TAAATCTTATCTTTACCTAAATTGCATCATC
189466 GTCTAGGACA
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
93 3 0.04
94 37 0.47
95 13 0.17
96 2 0.03
97 23 0.29
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.39
Consensus pattern (93 bp):
GGATACTCCAACCCAATTCTTATGAGGGAATACTCCACTCCTTTTTTAAACTTATCAATTTAAAT
CTTATCTTTACCTAAATTGCATCATCAA
Found at i:189481 original size:97 final size:94
Alignment explanation
Indices: 189295--189483 Score: 213
Period size: 97 Copynumber: 2.0 Consensus size: 94
189285 CTTCAACCCA
* * *
189295 ATTCTTCTGAGGGAATACTCCACTCCTTTTTTAAACTTGTCAATTTAAATCTTATCTTTACTTAA
1 ATTCTTATGAGGGAATACTCCACTCCTTTTTTAAACTTATCAATTTAAATCTTATCTTTACCTAA
*
189360 ATTGTCATCATCAAGGATACTCCAACCTT
66 ATTGTCATCATCAAGGACACTCCAACCTT
* * *
189389 ATTCTTATGA-GGAGATACTCCAAC-CCTATTTTTAAATTTATCACAATTTAAATCTTATTTTTG
1 ATTCTTATGAGGGA-ATACTCC-ACTCCT-TTTTTAAACTTAT--CAATTTAAATCTTATCTTTA
* * *
189452 CCTAAA-TGATCATCGTCTAGGACATTCCAACC
61 CCTAAATTG-TCATCATCAAGGACACTCCAACC
189484 CCATTTCTCC
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
93 3 0.04
94 19 0.24
95 13 0.16
96 2 0.03
97 42 0.53
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (94 bp):
ATTCTTATGAGGGAATACTCCACTCCTTTTTTAAACTTATCAATTTAAATCTTATCTTTACCTAA
ATTGTCATCATCAAGGACACTCCAACCTT
Found at i:192326 original size:677 final size:676
Alignment explanation
Indices: 189767--193078 Score: 4887
Period size: 676 Copynumber: 4.9 Consensus size: 676
189757 GATTATTTAT
* * * *
189767 ATTCATGTTTACAATAAACCACAAAAGTAATATTCCGTGTCATTATCTCTCTAGTGTTTGATACC
1 ATTCATGTTTACAAAAAACCACAAAAGTAATATTCCGTGTCGTTATCTCTCTAGTGTTTGACACG
* * * * * *
189832 TAATACTTAGTTTTCAAAATAAAATCCAAAAATTATTTTACATCTCTATGTTCGCTATCTCTCCA
66 AAATACCTAGTTTTCAAAATAAAATCTAAAAATTATTTTATATCTCTATGTTCGCCACCTCT-CA
* *
189897 -GGGCGCATATGAGATTAAAACTTTTTTCAAAACTTGGATTTATTTTTTTATGCAAAATTCATAC
130 GGGGTGCATATGAGATTAAAACTTTTCTCAAAACTTGGATTTA-TTTTTTATGCAAAATTCATAC
* *
189961 ATTTAAGGGGATTATATTGAAATAATGATAAACTAAAACCGAAAAAACCAATATCGAGTCAAAAC
194 ATTTAAGGGGATTATATTGAAATAATGATAAACTGAAACCGAAAAAACTAATATCGAGTCAAAAC
* * * * * * *
190026 ATAGTTAATAAGGTATCGATTTTAGGCGTCACGAGAAAGTTTGTATCTCTTTATGCGTAACTAAC
259 ATAGCTAGTAAGGTATCGATTTTGGGTGTCGCGAGAAAGTTTGTATCTTTTTACGCGTAACTAAC
* * *
190091 TCGCGAGCCCAACCAGTGAATCTTTGAATTACGTAAACCACGAGATCGATATCTTGAGTTTCGTA
324 TCCCGAGCCCAACCGGTGAATCTTTGAATTACGTAAACCACGAGATCGATGTCTTGAGTTTCGTA
* *
190156 ACTTAAAACATAAGTTTCAATAGACATCTAATTATGCCTAGCCCGAAATGATCAATGACGACTCC
389 ACTTAAAACATAAGTTTCAATAGGCATCTAATCATGCCTAGCCCGAAATGATCAATGACGACTCC
* * * * * * *
190221 AAAACTTCAATCACTTCATGGTAATTGCCAAGAATTGATTAGATGAGTAATTCATCTATCGATGT
454 AAAACTTCGATCACTTCGTGGTAACTGTCAAGAATCGATTAGATGGGTAATTCATCTACCGATGT
**
190286 TCCTCACTTCAATTAACACATTTCTTGTCACATCACAGAAATCCCTAATCACGAAAAATATTAAG
519 TCCTCACTTCAATTAACACATTTCTTGTCACGCCACAGAAATCCCTAATCACGAAAAATATTAAG
* *** * * *
190351 TCGAGCATGTCTTATCTTTCTTATATCTTTCTTATCATTGAGGTTGAGCACAGGCCACGATAAGG
584 TCGAGCATGTCTCATCTTTCTTATATCTTTCTTATCGCCGAGGTTAAGCACACGCCACGTTAAGG
*
190416 TTTAAATGTCACATTGAAGCTTATTTGC
649 TTTAAATGTCACATTGGAGCTTATTTGC
*
190444 ATTCATGTTTACAAAAAACCACAAAAGTAATATTCCGTGTCGTTATCTCTCTAGTATTTGACACG
1 ATTCATGTTTACAAAAAACCACAAAAGTAATATTCCGTGTCGTTATCTCTCTAGTGTTTGACACG
* *
190509 AAATACCTACTTTTCAAAATAAAATCTCAAAATTATTTTATATCTCTATGTTCGCCACCTCTTC-
66 AAATACCTAGTTTTCAAAATAAAATCTAAAAATTATTTTATATCTCTATGTTCGCCACCTC-TCA
190573 GGGGTGCATATGAGATTAAAACTTTTCTCAAAACTTGGATTTATTTTTTTATGCAAAATTCATAC
130 GGGGTGCATATGAGATTAAAACTTTTCTCAAAACTTGGATTTA-TTTTTTATGCAAAATTCATAC
*
190638 ATTTAA-GGGATTATATTGAAATAATGATAAATTGAAACCGAAAAAACTAATATCGAGTCAAAAC
194 ATTTAAGGGGATTATATTGAAATAATGATAAACTGAAACCGAAAAAACTAATATCGAGTCAAAAC
* * **
190702 AAAGCTAGTAAGATATCGATTTTGGGTGTCGCGAGAAAGTTTGTATCACTTTACGCGTAACTAAC
259 ATAGCTAGTAAGGTATCGATTTTGGGTGTCGCGAGAAAGTTTGTATCTTTTTACGCGTAACTAAC
* * *
190767 TCCCGAGCCCAACCGGTGAAACTTTGAATTATGTAAACCACGAAATCGATGTCTTGAGTTTCGTA
324 TCCCGAGCCCAACCGGTGAATCTTTGAATTACGTAAACCACGAGATCGATGTCTTGAGTTTCGTA
* *
190832 ACTTAAAACATAAGTTTCAATAGGCATCTAATCATGCCTAGCCCGAAATAATCAATGACGACTCT
389 ACTTAAAACATAAGTTTCAATAGGCATCTAATCATGCCTAGCCCGAAATGATCAATGACGACTCC
* * * *
190897 AAAACTTCGATCACTTCGTGTTAACTATCAAGAATCGATTGGATGGGTAATTTATCTACCGATGT
454 AAAACTTCGATCACTTCGTGGTAACTGTCAAGAATCGATTAGATGGGTAATTCATCTACCGATGT
* * * *
190962 TCCTCATTTCAATTAAGACATTTCTTGTCACGCCACAGAAATCCTTAATCATGAAAAATATTAAG
519 TCCTCACTTCAATTAACACATTTCTTGTCACGCCACAGAAATCCCTAATCACGAAAAATATTAAG
191027 TCGAGCATGTCTCATCTTTCTTATATCTTTCTTATCGCCGAGGTTAAGCACACGCCACGTTAAGG
584 TCGAGCATGTCTCATCTTTCTTATATCTTTCTTATCGCCGAGGTTAAGCACACGCCACGTTAAGG
*
191092 TTTATATGTCACATTGGAGCTTATTTGC
649 TTTAAATGTCACATTGGAGCTTATTTGC
*
191120 ATTCATGTTTACAAAAAACCACAAAAGTAATATTCCATGTCGTTATCTCTCTAGTGTTTGACACT
1 ATTCATGTTTACAAAAAACCACAAAAGTAATATTCCGTGTCGTTATCTCTCTAGTGTTTGACAC-
* * * *
191185 G-AATACCTAGTTTTCAAGATAAAATCTAGAAATTATTTTATATCTCTATGTTCGCCACTTCTCC
65 GAAATACCTAGTTTTCAAAATAAAATCTAAAAATTATTTTATATCTCTATGTTCGCCACCTCTCA
* * *
191249 GGGACT-CATATGAGATTAAAACTTTTTTAAAAACTTGGATTTATTTTTTATGCAAAATTCATAC
130 GGG-GTGCATATGAGATTAAAACTTTTCTCAAAACTTGGATTTATTTTTTATGCAAAATTCATAC
* *
191313 ATTTAAGGGGATTATATTAAAATAATGATAAACTGAAACCGAAAAAACCAATATCGAGTCAAAAC
194 ATTTAAGGGGATTATATTGAAATAATGATAAACTGAAACCGAAAAAACTAATATCGAGTCAAAAC
* * * *
191378 ATAACTAGTAAGGTATCGATTTCGAGTGTCACGAGAAAGTTTGTAT-TTCTTTACGCGTAACTAA
259 ATAGCTAGTAAGGTATCGATTTTGGGTGTCGCGAGAAAGTTTGTATCTT-TTTACGCGTAACTAA
** * * *
191442 CTCCCGAGCTTAACCAGTGAATCTTTGAATTACGTAAACCATGAGATCGGTGTCTTGAGTTTCGT
323 CTCCCGAGCCCAACCGGTGAATCTTTGAATTACGTAAACCACGAGATCGATGTCTTGAGTTTCGT
* * *
191507 AACTTAAAACATAAGTTTCAATAGGCATCTAATCATGCCTAGTCCGAAATGATCAATGATGATTC
388 AACTTAAAACATAAGTTTCAATAGGCATCTAATCATGCCTAGCCCGAAATGATCAATGACGACTC
* * * * *
191572 TAAAACTTCGATCACTTTGTGGTAACTGTAAACAATAGATTAGATGGGTAATTCATCTACCGATG
453 CAAAACTTCGATCACTTCGTGGTAACTGTCAAGAATCGATTAGATGGGTAATTCATCTACCGATG
* * * * *
191637 TTCCTCACTTCAATGAAGATATTTCTTGTCACGCCATAGAAATCCCTAATCATGAAAAATATTAA
518 TTCCTCACTTCAATTAACACATTTCTTGTCACGCCACAGAAATCCCTAATCACGAAAAATATTAA
* * *
191702 GTCGAACATGTCTCATTTTTCTTATATCTTTCTTATCGCCGAGGTTAAGCACATGCCACGTTAAG
583 GTCGAGCATGTCTCATCTTTCTTATATCTTTCTTATCGCCGAGGTTAAGCACACGCCACGTTAAG
*
191767 GTTTAAATGTCACATTGGATCTTATTTGC
648 GTTTAAATGTCACATTGGAGCTTATTTGC
* *
191796 ATTCATGTTTACAAAAAACCACAAAAGTAATATTCCTTGTCGTTATCTCTCTAGCGTTTGACACG
1 ATTCATGTTTACAAAAAACCACAAAAGTAATATTCCGTGTCGTTATCTCTCTAGTGTTTGACACG
* * *
191861 GAATACCTAGTTTTCAAAATAAAATCTAGAAATTGTTTTATATCTCTATGTTCGCCACCTCTCAG
66 AAATACCTAGTTTTCAAAATAAAATCTAAAAATTATTTTATATCTCTATGTTCGCCACCTCTCAG
* * *
191926 GGGTGCATATGAGACTAAAACTTTTCTCAAAACTTGGATTTACTTTTTTATACAAAATTCATATA
131 GGGTGCATATGAGATTAAAACTTTTCTCAAAACTTGGATTTA-TTTTTTATGCAAAATTCATACA
* *
191991 TTGAAGGGGATTATATTGAAATAATGATAAACTGAAACCAAAAAAACTAATATCGAGTCAAAACA
195 TTTAAGGGGATTATATTGAAATAATGATAAACTGAAACCGAAAAAACTAATATCGAGTCAAAACA
* *
192056 TAGCTAGTAATGTATCGATTTTGGGTGTCGCAAGAAAGTTTGTATCTTTTTACGCGTAACTAACT
260 TAGCTAGTAAGGTATCGATTTTGGGTGTCGCGAGAAAGTTTGTATCTTTTTACGCGTAACTAACT
* * *
192121 CCCAAGCCCAACCGGTGAATCTTTGAATTACGTAGACCACGAGATCGATGTCTTGAGTTTTGTAA
325 CCCGAGCCCAACCGGTGAATCTTTGAATTACGTAAACCACGAGATCGATGTCTTGAGTTTCGTAA
* * *
192186 CTCAAAACATAAATTTCAATAGGCATCTAATCATGCCTAGCCCAAAATGATCAATGACGACTCCA
390 CTTAAAACATAAGTTTCAATAGGCATCTAATCATGCCTAGCCCGAAATGATCAATGACGACTCCA
* * * * *
192251 AAACTTCGATCACTTTGTGGTAACTATCACGAATCGATTAGATGGGTAATTTATCTACCAATGTT
455 AAACTTCGATCACTTCGTGGTAACTGTCAAGAATCGATTAGATGGGTAATTCATCTACCGATGTT
*
192316 CCTCACTTCAATTAACACATTTCTTGTCACACCACAGAAAT-CCTAATCACGAAAAATATTAAGT
520 CCTCACTTCAATTAACACATTTCTTGTCACGCCACAGAAATCCCTAATCACGAAAAATATTAAGT
* * *
192380 CGAGCATGCCTCATTTTTCTTATATCTTTCTTATCGCCGAGGTTAAGCACACACCACGTTAAGGT
585 CGAGCATGTCTCATCTTTCTTATATCTTTCTTATCGCCGAGGTTAAGCACACGCCACGTTAAGGT
*
192445 TTAAATGTCACATTGGATCTTATTTGC
650 TTAAATGTCACATTGGAGCTTATTTGC
* *
192472 ATTCATGTTTACAAAAAACCACAAAAGTAATATTCCTTGTCGTTATCTCTCTAGTGTTTGACATG
1 ATTCATGTTTACAAAAAACCACAAAAGTAATATTCCGTGTCGTTATCTCTCTAGTGTTTGACACG
* * * *
192537 AAATACTTAGTTTTCAAAATAAAATCTAAAAATTGTTTTATATCTCTATGTTCACCACCTCTCAA
66 AAATACCTAGTTTTCAAAATAAAATCTAAAAATTATTTTATATCTCTATGTTCGCCACCTCTCAG
* * *
192602 AGGTGCATATGAGA--CAAACTTTTCTCAAAACTTGAATTTATTTTTTATGCAAAATTCATACAT
131 GGGTGCATATGAGATTAAAACTTTTCTCAAAACTTGGATTTATTTTTTATGCAAAATTCATACAT
*
192665 TGAAGGGGATTATATTGAAATAATGATAAACTGAAACCGAAAAAACTAATATCGAGTCAAAACAT
196 TTAAGGGGATTATATTGAAATAATGATAAACTGAAACCGAAAAAACTAATATCGAGTCAAAACAT
* * * * *** *
192730 AGCTAATAATGTATCGATTTTGGGTGTTGCGAGAAAATTTGTATCTTTTTACATTTAACTAACTT
261 AGCTAGTAAGGTATCGATTTTGGGTGTCGCGAGAAAGTTTGTATCTTTTTACGCGTAACTAACTC
* * * * * * * * * * *
192795 TCGAACCCAACCGATTTGAATCTTTAAATTATGTAGACTACGAAATCGATGTCTTAAATTTTGTA
326 CCGAGCCCAACCG--GTGAATCTTTGAATTACGTAAACCACGAGATCGATGTCTTGAGTTTCGTA
* * * * * *
192860 ACTCAAAACATAAGTTTCAATAAGCATCTAATCATGCTTAACCCGATATGATCAATAACGACTCC
389 ACTTAAAACATAAGTTTCAATAGGCATCTAATCATGCCTAGCCCGAAATGATCAATGACGACTCC
** * **
192925 AAAACTTCGATCACTTCGTAATAACTGTTAAGAATCGATTAGATAAGTAATTCATCTACCGATGT
454 AAAACTTCGATCACTTCGTGGTAACTGTCAAGAATCGATTAGATGGGTAATTCATCTACCGATGT
* * * * *
192990 TCTTCACTTCAATTAACACATTTTTTGTCACGTCACAGAAATCTCTAATCACGAAAAATATTAAA
519 TCCTCACTTCAATTAACACATTTCTTGTCACGCCACAGAAATCCCTAATCACGAAAAATATTAAG
* *
193055 TCGAGTATATCTCATCTTTCTTAT
584 TCGAGCATGTCTCATCTTTCTTAT
193079 TGTCGAGGTT
Statistics
Matches: 2395, Mismatches: 226, Indels: 29
0.90 0.09 0.01
Matches are distributed among these distances:
673 152 0.06
674 24 0.01
675 225 0.09
676 1461 0.61
677 530 0.22
678 3 0.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.33
Consensus pattern (676 bp):
ATTCATGTTTACAAAAAACCACAAAAGTAATATTCCGTGTCGTTATCTCTCTAGTGTTTGACACG
AAATACCTAGTTTTCAAAATAAAATCTAAAAATTATTTTATATCTCTATGTTCGCCACCTCTCAG
GGGTGCATATGAGATTAAAACTTTTCTCAAAACTTGGATTTATTTTTTATGCAAAATTCATACAT
TTAAGGGGATTATATTGAAATAATGATAAACTGAAACCGAAAAAACTAATATCGAGTCAAAACAT
AGCTAGTAAGGTATCGATTTTGGGTGTCGCGAGAAAGTTTGTATCTTTTTACGCGTAACTAACTC
CCGAGCCCAACCGGTGAATCTTTGAATTACGTAAACCACGAGATCGATGTCTTGAGTTTCGTAAC
TTAAAACATAAGTTTCAATAGGCATCTAATCATGCCTAGCCCGAAATGATCAATGACGACTCCAA
AACTTCGATCACTTCGTGGTAACTGTCAAGAATCGATTAGATGGGTAATTCATCTACCGATGTTC
CTCACTTCAATTAACACATTTCTTGTCACGCCACAGAAATCCCTAATCACGAAAAATATTAAGTC
GAGCATGTCTCATCTTTCTTATATCTTTCTTATCGCCGAGGTTAAGCACACGCCACGTTAAGGTT
TAAATGTCACATTGGAGCTTATTTGC
Found at i:194990 original size:2 final size:2
Alignment explanation
Indices: 194947--194975 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
194937 TTATGTTAGC
194947 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
194976 TTGCAAGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:196771 original size:20 final size:20
Alignment explanation
Indices: 196696--196773 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 20
196686 ATATTTATGA
196696 ATTAAT-AAATAATTAATATTT
1 ATTAATAAAATAA-TAAT-TTT
* * *
196717 ATTAA-AAACTAGTAAATTAT
1 ATTAATAAAATAAT-AATTTT
*
196737 ATTTATATGAAATAATAATTTT
1 A-TTA-ATAAAATAATAATTTT
196759 ATTAATAAAATAATA
1 ATTAATAAAATAATA
196774 GTAATCTATA
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
20 14 0.32
21 18 0.41
22 7 0.16
23 5 0.11
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (20 bp):
ATTAATAAAATAATAATTTT
Found at i:196917 original size:25 final size:24
Alignment explanation
Indices: 196889--196935 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
196879 TTTTATGTAT
*
196889 ATTTTAATGATATTTAATATTTAAA
1 ATTTTAATAATATTT-ATATTTAAA
*
196914 ATTTTAATAATGTTTATATTTA
1 ATTTTAATAATATTTATATTTA
196936 TCTAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (24 bp):
ATTTTAATAATATTTATATTTAAA
Found at i:202764 original size:18 final size:18
Alignment explanation
Indices: 202743--202777 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
202733 TTTTTTAATA
202743 ATTTAATTTTTTTTTCTT
1 ATTTAATTTTTTTTTCTT
**
202761 ATTTCTTTTTTTTTTCT
1 ATTTAATTTTTTTTTCT
202778 CGAATTTAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (18 bp):
ATTTAATTTTTTTTTCTT
Found at i:208197 original size:14 final size:13
Alignment explanation
Indices: 208162--208202 Score: 73
Period size: 13 Copynumber: 3.1 Consensus size: 13
208152 ACAATCCATC
208162 ATGTATCGATACA
1 ATGTATCGATACA
208175 ATGTATCGATACA
1 ATGTATCGATACA
208188 ATGTTATCGATACA
1 ATG-TATCGATACA
208202 A
1 A
208203 ACAGTGATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:208275 original size:19 final size:19
Alignment explanation
Indices: 208231--208317 Score: 96
Period size: 19 Copynumber: 4.8 Consensus size: 19
208221 CTGCCAGTTT
***
208231 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TAAA
208251 CATGTATCGATACAATAAA
1 CATGTATCGATACAATAAA
208270 CATGTATCGATAC-----A
1 CATGTATCGATACAATAAA
208284 -ATGTATCGATACAATAAA
1 CATGTATCGATACAATAAA
208302 CATGTATCGATACAAT
1 CATGTATCGATACAAT
208318 GTATCGATAC
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
13 12 0.21
14 1 0.02
18 1 0.02
19 29 0.50
20 15 0.26
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATAAA
Found at i:208289 original size:13 final size:13
Alignment explanation
Indices: 208271--208328 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
208261 TACAATAAAC
208271 ATGTATCGATACA
1 ATGTATCGATACA
208284 ATGTATCGATACA
1 ATGTATCGATACA
208297 A--TA---A-AC-
1 ATGTATCGATACA
208303 ATGTATCGATACA
1 ATGTATCGATACA
208316 ATGTATCGATACA
1 ATGTATCGATACA
208329 TGTTTATTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
6 1 0.03
7 2 0.05
8 3 0.08
11 3 0.08
12 2 0.05
13 27 0.71
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:208347 original size:32 final size:32
Alignment explanation
Indices: 208252--208328 Score: 154
Period size: 32 Copynumber: 2.4 Consensus size: 32
208242 ACAATTGTCC
208252 ATGTATCGATACAATAAACATGTATCGATACA
1 ATGTATCGATACAATAAACATGTATCGATACA
208284 ATGTATCGATACAATAAACATGTATCGATACA
1 ATGTATCGATACAATAAACATGTATCGATACA
208316 ATGTATCGATACA
1 ATGTATCGATACA
208329 TGTTTATTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.29
Consensus pattern (32 bp):
ATGTATCGATACAATAAACATGTATCGATACA
Found at i:209011 original size:25 final size:26
Alignment explanation
Indices: 208966--209019 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
208956 TTAAAGAGAT
* *
208966 TTTCTCCCCCTAGATTTAAAACAATA
1 TTTCTCCCCCTAGATTCAAAACAAAA
208992 TTTCTCCCCCTTA-A-TCAAAACAAAA
1 TTTCTCCCCC-TAGATTCAAAACAAAA
209017 TTT
1 TTT
209020 ATTTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.48
26 11 0.44
27 2 0.08
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.35
Consensus pattern (26 bp):
TTTCTCCCCCTAGATTCAAAACAAAA
Found at i:210914 original size:13 final size:13
Alignment explanation
Indices: 210896--210922 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
210886 ATAGTAACTC
210896 ATGTATCGATACA
1 ATGTATCGATACA
210909 ATGTATCGATACA
1 ATGTATCGATACA
210922 A
1 A
210923 GGAGTGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:217075 original size:20 final size:20
Alignment explanation
Indices: 217050--217100 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
217040 ACAAGCAATA
217050 TATCGATACAAT-CCATCATG
1 TATCGATACAATACCAT-ATG
*
217070 TATCGATACAATACCCTATG
1 TATCGATACAATACCATATG
217090 TATCGATACAA
1 TATCGATACAA
217101 ATAGTGGTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (20 bp):
TATCGATACAATACCATATG
Found at i:217187 original size:13 final size:13
Alignment explanation
Indices: 217169--217195 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
217159 TACAATGAAC
217169 ATGTATCGATACA
1 ATGTATCGATACA
217182 ATGTATCGATACA
1 ATGTATCGATACA
217195 A
1 A
217196 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:219976 original size:52 final size:52
Alignment explanation
Indices: 219897--220427 Score: 289
Period size: 52 Copynumber: 9.8 Consensus size: 52
219887 ACGATAAACA
* * *
219897 TGCCAATATGCTGATTCAAGGCCAGCGATATTAGTCTTAAAGATGACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGG
* * ** *
219949 TGCCAATGTGCTAATTCAAGGTTAGCGACATTGGACTTAAAGATGAGAAGAATGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC-T-----T-A-AAG-ATGACAAAGG
** * * *
220010 TGCTGATATGCTGATTCAAGGCTAGTGATATTGGACTTAAAGATGACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGG
* * *
220062 TGCTAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGAATGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC-T-----T-A-AAG-ATGACAAAGG
* ** * * * *
220123 TACGGATATGCTGATTAAAGGCCAACGATATTGGACTTAAAGATGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGG
* ** * *
220175 -CCTCAATATGCTGATTTTAGGCCAGCAACATTGGACTTAAAGATAAAAAGAATGATAAAGG
1 TGC-CAATATGCTGATTCAAGGCCAGCGACATTGGAC-T-----T--AAAG-ATGACAAAGG
* * * * * *
220236 TACCGATATGCTGATTCAAGGTCAGTGATATTGGATTTAAAGATGACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGG
* ** * * * * * *
220288 CGTTAATATGCTGATTCAAGGACAACGATATTGGACTT-AAGAAAGAAAAAAG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG-ATGACAAAGG
* * * * * **
220340 CGCCAATATGTTGATTCAAGACCAGCGATATTGGACTT-AAGA--AAAAAAA
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGG
* * *
220389 TCCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTA
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
220428 GAAAGAGATA
Statistics
Matches: 375, Mismatches: 73, Indels: 64
0.73 0.14 0.12
Matches are distributed among these distances:
49 37 0.10
51 5 0.01
52 185 0.49
53 13 0.03
54 2 0.01
55 3 0.01
58 3 0.01
59 2 0.01
60 13 0.03
61 111 0.30
62 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (52 bp):
TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGG
Found at i:220043 original size:61 final size:60
Alignment explanation
Indices: 219935--220281 Score: 262
Period size: 61 Copynumber: 6.0 Consensus size: 60
219925 TATTAGTCTT
* * * * **
219935 AAAG-ATGACAAAGGTGCCAATGTGCTAATTCAAGGTTAGCGACATTGGACTTAAAGATG
1 AAAGAATGATAAAGGTGCTAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* * * *
219994 AGAAGAATGATAAAGGTGCTGATATGCTGATTCAAGGCTAGTGATATTGGAC-T-----T-
1 A-AAGAATGATAAAGGTGCTAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* *
220048 AAAG-ATGACAAAGGTGCTAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
1 AAAGAATGATAAAGGTGCTAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* ** * * *
220107 AGAAGAATGATAAAGGTACGGATATGCTGATTAAAGGCCAACGATATTGGAC-T-----T-
1 A-AAGAATGATAAAGGTGCTAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* ** * *
220161 AAAG-ATGATAAAGG-CCTCAATATGCTGATTTTAGGCCAGCAACATTGGACTTAAAGATAA
1 AAAGAATGATAAAGGTGCT-AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-G
* ** * * * *
220221 AAAGAATGATAAAGGTACCGATATGCTGATTCAAGGTCAGTGATATTGGATTTAAAGATG
1 AAAGAATGATAAAGGTGCTAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
220281 A
1 A
220282 CAAAGGCGTT
Statistics
Matches: 225, Mismatches: 41, Indels: 43
0.73 0.13 0.14
Matches are distributed among these distances:
51 1 0.00
52 76 0.34
53 8 0.04
54 2 0.01
55 2 0.01
58 2 0.01
59 2 0.01
60 13 0.06
61 118 0.52
62 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.25
Consensus pattern (60 bp):
AAAGAATGATAAAGGTGCTAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
Found at i:220049 original size:113 final size:113
Alignment explanation
Indices: 219844--220427 Score: 586
Period size: 113 Copynumber: 5.3 Consensus size: 113
219834 AGTGTCGATA
* * ** * * * ** * *
219844 TGCTGATTCACGACCAGCGATGTT-GAGCTTGAAGATGAGAGGAACGATAAACATGCCAATATGC
1 TGCTGATTCAAGGCCAGCGACATTGGA-CTTAAAGATGAGAAGAATGATAAAGGTACCGATATGC
* *
219908 TGATTCAAGGCCAGCGATATTAGTCTTAAAGATGACAAAGGTGCCAATG
65 TGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGTGCCAATG
* ** * *
219957 TGCTAATTCAAGGTTAGCGACATTGGACTTAAAGATGAGAAGAATGATAAAGGTGCTGATATGCT
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGAATGATAAAGGTACCGATATGCT
* * *
220022 GATTCAAGGCTAGTGATATTGGACTTAAAGATGACAAAGGTGCTAATG
66 GATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGTGCCAATG
*
220070 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGAATGATAAAGGTACGGATATGCT
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGAATGATAAAGGTACCGATATGCT
* * * * *
220135 GATTAAAGGCCAACGATATTGGACTTAAAGATGATAAAGG-CCTCAATA
66 GATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGTGC-CAATG
** * * *
220183 TGCTGATTTTAGGCCAGCAACATTGGACTTAAAGATAAAAAGAATGATAAAGGTACCGATATGCT
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGAATGATAAAGGTACCGATATGCT
* * * * ** *
220248 GATTCAAGGTCAGTGATATTGGATTTAAAGATGACAAAGGCGTTAATA
66 GATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGTGCCAATG
* * * * *
220296 TGCTGATTCAAGGACAACGATATTGGACTT--A-A-GA-AAGAA--A-AAAGCG--CCAATATGT
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGAATGATAAAG-GTACCGATATGC
* * ** *
220351 TGATTCAAGACCAGCGATATTGGACTT-AAGA--AAAAAAATCCCAATG
65 TGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGTGCCAATG
*
220397 TGCTGATTCAAGGCCAGTGACATTGGACTTA
1 TGCTGATTCAAGGCCAGCGACATTGGACTTA
220428 GAAAGAGATA
Statistics
Matches: 394, Mismatches: 72, Indels: 21
0.81 0.15 0.04
Matches are distributed among these distances:
101 33 0.08
103 4 0.01
104 30 0.08
105 4 0.01
106 2 0.01
108 5 0.01
109 1 0.00
110 1 0.00
111 1 0.00
112 1 0.00
113 310 0.79
114 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (113 bp):
TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGAATGATAAAGGTACCGATATGCT
GATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGTGCCAATG
Found at i:220540 original size:32 final size:31
Alignment explanation
Indices: 220504--221236 Score: 493
Period size: 32 Copynumber: 23.2 Consensus size: 31
220494 GATACTACCA
* * *
220504 ACTTGTGTGGGCTTTTGAGAAGGATACCACTG
1 ACTTGTGTGGGC-TTTGAGAAGGTTGCCACCG
*
220536 ACTTGTGTGGGCTTTTGA-AAGGGGTTGCCATCG
1 ACTTGTGTGGGC-TTTGAGAA--GGTTGCCACCG
220569 ACTTGTGTGGGCTTT-AGAAGGGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAGAA---GGTTGCCACCG
* **
220602 ACTTGTGTGGGCTTTAGAGAAGGTTACCATTG
1 ACTTGTGTGGGCTTT-GAGAAGGTTGCCACCG
* *
220634 ACTTATGTGGGCTTTAGAAAAGGTTGCCACCG
1 ACTTGTGTGGGCTTT-GAGAAGGTTGCCACCG
* * *
220666 ACCTGTATGGGCTTTGAGAAGGGTTGCCACCA
1 ACTTGTGTGGGCTTTGAGAA-GGTTGCCACCG
* * * *
220698 ACTTATGTGGGCTTTGAGAGGGTTGTCACCA
1 ACTTGTGTGGGCTTTGAGAAGGTTGCCACCG
* * *
220729 ACATCTGTGGGCTTTGAGAAGGGTTGCCACTG
1 ACTTGTGTGGGCTTTGAGAA-GGTTGCCACCG
* *
220761 ACTTGTGTAGACTTTGAGAAGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAGAAGGTTGCCACCG
* *
220792 ACTTATGTGGGCTTTAAGAAGGTTGCCACC-
1 ACTTGTGTGGGCTTTGAGAAGGTTGCCACCG
* * *
220822 AGCTTGTATGGGCTTT-AGAAGGGTTGTCA-CT
1 A-CTTGTGTGGGCTTTGAGAA-GGTTGCCACCG
* * *
220853 AGCTTGTGTGGGCTTTGAAAAGGGTTACCACCA
1 A-CTTGTGTGGGCTTTGAGAA-GGTTGCCACCG
* *
220886 ATTTGTATGGGCTTTGAGAAGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAGAA-GGTTGCCACCG
**
220918 ACTTGTGTGGGCTTT-AGAAGGGTTGTAACC-
1 ACTTGTGTGGGCTTTGAGAA-GGTTGCCACCG
* * *
220948 AGCTTATGTAGGCTTT-AGACGAGGTTGCCACCA
1 A-CTTGTGTGGGCTTTGAGA--AGGTTGCCACCG
* * * * *
220981 ATTTGTGTGGGATTTAGGGAAAGGTTGGCATCG
1 ACTTGTGTGGGCTTT-GAG-AAGGTTGCCACCG
* *
221014 ACTTGTGTGGGCTTTGAGAAGGGTTGACACCA
1 ACTTGTGTGGGCTTTGAGAA-GGTTGCCACCG
* * *
221046 ACTTGTGTAGGC-TTCAAAAGAGATTGCCACC-
1 ACTTGTGTGGGCTTTGAGAAG-G-TTGCCACCG
* *
221077 AGCTTGTGTGAGCTTT-AGGAAAGGTTGCCACTG
1 A-CTTGTGTGGGCTTTGA-G-AAGGTTGCCACCG
* * * *
221110 ACTTATGTGGGCTTTAAGAAGGGTTACCA-CT
1 ACTTGTGTGGGCTTTGAGAA-GGTTGCCACCG
*
221141 AGCTTGTGTGGGCTTTAGGGAAAGGTTG---CC-
1 A-CTTGTGTGGGCTTT-GAG-AAGGTTGCCACCG
*
221171 -CTTGTGTGGGCTTTAAGGAAAGGTTG---CC-
1 ACTTGTGTGGGCTTTGA-G-AAGGTTGCCACCG
* *
221199 -CTTGTGTGGGCTTTAAGAAAGGTTGCCATCG
1 ACTTGTGTGGGCTTTGAG-AAGGTTGCCACCG
221230 ACTTGTG
1 ACTTGTG
221237 GACTTAAAAG
Statistics
Matches: 568, Mismatches: 93, Indels: 80
0.77 0.13 0.11
Matches are distributed among these distances:
27 9 0.02
28 41 0.07
30 9 0.02
31 145 0.26
32 271 0.48
33 82 0.14
34 6 0.01
35 5 0.01
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.30
Consensus pattern (31 bp):
ACTTGTGTGGGCTTTGAGAAGGTTGCCACCG
Found at i:221145 original size:64 final size:63
Alignment explanation
Indices: 220500--221236 Score: 539
Period size: 63 Copynumber: 11.7 Consensus size: 63
220490 AAGAGATACT
* * * * * *
220500 ACCAACTTGTGTGGGCTTTTGAGAAGGATACCACTGACTTGTGTGGGCTTTTGAA-AGGGGTTGC
1 ACCAGCTTGTGTGGGCTTTAGA-AAGGTTGCCACCGACTTGTGTGGGC-TTT-AAGAAGGGTTGC
220564 C
63 C
* * *
220565 ATC-GACTTGTGTGGGCTTTAGAAGGGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAA-GGTTA
1 ACCAG-CTTGTGTGGGCTTTAGAA--AGGTTGCCACCGACTTGTGTGGGCTTTA-AGAAGGGTTG
220628 CC
62 CC
** * * * *
220630 A-TTGACTTATGTGGGCTTTAGAAAAGGTTGCCACCGACCTGTATGGGCTTTGAGAAGGGTTGCC
1 ACCAG-CTTGTGTGGGCTTTAG-AAAGGTTGCCACCGACTTGTGTGGGCTTTAAGAAGGGTTGCC
* * * * * * * *
220694 ACCAACTTATGTGGGCTTT-GAGAGGGTTGTCACCAACATCTGTGGGCTTTGAGAAGGGTTGCC
1 ACCAGCTTGTGTGGGCTTTAGA-AAGGTTGCCACCGACTTGTGTGGGCTTTAAGAAGGGTTGCC
* * * *
220757 A-CTGACTTGTGTAGACTTT-GAGAAGGTTGCCACCGACTTATGTGGGCTTTAAGAA-GGTTGCC
1 ACCAG-CTTGTGTGGGCTTTAGA-AAGGTTGCCACCGACTTGTGTGGGCTTTAAGAAGGGTTGCC
* * * * *
220819 ACCAGCTTGTATGGGCTTTAGAAGGGTTGTCA-CTAGCTTGTGTGGGCTTTGAA-AAGGGTTACC
1 ACCAGCTTGTGTGGGCTTTAGAAAGGTTGCCACCGA-CTTGTGTGGGCTTT-AAGAAGGGTTGCC
** * * **
220882 ACCAATTTGTATGGGCTTTGAGAAGGGTTGCCACCGACTTGTGTGGGCTTT-AGAAGGGTTGTA
1 ACCAGCTTGTGTGGGCTTT-AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAAGAAGGGTTGCC
* * * * * * * * *
220945 ACCAGCTTATGTAGGCTTTAGACGAGGTTGCCACCAATTTGTGTGGGATTTAGGGAAAGGTTGGC
1 ACCAGCTTGTGTGGGCTTTAGA-AAGGTTGCCACCGACTTGTGTGGGCTTTA-AGAAGGGTTGCC
* * * * * * *
221010 ATC-GACTTGTGTGGGCTTTGAGAAGGGTTGACACCAACTTGTGTAGGCTTCAA-AAGAGATTGC
1 ACCAG-CTTGTGTGGGCTTT-AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAAGAAG-GGTTGC
221073 C
63 C
* * * *
221074 ACCAGCTTGTGTGAGCTTTAGGAAAGGTTGCCACTGACTTATGTGGGCTTTAAGAAGGGTTACC
1 ACCAGCTTGTGTGGGCTTTA-GAAAGGTTGCCACCGACTTGTGTGGGCTTTAAGAAGGGTTGCC
* *
221138 ACTAGCTTGTGTGGGCTTTAGGGAAAGGTTG---CC--CTTGTGTGGGCTTTAAGGAAAGGTTG-
1 ACCAGCTTGTGTGGGCTTTA--GAAAGGTTGCCACCGACTTGTGTGGGCTTTAA-GAAGGGTTGC
221197 -
63 C
*
221197 -CC--CTTGTGTGGGCTTTAAGAAAGGTTGCCATCGACTTGTG
1 ACCAGCTTGTGTGGGCTTT-AGAAAGGTTGCCACCGACTTGTG
221237 GACTTAAAAG
Statistics
Matches: 537, Mismatches: 99, Indels: 77
0.75 0.14 0.11
Matches are distributed among these distances:
55 9 0.02
56 14 0.03
57 1 0.00
58 2 0.00
60 21 0.04
61 9 0.02
62 49 0.09
63 158 0.29
64 142 0.26
65 106 0.20
66 26 0.05
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (63 bp):
ACCAGCTTGTGTGGGCTTTAGAAAGGTTGCCACCGACTTGTGTGGGCTTTAAGAAGGGTTGCC
Found at i:221175 original size:28 final size:27
Alignment explanation
Indices: 221143--221225 Score: 139
Period size: 28 Copynumber: 3.0 Consensus size: 27
221133 TTACCACTAG
221143 CTTGTGTGGGCTTTAGGGAAAGGTTGCC
1 CTTGTGTGGGCTTTA-GGAAAGGTTGCC
221171 CTTGTGTGGGCTTTAAGGAAAGGTTGCC
1 CTTGTGTGGGCTTT-AGGAAAGGTTGCC
*
221199 CTTGTGTGGGCTTTAAGAAAGGTTGCC
1 CTTGTGTGGGCTTTAGGAAAGGTTGCC
221226 ATCGACTTGT
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
27 12 0.23
28 40 0.75
29 1 0.02
ACGTcount: A:0.17, C:0.14, G:0.36, T:0.33
Consensus pattern (27 bp):
CTTGTGTGGGCTTTAGGAAAGGTTGCC
Found at i:221303 original size:34 final size:33
Alignment explanation
Indices: 221260--221377 Score: 119
Period size: 34 Copynumber: 3.5 Consensus size: 33
221250 GTGACGAAGC
*
221260 TGTGGACTTAAAAAGAAAAAAGGTGCCATGGAGT
1 TGTGGACTTAAAAAGAAAAAA-GTGCCAAGGAGT
** * * *
221294 TGTGGACTTAAATGGGGAAAATGTGACAAGGAGT
1 TGTGGACTTAAA-AAGAAAAAAGTGCCAAGGAGT
* * *
221328 TCTGGACTTTAAAAGAAAAAAGTGCCACGGAGT
1 TGTGGACTTAAAAAGAAAAAAGTGCCAAGGAGT
*
221361 CGTGGACTTAAAGAAGA
1 TGTGGACTTAAA-AAGA
221378 GATGCCACTA
Statistics
Matches: 65, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
33 24 0.37
34 36 0.55
35 5 0.08
ACGTcount: A:0.39, C:0.10, G:0.30, T:0.21
Consensus pattern (33 bp):
TGTGGACTTAAAAAGAAAAAAGTGCCAAGGAGT
Found at i:229909 original size:20 final size:20
Alignment explanation
Indices: 229884--229938 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
229874 AAAAACCCAG
229884 AATGTATCGATACAATGAAT-
1 AATGTATCGATACAAT-AATA
*
229904 AATGTATCGATACAAATAGTA
1 AATGTATCGATAC-AATAATA
229925 AATGTATCGATACA
1 AATGTATCGATACA
229939 TTTATTTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACAATAATA
Found at i:229930 original size:21 final size:21
Alignment explanation
Indices: 229884--229938 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
229874 AAAAACCCAG
229884 AATGTATCGATAC-AATGAAT
1 AATGTATCGATACAAATGAAT
*
229904 AATGTATCGATACAAAT-AGT
1 AATGTATCGATACAAATGAAT
229924 AAATGTATCGATACA
1 -AATGTATCGATACA
229939 TTTATTTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACAAATGAAT
Found at i:235434 original size:15 final size:15
Alignment explanation
Indices: 235416--235445 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
235406 CCAAATTGGG
235416 GAAGCTCAAAATGAA
1 GAAGCTCAAAATGAA
*
235431 GAAGCTCCAAATGAA
1 GAAGCTCAAAATGAA
235446 ATTGATGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.17, G:0.20, T:0.13
Consensus pattern (15 bp):
GAAGCTCAAAATGAA
Found at i:237515 original size:13 final size:13
Alignment explanation
Indices: 237497--237535 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
237487 ACATTTTTCT
237497 TTGTATCGATACA
1 TTGTATCGATACA
237510 TTGTATCGATACA
1 TTGTATCGATACA
*
237523 CTGTATCGATACA
1 TTGTATCGATACA
237536 AGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:239987 original size:20 final size:21
Alignment explanation
Indices: 239964--240020 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
239954 ACAATTCAAA
**
239964 GTATCGATACATGTTGCA-AT
1 GTATCGATACATGTTAAATAT
**
239984 GTATCGATACATGAAAAATAT
1 GTATCGATACATGTTAAATAT
240005 GTATCGATACATGTTA
1 GTATCGATACATGTTA
240021 GTGGGATTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (21 bp):
GTATCGATACATGTTAAATAT
Found at i:240084 original size:13 final size:13
Alignment explanation
Indices: 240066--240091 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
240056 TACACCAAGT
240066 ATGTATCGATACA
1 ATGTATCGATACA
240079 ATGTATCGATACA
1 ATGTATCGATACA
240092 CCAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:240110 original size:34 final size:32
Alignment explanation
Indices: 240048--240112 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
240038 TAGCCAAACT
**
240048 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
240080 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
240113 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:245684 original size:29 final size:25
Alignment explanation
Indices: 245638--245690 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 25
245628 TCTGAACATT
245638 ATTTTATTATTAATTTTAATTCTAAA
1 ATTTTATTATTAATTTTAA-TCTAAA
245664 ATTTTATATATATAAATTTTAATCTAA
1 ATTTTAT-TAT-T-AATTTTAATCTAA
245691 TCTGCTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 7 0.29
27 3 0.12
28 6 0.25
29 8 0.33
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (25 bp):
ATTTTATTATTAATTTTAATCTAAA
Found at i:246020 original size:26 final size:26
Alignment explanation
Indices: 245991--246041 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
245981 TAAAATAATA
*
245991 ATTAGCTATCCTATTTTTCTTTTTAG
1 ATTAACTATCCTATTTTTCTTTTTAG
*
246017 ATTAACTATGCTATTTTTCTTTTTA
1 ATTAACTATCCTATTTTTCTTTTTA
246042 TTTAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.14, G:0.06, T:0.59
Consensus pattern (26 bp):
ATTAACTATCCTATTTTTCTTTTTAG
Found at i:246692 original size:30 final size:30
Alignment explanation
Indices: 246652--246725 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
246642 TTAAGTTAAA
* *
246652 ATTAAAAGTTTATTTGAATATAGATGAAA-T
1 ATTAAGAGTTTATTTGAATATA-ATAAAAGT
*
246682 ATTAAGAGTTTATTTGCATATAATAAAAGT
1 ATTAAGAGTTTATTTGAATATAATAAAAGT
*
246712 A-TAAGAATTTATTT
1 ATTAAGAGTTTATTT
246726 AAATTAAATG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
29 17 0.44
30 22 0.56
ACGTcount: A:0.45, C:0.01, G:0.12, T:0.42
Consensus pattern (30 bp):
ATTAAGAGTTTATTTGAATATAATAAAAGT
Found at i:247763 original size:2 final size:2
Alignment explanation
Indices: 247756--247783 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
247746 TACTGCTTAC
247756 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
247784 TATGTACAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:250439 original size:16 final size:16
Alignment explanation
Indices: 250399--250429 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
250389 CCATATATTA
*
250399 TCTCGGTTTTGAATTT
1 TCTCGATTTTGAATTT
250415 TCTCGATTTTGAATT
1 TCTCGATTTTGAATT
250430 GTTGTCATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.13, G:0.16, T:0.55
Consensus pattern (16 bp):
TCTCGATTTTGAATTT
Found at i:255350 original size:15 final size:16
Alignment explanation
Indices: 255306--255351 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
255296 AATTTTCATG
255306 ACAAA-AGAAAAGAAA
1 ACAAAGAGAAAAGAAA
255321 ACAAAGAGAAAAGAAA
1 ACAAAGAGAAAAGAAA
*
255337 ACAAAG-GGAAAGAAA
1 ACAAAGAGAAAAGAAA
255352 TATGGAAGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 13 0.45
16 16 0.55
ACGTcount: A:0.74, C:0.07, G:0.20, T:0.00
Consensus pattern (16 bp):
ACAAAGAGAAAAGAAA
Found at i:256503 original size:21 final size:21
Alignment explanation
Indices: 256470--256510 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
256460 CTAAGTAAAA
256470 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
256491 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
256511 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:256575 original size:20 final size:20
Alignment explanation
Indices: 256550--256620 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
256540 ACCCTGAAAA
256550 GTATCGATACACATATAAAT
1 GTATCGATACACATATAAAT
* **
256570 GTATCGATACAAAT-TGCAT
1 GTATCGATACACATATAAAT
*
256589 AGTATCGATACACA-AAAATAT
1 -GTATCGATACACATATAA-AT
256610 GTATCGATACA
1 GTATCGATACA
256621 AGACATTGGC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.07
20 36 0.88
21 2 0.05
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
GTATCGATACACATATAAAT
Found at i:256670 original size:53 final size:53
Alignment explanation
Indices: 256590--256726 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
256580 AAATTGCATA
*
256590 GTATCGATACACAAAAATATGTATCGATACAAGACATTGGCAGTAGCCAAATTT
1 GTATCGATACAC-AAAATATGTATCGATACAAGACATTGGCAGTACCCAAATTT
* * *
256644 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTACCCAAATTT
1 GTATCGATACACAAAATATGTATCGATACAAGACATTGGCAGTACCCAAATTT
256697 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACAAAATATGTATCGATACA
256727 TTGGAAGTAG
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 66 0.85
54 12 0.15
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (53 bp):
GTATCGATACACAAAATATGTATCGATACAAGACATTGGCAGTACCCAAATTT
Found at i:259724 original size:13 final size:13
Alignment explanation
Indices: 259706--259730 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
259696 TTTTCCAGAT
259706 TGTATCGATACAA
1 TGTATCGATACAA
259719 TGTATCGATACA
1 TGTATCGATACA
259731 TTGCTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Done.