Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 129 of 208
Found at i:39544026 original size:43 final size:43
Alignment explanation
Indices: 39543736--39544042 Score: 154
Period size: 42 Copynumber: 7.2 Consensus size: 43
39543726 GCTTACAGAA
* * * * *
39543736 AAAAACTCCGCT-AAAGATCATGTTCTTTAGCGGCGCTAAG--A
1 AAAAACGCCGCTAAAAG-TAATGTTCTATAGCGGCGCTTAGTTC
* * **
39543777 AAATAATCGCCGCT-AAAGATCATGTTCTTTAGCGGCGCTTA-TGA
1 AAA-AA-CGCCGCTAAAAG-TAATGTTCTATAGCGGCGCTTAGTTC
* * * * **
39543821 AAAAACGCCGCT-AAAGATCACGTTCTTTAGCGGTGCTTAG-AA
1 AAAAACGCCGCTAAAAG-TAATGTTCTATAGCGGCGCTTAGTTC
* * * * **
39543863 AAAAACGCCGCT-AAAGATCATATTCTTTAGCAGCGCTTAG-GA
1 AAAAACGCCGCTAAAAG-TAATGTTCTATAGCGGCGCTTAGTTC
* * * *
39543905 AAAAACGCCGCT-AAAGATCATGTTCTTTAGCGGCGCTTTGGAT-
1 AAAAACGCCGCTAAAAG-TAATGTTCTATAGCGGCGC-TTAGTTC
*
39543948 GAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTT-GTTC
1 AAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAGTTC
* * * *
39543990 AAAAACGCCGCTAATAGTAGTGTT-TATTTAGTGGCGCTTATTTC
1 AAAAACGCCGCTAAAAGTAATGTTCTA--TAGCGGCGCTTAGTTC
*
39544034 ACAAACGCC
1 AAAAACGCC
39544043 ACTATTTGAT
Statistics
Matches: 230, Mismatches: 24, Indels: 21
0.84 0.09 0.08
Matches are distributed among these distances:
41 7 0.03
42 129 0.56
43 75 0.33
44 19 0.08
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (43 bp):
AAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAGTTC
Found at i:39544480 original size:12 final size:12
Alignment explanation
Indices: 39544459--39544494 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
39544449 TGAACCTCTA
*
39544459 CTTCTATCGCTG
1 CTTCTCTCGCTG
39544471 CTTCTCTCGCTG
1 CTTCTCTCGCTG
*
39544483 CTTCTCTTGCTG
1 CTTCTCTCGCTG
39544495 TGGCCTCTGC
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:0.03, C:0.36, G:0.17, T:0.44
Consensus pattern (12 bp):
CTTCTCTCGCTG
Found at i:39544504 original size:21 final size:21
Alignment explanation
Indices: 39544480--39544548 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
39544470 GCTTCTCTCG
* * *
39544480 CTGCTTCTCTTGCTGTGGCCT
1 CTGCTTCTCTCGCTGTAGCAT
39544501 CTGCTTCTCTCGCTGTAGCAT
1 CTGCTTCTCTCGCTGTAGCAT
**
39544522 CTGCTT-TCCTCGCTGCCGCAT
1 CTGCTTCT-CTCGCTGTAGCAT
39544543 CTGCTT
1 CTGCTT
39544549 TAAGTTGTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
20 1 0.02
21 41 0.98
ACGTcount: A:0.04, C:0.36, G:0.20, T:0.39
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGTAGCAT
Found at i:39550483 original size:39 final size:38
Alignment explanation
Indices: 39550414--39550491 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 38
39550404 CTAAAGAAAC
*
39550414 TGTGCCAAAACAAAATACCAAAAAATAATACCAAGTAA
1 TGTGCCAAAACAAAATACCAAAAAAGAATACCAAGTAA
** *
39550452 TGTGCCAAAACAATCCTACCAAAACAGAATACCAAGTAA
1 TGTGCCAAAACAA-AATACCAAAAAAGAATACCAAGTAA
39550491 T
1 T
39550492 CCACAAAGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
38 13 0.37
39 22 0.63
ACGTcount: A:0.53, C:0.22, G:0.09, T:0.17
Consensus pattern (38 bp):
TGTGCCAAAACAAAATACCAAAAAAGAATACCAAGTAA
Found at i:39551934 original size:17 final size:17
Alignment explanation
Indices: 39551912--39551950 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
39551902 AGAGTGTATA
39551912 ATTTAAATATTATCAA-T
1 ATTTAAA-ATTATCAATT
*
39551929 ATTTAAAATTATTAATT
1 ATTTAAAATTATCAATT
39551946 ATTTA
1 ATTTA
39551951 CAGTATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAAAATTATCAATT
Found at i:39552382 original size:7 final size:7
Alignment explanation
Indices: 39552370--39552414 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
39552360 AAAGCGACCT
39552370 AAACCCC
1 AAACCCC
39552377 AAACCCC
1 AAACCCC
**
39552384 AAACCTT
1 AAACCCC
39552391 AAACCCC
1 AAACCCC
39552398 AAACTCCC
1 AAAC-CCC
39552406 -AACCCC
1 AAACCCC
39552412 AAA
1 AAA
39552415 ACACTAAACC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 3 0.09
7 26 0.81
8 3 0.09
ACGTcount: A:0.44, C:0.49, G:0.00, T:0.07
Consensus pattern (7 bp):
AAACCCC
Found at i:39553083 original size:216 final size:216
Alignment explanation
Indices: 39552718--39553108 Score: 701
Period size: 216 Copynumber: 1.8 Consensus size: 216
39552708 TTTACATGAG
*
39552718 CGCCACTAATTCTAATATACATCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGAT
1 CGCCACTAATTCTAATATACATCAAGACCAAACGCTGCGTTTTGGTTAAGATAATTTGCGGCGAT
* *
39552783 TCTTACAAAGCATCTCTAATACTCTGCTTTAGCGGCCTTTTTCCGTAACCGCCACTAATTCTTAT
66 TCTTACAAAGCACCTCTAATACTCTCCTTTAGCGGCCTTTTTCCGTAACCGCCACTAATTCTTAT
39552848 ATACCTCAAGACAAAACGATGCGTTTTGGTTAAGATATTTTGCGGAACGCCGCTAATACTGTGCT
131 ATACCTCAAGACAAAACGATGCGTTTTGGTTAAGATATTTTGCGGAACGCCGCTAATACTGTGCT
39552913 ATAACGGCGTTTTCCCACAAT
196 ATAACGGCGTTTTCCCACAAT
* *
39552934 CGCCACTAATTCTAATATACATTAAGACCAAACGCTGCGTTTTGGTTAAGATAATTTGCGGCGTT
1 CGCCACTAATTCTAATATACATCAAGACCAAACGCTGCGTTTTGGTTAAGATAATTTGCGGCGAT
** *
39552999 TCTTACAAAGTGCCTCTAATACTCTCCTTTAGCGGCGTTTTTCCGTAACCGCCACTAATTCTTAT
66 TCTTACAAAGCACCTCTAATACTCTCCTTTAGCGGCCTTTTTCCGTAACCGCCACTAATTCTTAT
*
39553064 ATACCTCAAGACCAAACGATGCGTTTTGGTTAAGATATTTTGCGG
131 ATACCTCAAGACAAAACGATGCGTTTTGGTTAAGATATTTTGCGG
39553109 CGTTTACTAA
Statistics
Matches: 166, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
216 166 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.33
Consensus pattern (216 bp):
CGCCACTAATTCTAATATACATCAAGACCAAACGCTGCGTTTTGGTTAAGATAATTTGCGGCGAT
TCTTACAAAGCACCTCTAATACTCTCCTTTAGCGGCCTTTTTCCGTAACCGCCACTAATTCTTAT
ATACCTCAAGACAAAACGATGCGTTTTGGTTAAGATATTTTGCGGAACGCCGCTAATACTGTGCT
ATAACGGCGTTTTCCCACAAT
Found at i:39553100 original size:114 final size:113
Alignment explanation
Indices: 39552893--39553245 Score: 361
Period size: 114 Copynumber: 3.1 Consensus size: 113
39552883 TATTTTGCGG
* * * * * * * *
39552893 AACGCCGCTAATACTGTGCTATAACGGCGTTT-TCCCACAATCGCCACTAATTCTAATATACATT
1 AACGCCGCTAATAATATACTATAGCGGCGTTTAT--CATAAACGCCACTAATTCTAATATACCTC
* * *
39552957 AAGACCAAACGCTGCGTTTTGGTTAAGATAATTTGCGGCGTTT-CTTACAA
64 AAGACCAAACGATGCGTTTTGGTTAAGATATTTTGCGGCGTTTAC-TAAAA
** * * * * * * * * *
39553007 AGTGCCTCTAATACTCTCCTTTAGCGGCGTTTTTCCGTAACCGCCACTAATTCTTATATACCTCA
1 AACGCCGCTAATAATATACTATAGCGGCGTTTAT-CATAAACGCCACTAATTCTAATATACCTCA
39553072 AGACCAAACGATGCGTTTTGGTTAAGATATTTTGCGGCGTTTACTAAAA
65 AGACCAAACGATGCGTTTTGGTTAAGATATTTTGCGGCGTTTACTAAAA
* * **
39553121 AACGCCGCTAATAATATACTATAGCGGCGTTTATCATAAACGCCACCAAGTCTAATATACCTCGG
1 AACGCCGCTAATAATATACTATAGCGGCGTTTATCATAAACGCCACTAATTCTAATATACCTCAA
* * * * *
39553186 GAACAAACGATGCGTTTTGGCTAACATTTTTTGCGGCGCTTAC-AAATA
66 GACCAAACGATGCGTTTTGGTTAAGATATTTTGCGGCGTTTACTAAA-A
39553234 AACGCCGCTAAT
1 AACGCCGCTAAT
39553246 TATGCTATAT
Statistics
Matches: 200, Mismatches: 36, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
112 3 0.01
113 75 0.38
114 120 0.60
115 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (113 bp):
AACGCCGCTAATAATATACTATAGCGGCGTTTATCATAAACGCCACTAATTCTAATATACCTCAA
GACCAAACGATGCGTTTTGGTTAAGATATTTTGCGGCGTTTACTAAAA
Found at i:39553590 original size:15 final size:16
Alignment explanation
Indices: 39553572--39553630 Score: 63
Period size: 15 Copynumber: 3.9 Consensus size: 16
39553562 TTTAAAATAA
*
39553572 TAATATT-ATTATTAT
1 TAATATTCAATATTAT
39553587 TAATATT-AATATTA-
1 TAATATTCAATATTAT
*
39553601 TAATGTTCAATATTAT
1 TAATATTCAATATTAT
*
39553617 TAA-ATTCATTATTA
1 TAATATTCAATATTA
39553631 AAGTATTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
14 6 0.16
15 29 0.76
16 3 0.08
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (16 bp):
TAATATTCAATATTAT
Found at i:39553847 original size:23 final size:23
Alignment explanation
Indices: 39553821--39553868 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
39553811 ATAATAAATG
39553821 TTTATAGTATA-AAATATGAATAT
1 TTTA-AGTATATAAATATGAATAT
* *
39553844 TTTAATTATATAAATATGCATAT
1 TTTAAGTATATAAATATGAATAT
39553867 TT
1 TT
39553869 GTTTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (23 bp):
TTTAAGTATATAAATATGAATAT
Found at i:39556818 original size:40 final size:42
Alignment explanation
Indices: 39556748--39556840 Score: 138
Period size: 40 Copynumber: 2.3 Consensus size: 42
39556738 TTAAAATTAT
* * *
39556748 TTATATTAAA-AAACACTACCATAAATATAATAATTTTTTTA
1 TTATATTAAATAAACACTACAATAAATATAATAAATATTTTA
39556789 TTATATTAAATAAACAC-A-AATAAATATAATAAATATTTTA
1 TTATATTAAATAAACACTACAATAAATATAATAAATATTTTA
39556829 TTATATTAAATA
1 TTATATTAAATA
39556841 TAAATTTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
40 31 0.65
41 11 0.23
42 6 0.12
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (42 bp):
TTATATTAAATAAACACTACAATAAATATAATAAATATTTTA
Found at i:39562654 original size:39 final size:39
Alignment explanation
Indices: 39562577--39562717 Score: 198
Period size: 40 Copynumber: 3.6 Consensus size: 39
39562567 GAAAACAAAA
* *
39562577 AACCCAACACATT-AAAAAA-AAAAAACAAACAAACAAAG
1 AACCCAACACATTCAAAAAATAAATAACAAAC-AATAAAG
39562615 AACCCAACACATTCAAAAAATAAATAACAAACAATAAAG
1 AACCCAACACATTCAAAAAATAAATAACAAACAATAAAG
*
39562654 AACCCAACACATTCAAAAAAATAAATAACAAACAATAAAC
1 AACCCAACACATTC-AAAAAATAAATAACAAACAATAAAG
*
39562694 AACCCAGA-ATATTCAAAAAATAAA
1 AACCCA-ACACATTCAAAAAATAAA
39562718 AAAAGAACCC
Statistics
Matches: 95, Mismatches: 4, Indels: 7
0.90 0.04 0.07
Matches are distributed among these distances:
38 13 0.14
39 36 0.38
40 45 0.47
41 1 0.01
ACGTcount: A:0.66, C:0.21, G:0.02, T:0.11
Consensus pattern (39 bp):
AACCCAACACATTCAAAAAATAAATAACAAACAATAAAG
Found at i:39567700 original size:12 final size:12
Alignment explanation
Indices: 39567685--39567714 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
39567675 TCTTAGTCCC
*
39567685 CCTCTCCCTTTT
1 CCTCTCCCTCTT
39567697 CCTCTCCCTCTT
1 CCTCTCCCTCTT
39567709 CCTCTC
1 CCTCTC
39567715 TTCGTTCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (12 bp):
CCTCTCCCTCTT
Found at i:39569868 original size:29 final size:29
Alignment explanation
Indices: 39569804--39569862 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
39569794 AGCTGAAAAA
*
39569804 TAAAAAAATTATTAGAATAGATTGATTTT
1 TAAAAAAATTATTAGAATAAATTGATTTT
39569833 TAAAAAAATTA-TAGGAATAAATT-ATTTT
1 TAAAAAAATTATTA-GAATAAATTGATTTT
39569861 TA
1 TA
39569863 CGAAAACACT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (29 bp):
TAAAAAAATTATTAGAATAAATTGATTTT
Found at i:39572053 original size:14 final size:14
Alignment explanation
Indices: 39572034--39572060 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39572024 ATGCCATCGG
39572034 TGTATGGGACACAT
1 TGTATGGGACACAT
39572048 TGTATGGGACACA
1 TGTATGGGACACA
39572061 ATATAGTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.26
Consensus pattern (14 bp):
TGTATGGGACACAT
Found at i:39573294 original size:21 final size:21
Alignment explanation
Indices: 39573238--39573302 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 21
39573228 TATAAAACCT
*
39573238 AAATCCTAACCCTAAAAAAGA
1 AAATCCTAACCCTAAAAAATA
* **
39573259 AAA--ATATACTTTAAAAAATA
1 AAATCCTA-ACCCTAAAAAATA
39573279 AAATCCTAACCCTAAAAAAATA
1 AAATCCTAACCCT-AAAAAATA
39573301 AA
1 AA
39573303 GGGAAAAACG
Statistics
Matches: 33, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
19 2 0.06
20 13 0.39
21 6 0.18
22 12 0.36
ACGTcount: A:0.62, C:0.17, G:0.02, T:0.20
Consensus pattern (21 bp):
AAATCCTAACCCTAAAAAATA
Found at i:39575175 original size:11 final size:11
Alignment explanation
Indices: 39575159--39575217 Score: 86
Period size: 11 Copynumber: 5.5 Consensus size: 11
39575149 AACTTTTGAT
39575159 TAAAAAGATTA
1 TAAAAAGATTA
*
39575170 TAAAAA-AAT-
1 TAAAAAGATTA
39575179 TAAAAAGATTA
1 TAAAAAGATTA
39575190 TAAAAAGATTA
1 TAAAAAGATTA
*
39575201 TAAAAAAATTA
1 TAAAAAGATTA
39575212 TAAAAA
1 TAAAAA
39575218 TTATTAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
9 6 0.14
10 4 0.09
11 33 0.77
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.25
Consensus pattern (11 bp):
TAAAAAGATTA
Found at i:39575182 original size:20 final size:21
Alignment explanation
Indices: 39575157--39575217 Score: 88
Period size: 20 Copynumber: 2.9 Consensus size: 21
39575147 ACAACTTTTG
39575157 ATTAAAAAGATTATAAAAA-A
1 ATTAAAAAGATTATAAAAAGA
39575177 ATTAAAAAGATTATAAAAAGA
1 ATTAAAAAGATTATAAAAAGA
* *
39575198 TTATAAAAAAATTATAAAAA
1 AT-TAAAAAGATTATAAAAA
39575218 TTATTAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 19 0.51
21 2 0.05
22 16 0.43
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (21 bp):
ATTAAAAAGATTATAAAAAGA
Found at i:39575194 original size:31 final size:31
Alignment explanation
Indices: 39575159--39575221 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 31
39575149 AACTTTTGAT
39575159 TAAAAAGATTATAAAAAAATTA-AAAAGATTA
1 TAAAAAGATTATAAAAAAATTATAAAA-ATTA
39575190 TAAAAAGATTATAAAAAAATTATAAAAATTA
1 TAAAAAGATTATAAAAAAATTATAAAAATTA
39575221 T
1 T
39575222 TAAATATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (31 bp):
TAAAAAGATTATAAAAAAATTATAAAAATTA
Found at i:39575221 original size:9 final size:9
Alignment explanation
Indices: 39575173--39575272 Score: 71
Period size: 9 Copynumber: 10.6 Consensus size: 9
39575163 AAGATTATAA
39575173 AAAAATTA-
1 AAAAATTAT
39575181 AAAAGATTAT
1 AAAA-ATTAT
39575191 AAAAAGATTAT
1 -AAAA-ATTAT
39575202 AAAAAAATTAT
1 --AAAAATTAT
39575213 AAAAATTATT
1 AAAAATTA-T
*
39575223 AAATATT-T
1 AAAAATTAT
39575231 AAAAA-TAT
1 AAAAATTAT
* *
39575239 GAAACTTGAT
1 AAAAATT-AT
*
39575249 ATAAACTTAT
1 A-AAAATTAT
39575259 AAAAATTAT
1 AAAAATTAT
39575268 AAAAA
1 AAAAA
39575273 AAACATCAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
7 1 0.01
8 13 0.17
9 25 0.32
10 12 0.16
11 21 0.27
12 5 0.06
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:39575964 original size:20 final size:18
Alignment explanation
Indices: 39575931--39575994 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
39575921 TAATTTCAAG
*
39575931 TATTTTAAATAATTTTTA
1 TATTTTTAATAATTTTTA
39575949 TATTTTTATTATAATTTTTAA
1 TATTTTTA--ATAATTTTT-A
*
39575970 TAATTTTAATAATTTTCTA
1 TATTTTTAATAATTTT-TA
39575989 -ATTTTT
1 TATTTTT
39575995 TATGATTTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 12 0.31
19 9 0.23
20 10 0.26
21 8 0.21
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTTTTAATAATTTTTA
Found at i:39575978 original size:9 final size:9
Alignment explanation
Indices: 39575932--39575985 Score: 54
Period size: 9 Copynumber: 5.6 Consensus size: 9
39575922 AATTTCAAGT
39575932 ATTTTAAATA
1 ATTTT-AATA
*
39575942 ATTTTTATA
1 ATTTTAATA
*
39575951 TTTTTATTATA
1 ATTTTA--ATA
39575962 ATTTTTAATA
1 A-TTTTAATA
39575972 ATTTTAATA
1 ATTTTAATA
39575981 ATTTT
1 ATTTT
39575986 CTAATTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
9 20 0.54
10 9 0.24
11 3 0.08
12 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
ATTTTAATA
Found at i:39575994 original size:9 final size:9
Alignment explanation
Indices: 39575939--39575994 Score: 51
Period size: 10 Copynumber: 6.0 Consensus size: 9
39575929 AGTATTTTAA
39575939 ATAATTTTT
1 ATAATTTTT
*
39575948 ATATTTTTATT
1 ATA-ATTT-TT
39575959 ATAATTTTT
1 ATAATTTTT
*
39575968 AATAATTTTA
1 -ATAATTTTT
39575978 ATAA-TTTT
1 ATAATTTTT
*
39575986 CTAATTTTT
1 ATAATTTTT
39575995 TATGATTTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
8 6 0.16
9 13 0.34
10 14 0.37
11 5 0.13
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (9 bp):
ATAATTTTT
Found at i:39575994 original size:18 final size:17
Alignment explanation
Indices: 39575932--39575994 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 17
39575922 AATTTCAAGT
*
39575932 ATTTTAAATAATTTTTA
1 ATTTTTAATAATTTTTA
39575949 TATTTTTATTATAATTTTTA
1 -ATTTTTA--ATAATTTTTA
39575969 ATAATTTTAATAATTTTCTA
1 AT--TTTTAATAATTTT-TA
39575989 ATTTTT
1 ATTTTT
39575995 TATGATTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
18 10 0.26
19 10 0.26
20 14 0.36
21 5 0.13
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTTTAATAATTTTTA
Found at i:39575995 original size:19 final size:18
Alignment explanation
Indices: 39575933--39575996 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 18
39575923 ATTTCAAGTA
*
39575933 TTTTAAATAATTTTTATAT
1 TTTTTAATAATTTTTA-AT
*
39575952 TTTTATTATAATTTTTAAT
1 TTTT-TAATAATTTTTAAT
*
39575971 AATTTTAATAATTTTCTAAT
1 -TTTTTAATAATTTT-TAAT
39575991 TTTTTA
1 TTTTTA
39575997 TGATTTTCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
19 20 0.54
20 17 0.46
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTTAATAATTTTTAAT
Found at i:39579845 original size:29 final size:29
Alignment explanation
Indices: 39579796--39579860 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
39579786 GCTTCAAATT
* *
39579796 TTTTTCTTAGATCGCCGCAAAGGCTTTCA
1 TTTTTCTTAGATCGCCACAAAGGCTTCCA
* *
39579825 TTTTTCTTAGATTGCCACAAAGTCTTCCA
1 TTTTTCTTAGATCGCCACAAAGGCTTCCA
39579854 TTTTTCT
1 TTTTTCT
39579861 AGTGTGTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.45
Consensus pattern (29 bp):
TTTTTCTTAGATCGCCACAAAGGCTTCCA
Found at i:39585600 original size:14 final size:14
Alignment explanation
Indices: 39585583--39585611 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39585573 ATGTATGATC
39585583 ATTTTAGTATAGTT
1 ATTTTAGTATAGTT
39585597 ATTTTAGTATAGTT
1 ATTTTAGTATAGTT
39585611 A
1 A
39585612 AATCTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (14 bp):
ATTTTAGTATAGTT
Found at i:39591938 original size:20 final size:20
Alignment explanation
Indices: 39591893--39591940 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
39591883 TAATATTTAA
39591893 TTATATTTAAATAAAATTAT
1 TTATATTTAAATAAAATTAT
* **
39591913 TAATATTTATTTATAAATT-T
1 TTATATTTAAATA-AAATTAT
39591933 TTATATTT
1 TTATATTT
39591941 TTATTCAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATATTTAAATAAAATTAT
Found at i:39595489 original size:34 final size:34
Alignment explanation
Indices: 39595451--39595531 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 34
39595441 AACTATATTT
*
39595451 TTATGCGAATCT-TTGCTAAGTGCAAACTATGCTG
1 TTATGCGAACCTATT-CTAAGTGCAAACTATGCTG
* * * *
39595485 TTATGTGAACCTATTCTATGTGCGAACTATGTTG
1 TTATGCGAACCTATTCTAAGTGCAAACTATGCTG
*
39595519 TTATGCAAACCTA
1 TTATGCGAACCTA
39595532 CGTTTTATGT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
34 37 0.95
35 2 0.05
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (34 bp):
TTATGCGAACCTATTCTAAGTGCAAACTATGCTG
Found at i:39595563 original size:17 final size:17
Alignment explanation
Indices: 39595509--39595566 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
39595499 TCTATGTGCG
39595509 AACTATGTTGTTATGCA
1 AACTATGTTGTTATGCA
* **
39595526 AACCTACGTT-TTATGTG
1 AA-CTATGTTGTTATGCA
*
39595543 AACTGTGTTGTTATGCA
1 AACTATGTTGTTATGCA
39595560 AACTATG
1 AACTATG
39595567 CTAGGTACGA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
16 5 0.16
17 20 0.65
18 6 0.19
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.40
Consensus pattern (17 bp):
AACTATGTTGTTATGCA
Found at i:39601933 original size:28 final size:28
Alignment explanation
Indices: 39601896--39601959 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 28
39601886 TTAATATAAA
39601896 TATAA-ATATA-AA-TATATATAATTATTAT
1 TATAACATATAGAATTA-ATATAATT-TT-T
39601924 T-TAACATATAGAATTAATATAATTTTT
1 TATAACATATAGAATTAATATAATTTTT
39601951 TATAACATA
1 TATAACATA
39601960 ATATATTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
27 5 0.16
28 15 0.47
29 10 0.31
30 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (28 bp):
TATAACATATAGAATTAATATAATTTTT
Found at i:39610714 original size:15 final size:15
Alignment explanation
Indices: 39610687--39610726 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
39610677 ACACTTTCCA
39610687 TAAAATTAT-AAATT
1 TAAAATTATAAAATT
* *
39610701 TTAAATTTTAAAATT
1 TAAAATTATAAAATT
39610716 TAAAATTATAA
1 TAAAATTATAA
39610727 CTCATCATAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAAATTATAAAATT
Found at i:39611465 original size:13 final size:13
Alignment explanation
Indices: 39611447--39611472 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39611437 AAAATGCATG
39611447 TATATATATTATA
1 TATATATATTATA
39611460 TATATATATTATA
1 TATATATATTATA
39611473 ATAATAATTA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATTATA
Found at i:39612301 original size:25 final size:25
Alignment explanation
Indices: 39612253--39612301 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
39612243 CATAATTGAA
* * *
39612253 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
39612278 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
39612302 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:39612760 original size:43 final size:43
Alignment explanation
Indices: 39612696--39612781 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
39612686 TATGTGATTG
39612696 ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAGAAA
1 ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAGAAA
* *
39612739 ATATTGAAATGGCAAATATGAGAAATGATTATGAGATGAGAAA
1 ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAGAAA
39612782 TGAAATATGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.50, C:0.02, G:0.24, T:0.23
Consensus pattern (43 bp):
ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAGAAA
Found at i:39612765 original size:16 final size:16
Alignment explanation
Indices: 39612701--39612765 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 16
39612691 GATTGATATT
*
39612701 GAAATGGCAAAGATGA
1 GAAATGGCAAATATGA
39612717 GAAAT-G--AATATGA
1 GAAATGGCAAATATGA
* *
39612730 G--ATGAGAAAATAT-T
1 GAAATG-GCAAATATGA
39612744 GAAATGGCAAATATGA
1 GAAATGGCAAATATGA
39612760 GAAATG
1 GAAATG
39612766 ATTATGAGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
11 2 0.05
13 8 0.21
14 1 0.03
15 13 0.34
16 14 0.37
ACGTcount: A:0.51, C:0.03, G:0.26, T:0.20
Consensus pattern (16 bp):
GAAATGGCAAATATGA
Found at i:39614162 original size:49 final size:49
Alignment explanation
Indices: 39614090--39614186 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
39614080 TCAAGAAGGG
* *
39614090 ATAAATAGTGATAAGAGTGTAGACAGTGAAAGACTAAGTTTAGCAATGT
1 ATAAATAGTGATAAGAGTGTAGACAGTGAAAGACCAAGTTTAGAAATGT
*
39614139 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGAAATG
1 ATAAATAGTGATAAGAGTGTAGACAGTGAAAGACCAAGTTTAGAAATG
39614187 CATAGCATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.43, C:0.06, G:0.26, T:0.25
Consensus pattern (49 bp):
ATAAATAGTGATAAGAGTGTAGACAGTGAAAGACCAAGTTTAGAAATGT
Found at i:39623244 original size:19 final size:19
Alignment explanation
Indices: 39623202--39623252 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
39623192 AAATTACAAA
39623202 AAAAATTCAAAATAATTTTT
1 AAAAATTCAAAAT-ATTTTT
39623222 -AAAATTCAAAAT-TTTTAT
1 AAAAATTCAAAATATTTT-T
39623240 AAAAATTCTAAAA
1 AAAAATTC-AAAA
39623253 AATATATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 4 0.14
18 1 0.04
19 19 0.68
20 4 0.14
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATATTTTT
Found at i:39627617 original size:11 final size:11
Alignment explanation
Indices: 39627603--39627638 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
39627593 AATAGTATTG
39627603 AAATAGTGCCC
1 AAATAGTGCCC
39627614 AAATAGTGCCC
1 AAATAGTGCCC
*
39627625 AAATAGTACCC
1 AAATAGTGCCC
39627636 AAA
1 AAA
39627639 CATGAAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.44, C:0.25, G:0.14, T:0.17
Consensus pattern (11 bp):
AAATAGTGCCC
Found at i:39632537 original size:54 final size:54
Alignment explanation
Indices: 39632479--39632586 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
39632469 ACACAAAATG
39632479 TTCACTTAACTAGAACTAATTTAAAATGTTCAATATGATCATTTATAAAGAAAA
1 TTCACTTAACTAGAACTAATTTAAAATGTTCAATATGATCATTTATAAAGAAAA
* *
39632533 TTCACTTATCTAGAACTAATTTAACATGTTCAATATGATCATTTATAAAGAAAA
1 TTCACTTAACTAGAACTAATTTAAAATGTTCAATATGATCATTTATAAAGAAAA
39632587 ATATTATCAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.36
Consensus pattern (54 bp):
TTCACTTAACTAGAACTAATTTAAAATGTTCAATATGATCATTTATAAAGAAAA
Found at i:39634528 original size:20 final size:20
Alignment explanation
Indices: 39634487--39634530 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
39634477 AATGAAGTGC
* *
39634487 AAATGATTTTAACCAAATTA
1 AAATGATTTTAAACAAAGTA
39634507 AAATGATTTTCAAAC-AAGTA
1 AAATGATTTT-AAACAAAGTA
39634527 AAAT
1 AAAT
39634531 TTGCTCTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.32
Consensus pattern (20 bp):
AAATGATTTTAAACAAAGTA
Found at i:39649207 original size:7 final size:7
Alignment explanation
Indices: 39649197--39649222 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
39649187 TGTATTTTGT
39649197 ATTTTCC
1 ATTTTCC
39649204 ATTTTCC
1 ATTTTCC
39649211 ATTTTCC
1 ATTTTCC
39649218 ATTTT
1 ATTTT
39649223 GGGAATGGCC
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:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (7 bp):
ATTTTCC
Found at i:39649207 original size:14 final size:14
Alignment explanation
Indices: 39649190--39649223 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
39649180 ATTATTTTGT
*
39649190 ATTTTGTATTTTCC
1 ATTTTGCATTTTCC
*
39649204 ATTTTCCATTTTCC
1 ATTTTGCATTTTCC
39649218 ATTTTG
1 ATTTTG
39649224 GGAATGGCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.15, C:0.18, G:0.06, T:0.62
Consensus pattern (14 bp):
ATTTTGCATTTTCC
Found at i:39652379 original size:16 final size:16
Alignment explanation
Indices: 39652358--39652391 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
39652348 TATAATTTAA
39652358 AATTAATCATT-TAAAC
1 AATTAATC-TTGTAAAC
39652374 AATTAATCTTGTAAAC
1 AATTAATCTTGTAAAC
39652390 AA
1 AA
39652392 CAGGTTGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 15 0.88
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (16 bp):
AATTAATCTTGTAAAC
Found at i:39654336 original size:28 final size:28
Alignment explanation
Indices: 39654296--39654349 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
39654286 TAAAAACTTT
39654296 TGTTCAATCATAAGTAAACATGATATAA
1 TGTTCAATCATAAGTAAACATGATATAA
39654324 TGTTCAATCATAAGTAAACATGATAT
1 TGTTCAATCATAAGTAAACATGATAT
39654350 TAACTTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (28 bp):
TGTTCAATCATAAGTAAACATGATATAA
Found at i:39664709 original size:23 final size:23
Alignment explanation
Indices: 39664640--39664709 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
39664630 TCATTAACAT
*
39664640 TGTTTGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* **
39664664 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCAATTAA
*
39664687 TGTTCGTGAACATATTCAATTAA
1 TGTTCGTGAACATGTTCAATTAA
39664710 GTTAAATGAA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:39668497 original size:18 final size:18
Alignment explanation
Indices: 39668460--39668497 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
39668450 TTGTGAGGGG
* *
39668460 GATATGGGAAGTGAGGAA
1 GATATGGGAAGTCAGAAA
39668478 GATATGGGAAGTCAGAAA
1 GATATGGGAAGTCAGAAA
39668496 GA
1 GA
39668498 ATCATGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.39, T:0.16
Consensus pattern (18 bp):
GATATGGGAAGTCAGAAA
Found at i:39672196 original size:14 final size:14
Alignment explanation
Indices: 39672177--39672205 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39672167 GTCCAAGTTA
39672177 CAAAAATCGCCATT
1 CAAAAATCGCCATT
39672191 CAAAAATCGCCATT
1 CAAAAATCGCCATT
39672205 C
1 C
39672206 GGGCGAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.31, G:0.07, T:0.21
Consensus pattern (14 bp):
CAAAAATCGCCATT
Found at i:39677045 original size:33 final size:33
Alignment explanation
Indices: 39677003--39677073 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
39676993 ACCTATATTC
* *
39677003 CAGTCACATAGGTCTCCTTCACTTGCCT-CACAA
1 CAGTCACATAGGTCCCCTTCACCTG-CTACACAA
*
39677036 CAGTCACATATGTCCCCTTCACCTGCTACACAA
1 CAGTCACATAGGTCCCCTTCACCTGCTACACAA
39677069 CAGTC
1 CAGTC
39677074 CTCCTCACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 2 0.06
33 32 0.94
ACGTcount: A:0.25, C:0.38, G:0.11, T:0.25
Consensus pattern (33 bp):
CAGTCACATAGGTCCCCTTCACCTGCTACACAA
Found at i:39686628 original size:21 final size:21
Alignment explanation
Indices: 39686604--39686659 Score: 51
Period size: 24 Copynumber: 2.5 Consensus size: 21
39686594 GATCAAAGCT
39686604 AAAGAGAAAGTAGAAAAGA-AA
1 AAAGAGAAAGTA-AAAAGACAA
*
39686625 AAAGTAGCAGAAGTAAAGAGACAA
1 AAAG-AG-A-AAGTAAAAAGACAA
*
39686649 AAAGAAAAAGT
1 AAAGAGAAAGT
39686660 CTTGGAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
21 8 0.28
22 3 0.10
23 7 0.24
24 11 0.38
ACGTcount: A:0.66, C:0.04, G:0.23, T:0.07
Consensus pattern (21 bp):
AAAGAGAAAGTAAAAAGACAA
Found at i:39689257 original size:36 final size:36
Alignment explanation
Indices: 39689175--39689258 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 36
39689165 ATACTGTCTG
* * * * *
39689175 TTTGATGTATTTCGGTTGGAGTAGCTCTTATGAGCA
1 TTTGGTGTGTTTCAGTTGGACTAACTCTTATGAGCA
* *
39689211 ATT-GTCGTGTTTCAGTTGGACTAACTCTTGTGAGCA
1 TTTGGT-GTGTTTCAGTTGGACTAACTCTTATGAGCA
39689247 TTTGGTGTGTTT
1 TTTGGTGTGTTT
39689259 TGGAGGGATT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
35 1 0.03
36 35 0.92
37 2 0.05
ACGTcount: A:0.17, C:0.12, G:0.27, T:0.44
Consensus pattern (36 bp):
TTTGGTGTGTTTCAGTTGGACTAACTCTTATGAGCA
Found at i:39690608 original size:15 final size:16
Alignment explanation
Indices: 39690590--39690632 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 16
39690580 AAATAAGATC
39690590 AATATA-CATAATAAA
1 AATATATCATAATAAA
39690605 AATA-ATCAT-ATAAA
1 AATATATCATAATAAA
39690619 AA-ATATCA-AATAAA
1 AATATATCATAATAAA
39690633 TGACAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
13 1 0.04
14 17 0.68
15 7 0.28
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (16 bp):
AATATATCATAATAAA
Found at i:39692601 original size:132 final size:132
Alignment explanation
Indices: 39692437--39693263 Score: 1366
Period size: 132 Copynumber: 6.3 Consensus size: 132
39692427 TTGTAGCTTT
* * * *
39692437 AACCTTCTCCACCGCTACTCAGGGAGACAAGGCTTGGTGGCTTTAATCTGCTTCCCACTATCTTG
1 AACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTG
* **
39692502 GAAGGATAAGATTTTCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCT
66 GAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCT
39692567 TC
131 TC
39692569 AACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTG
1 AACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTG
*
39692634 GAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCT
66 GAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCT
39692699 TC
131 TC
* *
39692701 AACCTTCTCTGCTGCTGCTCAGGGAGACAAGGTTTGGTGGCTTAAATCTGCTTCCCACTATCTTG
1 AACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTG
* * *
39692766 GAAAGATAAGATTCGCCGTCTTAGATCTGCTCCACTACTGCTTAGGGAGATGAGATCTATAATCT
66 GAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCT
39692831 TC
131 TC
*
39692833 AACCTTCTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTG
1 AACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTG
* *
39692898 GAAAGATAAGATTCGCCGTCTTCGATCTACTCCACAACTGCTTAGGGAGATAAGATCTACAATCT
66 GAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCT
39692963 TC
131 TC
*
39692965 AACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTG
1 AACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTG
* * *
39693030 GAAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTACTTAGGGAGATAAGATCTACAATCT
66 GAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCT
39693095 TC
131 TC
* *
39693097 AACCTACTCCGCTGCTGCTCAGGGAGACAAGGTTTGGTGGCTTAAATCTGCTTCCCACTATCTTG
1 AACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTG
** * * * * *
39693162 GAAAGATAAGATTTACCGTCCTCGATCTACTCCACTACTACTTAGGGAGATAAGATCTACGATCG
66 GAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCT
39693227 TC
131 TC
* * *
39693229 AACCTACTTCGCTGTTGCTCAGGGAGACAAGGCTT
1 AACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTT
39693264 AGTGTTTCAC
Statistics
Matches: 658, Mismatches: 37, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 658 1.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (132 bp):
AACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTG
GAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCT
TC
Found at i:39702266 original size:12 final size:12
Alignment explanation
Indices: 39702251--39702284 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
39702241 GGAATAATTG
39702251 AACAAATAAACA
1 AACAAATAAACA
*
39702263 AACAAACAAACA
1 AACAAATAAACA
39702275 AACAAATAAA
1 AACAAATAAA
39702285 TCGACCACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.76, C:0.18, G:0.00, T:0.06
Consensus pattern (12 bp):
AACAAATAAACA
Found at i:39702285 original size:4 final size:4
Alignment explanation
Indices: 39702251--39702280 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
39702241 GGAATAATTG
*
39702251 AACA AATA AACA AACA AACA AACA AACA AA
1 AACA AACA AACA AACA AACA AACA AACA AA
39702281 TAAATCGACC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.77, C:0.20, G:0.00, T:0.03
Consensus pattern (4 bp):
AACA
Found at i:39702490 original size:9 final size:9
Alignment explanation
Indices: 39702476--39702506 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
39702466 TAACATAGTT
39702476 TAAAATAAA
1 TAAAATAAA
39702485 TAAAATAAA
1 TAAAATAAA
39702494 T-AAATAAA
1 TAAAATAAA
39702502 TAAAA
1 TAAAA
39702507 AACACAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
TAAAATAAA
Found at i:39705393 original size:96 final size:96
Alignment explanation
Indices: 39705212--39705398 Score: 250
Period size: 96 Copynumber: 1.9 Consensus size: 96
39705202 CTACACGATG
* * * *
39705212 CTGCTCACACAAGCTATCTAGTATCCGCAACTAATGTCGGACCTCAGCCATCGATAGGACATTCA
1 CTGCTCACACAAGCTATCTAGTATCCACAACTAATGTCGAAACTCAGCCACCGATAGGACATTCA
* *
39705277 AGACCAGCATCAGAACCATGGTAACCTGGGT
66 AGACCAGCACCAGAAACATGGTAACCTGGGT
* * *
39705308 CTGCTTACACAAGCTGT-TGAGTATCCACAACTAATGTCGAAACTCAGCCACCGGTAGGACATTC
1 CTGCTCACACAAGCTATCT-AGTATCCACAACTAATGTCGAAACTCAGCCACCGATAGGACATTC
* * *
39705372 AAGACTAGTACCCGAAACATGGTAACC
65 AAGACCAGCACCAGAAACATGGTAACC
39705399 CTAATGACAT
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
95 1 0.01
96 77 0.99
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (96 bp):
CTGCTCACACAAGCTATCTAGTATCCACAACTAATGTCGAAACTCAGCCACCGATAGGACATTCA
AGACCAGCACCAGAAACATGGTAACCTGGGT
Found at i:39708253 original size:28 final size:28
Alignment explanation
Indices: 39708213--39708273 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
39708203 TTTTACTATT
*
39708213 TTTTACAATATTTTATAATTTCTAATAA
1 TTTTACAACATTTTATAATTTCTAATAA
*
39708241 TTTTACAACATTTTATAATTTCTAATAT
1 TTTTACAACATTTTATAATTTCTAATAA
39708269 TTTTA
1 TTTTA
39708274 TAATTTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTTACAACATTTTATAATTTCTAATAA
Found at i:39708366 original size:23 final size:23
Alignment explanation
Indices: 39708326--39708397 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 23
39708316 TTTAAACAAG
*
39708326 TATATATA-TTATAA-TTTTATT
1 TATATATATTTTTAATTTTTATT
*
39708347 TATATATATTTTTAATTTTTA-A
1 TATATATATTTTTAATTTTTATT
*
39708369 TA-ATAAATTTTATAACTTTTATATT
1 TATATATATTTT-TAA-TTTT-TATT
39708394 TATA
1 TATA
39708398 AAGACTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
21 16 0.40
22 10 0.25
23 9 0.22
24 2 0.05
25 2 0.05
26 1 0.03
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (23 bp):
TATATATATTTTTAATTTTTATT
Found at i:39711134 original size:66 final size:66
Alignment explanation
Indices: 39710991--39711140 Score: 187
Period size: 66 Copynumber: 2.3 Consensus size: 66
39710981 AGCAAATTAC
* * * *
39710991 ACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGC
1 ACAACTTAAAGCAGATGCAACAGCGAGAGAAGCTGAGGCTCAAAAAAGATATGAAGAACTCCAGC
39711056 T
66 T
* * *
39711057 ACAACTGAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGCTCAACGAAAG-TATGAAGAACTCCAG
1 ACAACTTAAAGCAGATGCAACAGCGAGAGAAGCTGAGGCTCAA-AAAAGATATGAAGAACTCCAG
39711121 C-
65 CT
* *
39711122 AGTAGCTTAAAGCAGATGC
1 A-CAACTTAAAGCAGATGC
39711141 GGNNNNNNNN
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
65 1 0.01
66 67 0.93
67 4 0.06
ACGTcount: A:0.41, C:0.19, G:0.26, T:0.14
Consensus pattern (66 bp):
ACAACTTAAAGCAGATGCAACAGCGAGAGAAGCTGAGGCTCAAAAAAGATATGAAGAACTCCAGC
T
Found at i:39711802 original size:43 final size:43
Alignment explanation
Indices: 39711692--39711807 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 43
39711682 NNNNNNNNNN
* *
39711692 TATAGATCAGGGTCTATTGCGGCGTTTGAGGGGAAAGCGCCGC
1 TATAGATCAAGGTCTATTGCGGCGTTTGAGGGCAAAGCGCCGC
* * * * * *
39711735 TAAAGAT-TAGGTTCT-TTCGTGGCGTTTGTGGTCAAAGTGCCGC
1 TATAGATCAAGG-TCTATT-GCGGCGTTTGAGGGCAAAGCGCCGC
39711778 TATAGATCAAGGTCTATTGCGGCGTTTGAG
1 TATAGATCAAGGTCTATTGCGGCGTTTGAG
39711808 AAAAAAACGC
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
42 4 0.07
43 48 0.84
44 5 0.09
ACGTcount: A:0.21, C:0.16, G:0.33, T:0.30
Consensus pattern (43 bp):
TATAGATCAAGGTCTATTGCGGCGTTTGAGGGCAAAGCGCCGC
Found at i:39711820 original size:43 final size:43
Alignment explanation
Indices: 39711692--39711822 Score: 122
Period size: 43 Copynumber: 3.0 Consensus size: 43
39711682 NNNNNNNNNN
* **
39711692 TATAGATCAGGGTCTATTGCGGCGTTTGAGGGGAAAGCGCCGC
1 TATAGATCAAGGTCTATTGCGGCGTTTGAGGAAAAAGCGCCGC
* * * * ** *
39711735 TAAAGAT-TAGGTTCT-TTCGTGGCGTTTGTGGTCAAAGTGCCGC
1 TATAGATCAAGG-TCTATT-GCGGCGTTTGAGGAAAAAGCGCCGC
* *
39711778 TATAGATCAAGGTCTATTGCGGCGTTTGAGAAAAAAACGCCGC
1 TATAGATCAAGGTCTATTGCGGCGTTTGAGGAAAAAGCGCCGC
39711821 TA
1 TA
39711823 AAGACCCTGA
Statistics
Matches: 67, Mismatches: 17, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
42 4 0.06
43 58 0.87
44 5 0.07
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (43 bp):
TATAGATCAAGGTCTATTGCGGCGTTTGAGGAAAAAGCGCCGC
Found at i:39711843 original size:43 final size:43
Alignment explanation
Indices: 39711796--39711890 Score: 145
Period size: 43 Copynumber: 2.2 Consensus size: 43
39711786 AAGGTCTATT
* *
39711796 GCGGCGTTTGAGAAAAAAACGCCGCTAAAGACCCTGATCTTTA
1 GCGGCGCTTGACAAAAAAACGCCGCTAAAGACCCTGATCTTTA
* **
39711839 GCGGCGCTTGTCCCAAAAACGCCGCTAAAGACCCTGATCTTTA
1 GCGGCGCTTGACAAAAAAACGCCGCTAAAGACCCTGATCTTTA
39711882 GCGGCGCTT
1 GCGGCGCTT
39711891 CCACTAAAGC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.21
Consensus pattern (43 bp):
GCGGCGCTTGACAAAAAAACGCCGCTAAAGACCCTGATCTTTA
Found at i:39714765 original size:18 final size:17
Alignment explanation
Indices: 39714742--39714774 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
39714732 GTTTATTTTA
39714742 AATTTTTTGTACATATT
1 AATTTTTTGTACATATT
39714759 AATTTTTTGTACATAT
1 AATTTTTTGTACATAT
39714775 AAAGTAGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (17 bp):
AATTTTTTGTACATATT
Found at i:39715764 original size:128 final size:127
Alignment explanation
Indices: 39715564--39715808 Score: 368
Period size: 128 Copynumber: 1.9 Consensus size: 127
39715554 TATATTTAAT
** * * **
39715564 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTATTCAAGCGCTGCTAAAGAACATGTTCTTT
1 CGCCGCTAAAGAACATGGCCTTTAGCGGCATTTTTATTCAAGCGCCGCTAAAGAACATGACCTTT
* * *
39715629 AGCGGCGTTTTTATT-CAAGCGCCGCTAAAGAACATGATCTTTAGTGGCGTTTAATTTTAAAG
66 AGAGGCGTTTTT-TTCCAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTAATTTTAAAG
39715691 CGCCGCTAAAGAACATGGCCTTTAGCGGCATTTGGTT-TTCAAGCGCCGCTAAAGAACATGACCT
1 CGCCGCTAAAGAACATGGCCTTTAGCGGCATTT--TTATTCAAGCGCCGCTAAAGAACATGACCT
39715755 TTAGAGGCGTTTTTTTCCAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTT
64 TTAGAGGCGTTTTTTTCCAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTT
39715809 TTATCTGTAA
Statistics
Matches: 106, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
127 32 0.30
128 72 0.68
129 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (127 bp):
CGCCGCTAAAGAACATGGCCTTTAGCGGCATTTTTATTCAAGCGCCGCTAAAGAACATGACCTTT
AGAGGCGTTTTTTTCCAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTAATTTTAAAG
Found at i:39715809 original size:42 final size:41
Alignment explanation
Indices: 39715564--39715810 Score: 332
Period size: 42 Copynumber: 5.9 Consensus size: 41
39715554 TATATTTAAT
**
39715564 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTATTCAAG
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTT-TTCAAG
* **
39715606 CGCTGCTAAAGAACATGTTCTTTAGCGGCGTTTTTATTCAAG
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTT-TTCAAG
* * *
39715648 CGCCGCTAAAGAACATGATCTTTAGTGGCGTTTAATTTTAAAG
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTT--TTTTCAAG
* *
39715691 CGCCGCTAAAGAACATGGCCTTTAGCGGCATTTGGTTTTCAAG
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTT--TTTTCAAG
*
39715734 CGCCGCTAAAGAACATGACCTTTAGAGGCGTTTTTTTCCAAG
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTT-CAAG
39715776 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTT
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTT
39715811 ATCTGTAAAC
Statistics
Matches: 186, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
41 4 0.02
42 109 0.59
43 71 0.38
44 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (41 bp):
CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTCAAG
Found at i:39719984 original size:90 final size:90
Alignment explanation
Indices: 39719831--39720130 Score: 376
Period size: 90 Copynumber: 3.3 Consensus size: 90
39719821 ACTACTATTC
* ** *
39719831 AAAATGTTCGTATTATTTTTGTATCCGTAAATC-AATTTTAGTCCGTATTATTTGTTGGTCGAAT
1 AAAATGTTCGTATTATCTTTGTATATGTAAA-CAAATTTTAGTCCGTATTATTTATTGGTCGAAT
39719895 TTTATATTTTCGTATATCAGTTTTGT
65 TTTATATTTTCGTATATCAGTTTTGT
* * * **
39719921 AAAATGTTTGTATTATCTTTGGATATGTAAA-AATATTTTAGACCGTATTATTTACCGGTCGAAT
1 AAAATGTTCGTATTATCTTTGTATATGTAAACAA-ATTTTAGTCCGTATTATTTATTGGTCGAAT
* *
39719985 TTTATATTTTCGTATATCAATTTTCT
65 TTTATATTTTCGTATATCAGTTTTGT
* *
39720011 AAAATGTTCGTATTATTTTTGTATATGTAAATCAAA-TTTAGTCGGTATTATTTATTGGTCGAAT
1 AAAATGTTCGTATTATCTTTGTATATGTAAA-CAAATTTTAGTCCGTATTATTTATTGGTCGAAT
* *
39720075 TATATATTTTCATATA-CTAGTTTTGT
65 TTTATATTTTCGTATATC-AGTTTTGT
* *
39720101 AGAATGTTCGTATTTTC-TTGTATATGTAAA
1 AAAATGTTCGTATTATCTTTGTATATGTAAA
39720131 TTTTTTTGTT
Statistics
Matches: 180, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
89 15 0.08
90 162 0.90
91 1 0.01
92 2 0.01
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.49
Consensus pattern (90 bp):
AAAATGTTCGTATTATCTTTGTATATGTAAACAAATTTTAGTCCGTATTATTTATTGGTCGAATT
TTATATTTTCGTATATCAGTTTTGT
Found at i:39725874 original size:38 final size:38
Alignment explanation
Indices: 39725795--39725911 Score: 114
Period size: 38 Copynumber: 3.1 Consensus size: 38
39725785 CTGGCACCTG
* * * *
39725795 CTGAAGTCAGCCACTTA-TAGGCCATGGCCTGACACGGC
1 CTGAAGCCAGCCACTTAGT-GGCCAAGGCCTGACATGAC
*
39725833 CTGAAGCCAGCCACTTAGTGGCCAAGGCCTGACATAAC
1 CTGAAGCCAGCCACTTAGTGGCCAAGGCCTGACATGAC
* * *
39725871 CTGAAACCTA-TCATTTAAG-GGCCAAGGCCTGACATGAC
1 CTGAAGCC-AGCCACTT-AGTGGCCAAGGCCTGACATGAC
39725909 CTG
1 CTG
39725912 CAGCTTATCC
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
38 63 0.94
39 4 0.06
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.19
Consensus pattern (38 bp):
CTGAAGCCAGCCACTTAGTGGCCAAGGCCTGACATGAC
Found at i:39726081 original size:18 final size:17
Alignment explanation
Indices: 39726023--39726090 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 17
39726013 TTTATAAAAT
39726023 TTAAATTTATTACTTTAAA
1 TTAAATTTATT--TTTAAA
* *
39726042 TTAATTATTTGTTTTTTCAA
1 TTAA--ATTT-ATTTTTAAA
39726062 TTAAATGTTATTTTTAAA
1 TTAAAT-TTATTTTTAAA
39726080 TTAAATTTATT
1 TTAAATTTATT
39726091 GCATTAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
17 5 0.12
18 15 0.37
19 6 0.15
20 9 0.22
21 4 0.10
22 2 0.05
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (17 bp):
TTAAATTTATTTTTAAA
Found at i:39726127 original size:69 final size:64
Alignment explanation
Indices: 39726042--39726179 Score: 179
Period size: 69 Copynumber: 2.1 Consensus size: 64
39726032 TTACTTTAAA
* * *
39726042 TTAATTATTTGTTTTTTCAATTAAATGT-TATTTTTAAATTAAATTTATTGCATTAAATTGATTT
1 TTAAATATTTATTTTTTCAATTAAAT-TATA-TTTTAAA-T--ATTTATTGCATTAAATTGA-TA
39726106 ATCAT
60 ATCAT
*
39726111 TTAAATATTTATTTTTTCAATTAAATTATATTTTAAATATTTATTGCTTTAAATTGATAATCAT
1 TTAAATATTTATTTTTTCAATTAAATTATATTTTAAATATTTATTGCATTAAATTGATAATCAT
39726175 TTAAA
1 TTAAA
39726180 AGTTATATCT
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
64 11 0.17
65 18 0.28
67 1 0.02
68 8 0.12
69 26 0.41
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (64 bp):
TTAAATATTTATTTTTTCAATTAAATTATATTTTAAATATTTATTGCATTAAATTGATAATCAT
Found at i:39726178 original size:32 final size:32
Alignment explanation
Indices: 39726084--39726179 Score: 106
Period size: 32 Copynumber: 3.0 Consensus size: 32
39726074 TTTAAATTAA
*
39726084 ATTTATTGCATTAAATTGATTTATCATTTAAAT
1 ATTTATTGCTTTAAATTGA-TTATCATTTAAAT
* * *
39726117 ATTTATT-TTTTCAATTAAATTAT-ATTTTAAAT
1 ATTTATTGCTTTAAATT-GATTATCA-TTTAAAT
*
39726149 ATTTATTGCTTTAAATTGATAATCATTTAAA
1 ATTTATTGCTTTAAATTGATTATCATTTAAA
39726180 AGTTATATCT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
31 1 0.02
32 34 0.67
33 16 0.31
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.53
Consensus pattern (32 bp):
ATTTATTGCTTTAAATTGATTATCATTTAAAT
Found at i:39729058 original size:54 final size:53
Alignment explanation
Indices: 39728997--39729158 Score: 195
Period size: 52 Copynumber: 3.1 Consensus size: 53
39728987 CCAGCACATA
39728997 AAATTTTTTTTAAATCTGGTACAAGGGTGCTGGCCATCAATGTCCCAACACCC
1 AAATTTTTTTTAAATCTGGTACAAGGGTGCTGGCCATCAATGTCCCAACACCC
* * * * *
39729050 -AATTTTTTTAAAAAATATGGTACAAGGGTGCTAGCCATCAATGTCCTAGCACCC
1 AAATTTTTTT--TAAATCTGGTACAAGGGTGCTGGCCATCAATGTCCCAACACCC
* * * *
39729104 AAAATTTTTTT-AATCTGGTACAAGGGTG-TCGACCATTAGTGTCCCAACACCC
1 AAATTTTTTTTAAATCTGGTACAAGGGTGCT-GGCCATCAATGTCCCAACACCC
39729156 AAA
1 AAA
39729159 AAAAATATTT
Statistics
Matches: 91, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
51 1 0.01
52 44 0.48
54 38 0.42
55 8 0.09
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (53 bp):
AAATTTTTTTTAAATCTGGTACAAGGGTGCTGGCCATCAATGTCCCAACACCC
Found at i:39729147 original size:52 final size:52
Alignment explanation
Indices: 39728975--39729159 Score: 187
Period size: 54 Copynumber: 3.5 Consensus size: 52
39728965 AGGGGTGCTA
* * **
39728975 ACCATCAGTGTCCCAGCACATAAAATTTTTTTTAAATCTGGTACAAGGGTGCTG
1 ACCATCAATGTCCCAACACCCAAAA-TTTTTTTAAATCTGGTACAAGGGTGC-G
* * *
39729029 GCCATCAATGTCCCAACACCC--AATTTTTTTAAAAAATATGGTACAAGGGTGCT
1 ACCATCAATGTCCCAACACCCAAAATTTTTTT---AAATCTGGTACAAGGGTGCG
* *
39729082 AGCCATCAATGTCCTAGCACCCAAAATTTTTTT-AATCTGGTACAAGGGTGTCG
1 A-CCATCAATGTCCCAACACCCAAAATTTTTTTAAATCTGGTACAAGGGTG-CG
* *
39729135 ACCATTAGTGTCCCAACACCCAAAA
1 ACCATCAATGTCCCAACACCCAAAA
39729160 AAAATATTTT
Statistics
Matches: 108, Mismatches: 16, Indels: 16
0.77 0.11 0.11
Matches are distributed among these distances:
51 7 0.06
52 38 0.35
53 2 0.02
54 52 0.48
56 9 0.08
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (52 bp):
ACCATCAATGTCCCAACACCCAAAATTTTTTTAAATCTGGTACAAGGGTGCG
Found at i:39729879 original size:21 final size:21
Alignment explanation
Indices: 39729843--39729882 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
39729833 GTAGAATTGT
39729843 AGAAATATGTTGTTTTTTTTG
1 AGAAATATGTTGTTTTTTTTG
39729864 AGAAAGTATGTT-TTTTTTT
1 AGAAA-TATGTTGTTTTTTT
39729883 AAATTTACCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.25, C:0.00, G:0.17, T:0.57
Consensus pattern (21 bp):
AGAAATATGTTGTTTTTTTTG
Found at i:39730223 original size:16 final size:15
Alignment explanation
Indices: 39730180--39730224 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
39730170 ACTCATTCCC
*
39730180 CAATCCT-AAATTCT
1 CAATCCTCAAATTTT
39730194 CAATCCTC-AATTTT
1 CAATCCTCAAATTTT
39730208 CAATCCTCCAAATTTT
1 CAATCCT-CAAATTTT
39730224 C
1 C
39730225 GGGTTTAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 19 0.70
15 1 0.04
16 7 0.26
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (15 bp):
CAATCCTCAAATTTT
Found at i:39731835 original size:20 final size:20
Alignment explanation
Indices: 39731810--39731848 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
39731800 ATTTGATTTG
*
39731810 TTAAAATCATTTTAACTTGT
1 TTAAAATAATTTTAACTTGT
39731830 TTAAAATAATTTTAACTTG
1 TTAAAATAATTTTAACTTG
39731849 ATTTTAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (20 bp):
TTAAAATAATTTTAACTTGT
Found at i:39732003 original size:23 final size:22
Alignment explanation
Indices: 39731953--39732003 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
39731943 ATTTTGTTCA
39731953 ATTTTAATTTTCATTCAAAAAC
1 ATTTTAATTTTCATTCAAAAAC
* *
39731975 ACTTTAATTTGTTATATC-AAAAC
1 ATTTTAATTT-TCAT-TCAAAAAC
39731998 ATTTTA
1 ATTTTA
39732004 TCAAATAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 9 0.38
23 13 0.54
24 2 0.08
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (22 bp):
ATTTTAATTTTCATTCAAAAAC
Found at i:39732341 original size:43 final size:43
Alignment explanation
Indices: 39732293--39732378 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
39732283 GGAGATAAGT
39732293 GGTCAGTTCAACATAATAAATAGATAAGAGTGAATGAGAAATG
1 GGTCAGTTCAACATAATAAATAGATAAGAGTGAATGAGAAATG
39732336 GGTCAGTTCAACATAATAAATAGATAAGAGTGAATGAGAAATG
1 GGTCAGTTCAACATAATAAATAGATAAGAGTGAATGAGAAATG
39732379 AACTAAAACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.47, C:0.07, G:0.23, T:0.23
Consensus pattern (43 bp):
GGTCAGTTCAACATAATAAATAGATAAGAGTGAATGAGAAATG
Found at i:39732748 original size:18 final size:18
Alignment explanation
Indices: 39732725--39732761 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
39732715 TGAAGCCGGA
*
39732725 GAAGGAACATGTTTGGGT
1 GAAGGAACATGCTTGGGT
39732743 GAAGGAACATGCTTGGGT
1 GAAGGAACATGCTTGGGT
39732761 G
1 G
39732762 TCAGAAAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.08, G:0.41, T:0.24
Consensus pattern (18 bp):
GAAGGAACATGCTTGGGT
Found at i:39742898 original size:12 final size:12
Alignment explanation
Indices: 39742883--39742910 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
39742873 ATGAACTTGA
39742883 CAAAGAACAATT
1 CAAAGAACAATT
39742895 CAAAGAACAATT
1 CAAAGAACAATT
39742907 CAAA
1 CAAA
39742911 AAATAAACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.18, G:0.07, T:0.14
Consensus pattern (12 bp):
CAAAGAACAATT
Found at i:39752451 original size:22 final size:22
Alignment explanation
Indices: 39752432--39752510 Score: 113
Period size: 22 Copynumber: 3.6 Consensus size: 22
39752422 CATTCATGTT
**
39752432 TAACGTACTAAGCTCTCATGTT
1 TAACGTACTAAGCTCTCATGGC
* * *
39752454 TAACGAACTAAACCCTCATGGC
1 TAACGTACTAAGCTCTCATGGC
39752476 TAACGTACTAAGCTCTCATGGC
1 TAACGTACTAAGCTCTCATGGC
39752498 TAACGTACTAAGC
1 TAACGTACTAAGC
39752511 AATCACTTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.27
Consensus pattern (22 bp):
TAACGTACTAAGCTCTCATGGC
Found at i:39755791 original size:17 final size:16
Alignment explanation
Indices: 39755758--39755794 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
39755748 TAGTCGTTTG
39755758 TTTATTTTTTTTCTTA
1 TTTATTTTTTTTCTTA
*
39755774 TTTATTTATTTTTGTTA
1 TTTATTT-TTTTTCTTA
39755791 TTTA
1 TTTA
39755795 AATTCTCTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (16 bp):
TTTATTTTTTTTCTTA
Found at i:39756532 original size:21 final size:21
Alignment explanation
Indices: 39756485--39756532 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
39756475 AATTTAATTT
*
39756485 TTTTTTCTTTTATGTTCTTTA
1 TTTTTCCTTTTATGTTCTTTA
**
39756506 ACTTTCCTTTT-TGTTTCTTTA
1 TTTTTCCTTTTATG-TTCTTTA
39756527 TTTTTC
1 TTTTTC
39756533 ATGCTCTTCT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.08, C:0.15, G:0.04, T:0.73
Consensus pattern (21 bp):
TTTTTCCTTTTATGTTCTTTA
Found at i:39757901 original size:19 final size:20
Alignment explanation
Indices: 39757879--39757920 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
39757869 TAGCGAAATG
* *
39757879 ATAGTAAAACAAAGA-AAAA
1 ATAGTAAAAAAAAAACAAAA
39757898 ATAGTAAAAAAAAAACAAAA
1 ATAGTAAAAAAAAAACAAAA
39757918 ATA
1 ATA
39757921 TTTTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.12
Consensus pattern (20 bp):
ATAGTAAAAAAAAAACAAAA
Found at i:39763839 original size:19 final size:20
Alignment explanation
Indices: 39763815--39763860 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
39763805 TGTTATATTT
* *
39763815 TGATTAATTAAG-TAAAATA
1 TGATTAATTAAGAAAAAACA
39763834 TGATTAATTAAGAAAAAACA
1 TGATTAATTAAGAAAAAACA
39763854 TGATTAA
1 TGATTAA
39763861 ATAATTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.33
Consensus pattern (20 bp):
TGATTAATTAAGAAAAAACA
Found at i:39772251 original size:13 final size:13
Alignment explanation
Indices: 39772233--39772259 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39772223 TTGTTTCAAA
39772233 GAATGTTTTTTAT
1 GAATGTTTTTTAT
39772246 GAATGTTTTTTAT
1 GAATGTTTTTTAT
39772259 G
1 G
39772260 TCCTTCATTT
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:0.22, C:0.00, G:0.19, T:0.59
Consensus pattern (13 bp):
GAATGTTTTTTAT
Found at i:39775059 original size:4 final size:4
Alignment explanation
Indices: 39775050--39775077 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
39775040 TTTGACTAAA
39775050 TGAT TGAT TGAT TGAT TGAT TGAT TGAT
1 TGAT TGAT TGAT TGAT TGAT TGAT TGAT
39775078 ATTGTCATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGAT
Found at i:39787943 original size:47 final size:46
Alignment explanation
Indices: 39787881--39788032 Score: 207
Period size: 47 Copynumber: 3.2 Consensus size: 46
39787871 GGAAGAAGTG
* * *
39787881 GTTTATCTACAAAAGTGGTAGCTTGTTCACAATTTTATAAAGTGGTA
1 GTTTATCTGCAAAAGTGGT-GCTTGTCCACAATTTTATTAAGTGGTA
*
39787928 GTTTTTCTGCAAAAGTGGTGGCTTGTCCACAATTTTATTAAGTGGTA
1 GTTTATCTGCAAAAGTGGT-GCTTGTCCACAATTTTATTAAGTGGTA
* *
39787975 GTTTATCTGAAAAAGTGGTGATTTGTCCAC-ATTATTATTAAGTGGTA
1 GTTTATCTGCAAAAGTGGTG-CTTGTCCACAATT-TTATTAAGTGGTA
39788022 GTTTATCTGCA
1 GTTTATCTGCA
39788033 TTACTGTTAC
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
46 4 0.04
47 90 0.96
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (46 bp):
GTTTATCTGCAAAAGTGGTGCTTGTCCACAATTTTATTAAGTGGTA
Found at i:39792486 original size:47 final size:47
Alignment explanation
Indices: 39792417--39792670 Score: 348
Period size: 47 Copynumber: 5.4 Consensus size: 47
39792407 ACGGAGGAAG
* * * *
39792417 AAGTGGCAGTTTATCTACAAAAGTGGTAGCTTGTCCAGAATATTATA
1 AAGTGGCAGTTTATCTGCAAAAGTGGTGGCTTGTCCACAATTTTATA
* *
39792464 AAGTGACAGTTTATCTGCAAAAGTGGTGACTTGTCCACAATTTTATTA
1 AAGTGGCAGTTTATCTGCAAAAGTGGTGGCTTGTCCACAATTTTA-TA
* * *
39792512 AA-TGGCAGTTTATTTGCAAAAGTGGGGGCTTGTCCACCATTTTATA
1 AAGTGGCAGTTTATCTGCAAAAGTGGTGGCTTGTCCACAATTTTATA
* * *
39792558 AAGTGGCAGTTTATTTGCAAAAGTGGTGGCTTGTCCACAATTTTTTT
1 AAGTGGCAGTTTATCTGCAAAAGTGGTGGCTTGTCCACAATTTTATA
* * * *
39792605 AAGTGGCAGTTTATTTGTAAAAGTGGTGGCTTGTCCACAATATTATT
1 AAGTGGCAGTTTATCTGCAAAAGTGGTGGCTTGTCCACAATTTTATA
39792652 AAGTGGCAGTTTATCTGCA
1 AAGTGGCAGTTTATCTGCA
39792671 TTATTGTGAC
Statistics
Matches: 185, Mismatches: 20, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
46 4 0.02
47 177 0.96
48 4 0.02
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.36
Consensus pattern (47 bp):
AAGTGGCAGTTTATCTGCAAAAGTGGTGGCTTGTCCACAATTTTATA
Found at i:39795973 original size:7 final size:7
Alignment explanation
Indices: 39795961--39795990 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
39795951 AATACCATCA
39795961 ATATGTG
1 ATATGTG
39795968 ATATGTG
1 ATATGTG
*
39795975 ATTTGTG
1 ATATGTG
39795982 ATATGTG
1 ATATGTG
39795989 AT
1 AT
39795991 GATGAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.47
Consensus pattern (7 bp):
ATATGTG
Found at i:39805105 original size:14 final size:14
Alignment explanation
Indices: 39805082--39805117 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
39805072 AACTCTCTAA
39805082 AGAAAATTGTAGAG
1 AGAAAATTGTAGAG
*
39805096 AGAAAGTTGTAGAG
1 AGAAAATTGTAGAG
39805110 AGAAAATT
1 AGAAAATT
39805118 CTCTAAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.28, T:0.22
Consensus pattern (14 bp):
AGAAAATTGTAGAG
Found at i:39807966 original size:11 final size:11
Alignment explanation
Indices: 39807942--39807990 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
39807932 AACTAATCCT
39807942 CTCTCAATTTTC
1 CTCTCAA-TTTC
*
39807954 CTTTCAATTTC
1 CTCTCAATTTC
*
39807965 CTCTAAATTTC
1 CTCTCAATTTC
*
39807976 CTCTCAATTTG
1 CTCTCAATTTC
39807987 CTCT
1 CTCT
39807991 TAAATTCCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 26 0.81
12 6 0.19
ACGTcount: A:0.18, C:0.31, G:0.02, T:0.49
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:39807982 original size:22 final size:23
Alignment explanation
Indices: 39807950--39807996 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
39807940 CTCTCTCAAT
*
39807950 TTTCCTTTCAATTTCCTC-TAAA
1 TTTCCTCTCAATTTCCTCTTAAA
*
39807972 TTTCCTCTCAATTTGCTCTTAAA
1 TTTCCTCTCAATTTCCTCTTAAA
39807995 TT
1 TT
39807997 CCTTCCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.51
Consensus pattern (23 bp):
TTTCCTCTCAATTTCCTCTTAAA
Found at i:39808058 original size:51 final size:51
Alignment explanation
Indices: 39807977--39808076 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
39807967 CTAAATTTCC
*
39807977 TCTCAATTTGCTCTTAAATTCCTTCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTGCTCTCAAATTCCTTCCAAATTTCTCTCAAATCCATATTTAA
* * * *
39808028 TCTCAATTTGCTCTCAAGTTCC-TCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAAATTCCTTC-CAAATTTCTCTCAAATCCATATTT
39808077 TTAAATAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 2 0.05
51 41 0.95
ACGTcount: A:0.26, C:0.26, G:0.03, T:0.45
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAAATTCCTTCCAAATTTCTCTCAAATCCATATTTAA
Found at i:39808091 original size:14 final size:14
Alignment explanation
Indices: 39808074--39808119 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
39808064 TAAATCCCTA
*
39808074 TTTTTAAATAATTT
1 TTTTTAAAAAATTT
* *
39808088 TTTTAAAAAAATTA
1 TTTTTAAAAAATTT
39808102 TTTTTAAAAAATTT
1 TTTTTAAAAAATTT
39808116 TTTT
1 TTTT
39808120 AAACCGTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTTAAAAAATTT
Found at i:39809220 original size:7 final size:7
Alignment explanation
Indices: 39809208--39809233 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
39809198 TAGTCGATTG
39809208 GTATTTA
1 GTATTTA
39809215 GTATTTA
1 GTATTTA
39809222 GTATTTA
1 GTATTTA
39809229 GTATT
1 GTATT
39809234 ATGTATATAA
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:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:39809901 original size:18 final size:18
Alignment explanation
Indices: 39809859--39809901 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
39809849 TGCCAGGTAC
*
39809859 GTTTCCTAACCCTTTTAT
1 GTTTCCTAACCCTTATAT
* *
39809877 ATATCCTAACCCTTATAT
1 GTTTCCTAACCCTTATAT
39809895 GTTTCCT
1 GTTTCCT
39809902 TTTCCGAGTC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.28, G:0.05, T:0.47
Consensus pattern (18 bp):
GTTTCCTAACCCTTATAT
Found at i:39810199 original size:21 final size:21
Alignment explanation
Indices: 39810157--39810201 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
39810147 AAATGCCCTA
*
39810157 CCGGAAGAACCAGAATCCCCG
1 CCGGAAGAACCACAATCCCCG
*
39810178 CCGGAGGAACCACAA-CCGCCG
1 CCGGAAGAACCACAATCC-CCG
39810199 CCG
1 CCG
39810202 AAAGCTGGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.29, C:0.42, G:0.27, T:0.02
Consensus pattern (21 bp):
CCGGAAGAACCACAATCCCCG
Found at i:39810493 original size:27 final size:27
Alignment explanation
Indices: 39810452--39810505 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
39810442 ACAAAACTTA
39810452 AACCCTTAACCT-AAAACCCGTAACCCT
1 AACCCTTAACCTAAAAACCC-TAACCCT
*
39810479 AACCCTTAACTTAAAAACCCTAACCCT
1 AACCCTTAACCTAAAAACCCTAACCCT
39810506 TAAATTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.39, C:0.39, G:0.02, T:0.20
Consensus pattern (27 bp):
AACCCTTAACCTAAAAACCCTAACCCT
Found at i:39810530 original size:22 final size:22
Alignment explanation
Indices: 39810473--39810944 Score: 583
Period size: 22 Copynumber: 22.0 Consensus size: 22
39810463 TAAAACCCGT
39810473 AACCCT-AACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
39810494 AACCCT-AACCCTTAAATTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
39810515 AACCCTAAATCTTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* * *
39810537 AATCATAAACCCTTAACCTAAA
1 AACCCTAAACCCTTAACTTAAA
39810559 AACCCT-AACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
39810580 AACCCTAAATCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
39810602 AACCCT-AACTCCTTTACTTAAA
1 AACCCTAAAC-CCTTAACTTAAA
*
39810624 AACCCTAAACCCTTAAATTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
39810646 AATCCTAAACTCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
39810668 AACCCT-AACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
39810689 AACACTAAACCCTGAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
39810711 AACCCT-AACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
39810732 AACACTAAACCCTTAAATTAAA
1 AACCCTAAACCCTTAACTTAAA
*
39810754 AACCCTAAACCCTTAAATTAAA
1 AACCCTAAACCCTTAACTTAAA
*
39810776 AATCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
39810798 AACCCT-AACCCTTAACTTTAA
1 AACCCTAAACCCTTAACTTAAA
39810819 AACCCTAAA-CCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*** *
39810840 AATTGT-AACCCTTAAATTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
39810861 AACCCTAAACTCTTAACTT-TA
1 AACCCTAAACCCTTAACTTAAA
* * *
39810882 AACCGT-AACCCTTAAATAAAA
1 AACCCTAAACCCTTAACTTAAA
*
39810903 AACCCT-AACACTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
39810924 AACCCT-AACCTTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
39810945 TATAATTTGA
Statistics
Matches: 386, Mismatches: 55, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.03
21 177 0.46
22 195 0.51
23 3 0.01
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.26
Consensus pattern (22 bp):
AACCCTAAACCCTTAACTTAAA
Found at i:39810574 original size:43 final size:43
Alignment explanation
Indices: 39810473--39810944 Score: 596
Period size: 43 Copynumber: 11.0 Consensus size: 43
39810463 TAAAACCCGT
*
39810473 AACCCT-AACCCTTAACTTAAAAACCCTAACCCTTAAATTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * * * *
39810515 AACCCTAAATCTTTAACTTAAAAATCATAAACCCTTAACCTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
*
39810559 AACCCT-AACCCTTAACTTAAAAACCCTAAATCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
* *
39810602 AACCCT-AACTCCTTTACTTAAAAACCCTAAACCCTTAAATTAAA
1 AACCCTAAAC-CCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
* *
39810646 AATCCTAAACTCTTAACTTAAAAACCCTAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* *
39810689 AACACTAAACCCTGAACTTAAAAACCCTAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * *
39810732 AACACTAAACCCTTAAATTAAAAACCCTAAACCCTTAAATTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
* *
39810776 AATCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTTAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
*** *
39810819 AACCCTAAA-CCTTAACTTAAAAATTGTAACCCTTAAATTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * * * *
39810861 AACCCTAAACTCTTAACTT-TAAACCGTAACCCTTAAATAAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* *
39810903 AACCCT-AACACTTAACTTAAAAACCCTAACCTTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
39810945 TATAATTTGA
Statistics
Matches: 375, Mismatches: 48, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
41 11 0.03
42 86 0.23
43 165 0.44
44 110 0.29
45 3 0.01
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.26
Consensus pattern (43 bp):
AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
Found at i:39814513 original size:127 final size:126
Alignment explanation
Indices: 39814076--39814770 Score: 974
Period size: 127 Copynumber: 5.5 Consensus size: 126
39814066 CCCAAACATG
* * * *
39814076 CTACTGTAGCAAAAACGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGG
1 CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * * * *
39814141 TAGAAGCG--ATTTTATACTATTTGCTCAAAAACGTCAAGTCAAAATTATTTTTCCAGGAC
66 TTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* * *
39814200 CTACTGTAGCAAAAGTGCGTCCACGAGGACGCGATTTCACAAATTCTTCTCA-AATAGCATCCTG
1 CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTG
* *
39814264 CTT-ACAGCGTTGTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTT-CAGGAC
65 CTTGA-AGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
*
39814325 CTACTGTAGCAAAAGCGCATCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
39814390 TTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCTA-GAC
66 TTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCC-AGGAC
* * *
39814452 CAACTGTAGCAAAAGCGCATCCACGAGGGCGTGATTTCACAAATTCTTCTCATAAAGCATCCTAC
1 CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
*
39814517 TTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCCTA-GAC
66 TTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCC-AGGAC
* * * *
39814579 CAACTGTAGCAAAAGCGTATCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAACATCCTTC
1 CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
*
39814644 TTGAAGCG-TTTTTTAAACTATTTACTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
66 TTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* * * * * * * * *
39814704 CTACTATAGCAAAAGCGCGTACACGTGGGCGCGACTTCAAAAATCCTTCTGATAAATCATCCTGC
1 CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
39814769 TT
66 TT
39814771 TGATTTTATC
Statistics
Matches: 522, Mismatches: 39, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
123 3 0.01
124 63 0.12
125 174 0.33
126 86 0.16
127 195 0.37
128 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
Found at i:39814542 original size:252 final size:252
Alignment explanation
Indices: 39814076--39814766 Score: 991
Period size: 252 Copynumber: 2.7 Consensus size: 252
39814066 CCCAAACATG
* * *
39814076 CTACTGTAGCAAAAACGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGG
1 CTACTGTAGCAAAAGCGCATCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * * * *
39814141 TAGAAGCG-ATTTTATACTATTTGCTCAAAAACGTCAAGTCAAAATTATTTTTCCAGGACCTACT
66 TTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACT
* * *
39814205 GTAGCAAAAGTGCGTCCACGAGGACGCGATTTCACAAATTCTTCTCA-AATAGCATCCTGCTTAC
131 GTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTACTTAC
* *
39814269 AGCGTTGTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TT-C-AGGAC
195 AGCGTTGTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCCTA-GAC
39814325 CTACTGTAGCAAAAGCGCATCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCATCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
*
39814390 TTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCTA-GACCA
66 TTGAAGCG-TTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCC-AGGACCT
* *
39814454 ACTGTAGCAAAAGCGCATCCACGAGGGCGTGATTTCACAAATTCTTCTCATAAAGCATCCTACTT
128 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTACTT
*
39814519 GA-AGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCCTAGAC
193 -ACAGCGTTGTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCCTAGAC
* * * * *
39814579 CAACTGTAGCAAAAGCGTATCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAACATCCTTC
1 CTACTGTAGCAAAAGCGCATCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
*
39814644 TTGAAGCGTTTTTTAAACTATTTACTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACT
66 TTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACT
* * * * * * * *
39814709 ATAGCAAAAGCGCGTACACGTGGGCGCGACTTCAAAAATCCTTCTGATAAATCATCCT
131 GTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCT
39814767 GCTTTGATTT
Statistics
Matches: 397, Mismatches: 35, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
249 69 0.17
251 38 0.10
252 169 0.43
253 48 0.12
254 72 0.18
255 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.30
Consensus pattern (252 bp):
CTACTGTAGCAAAAGCGCATCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACT
GTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTACTTACA
GCGTTGTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCCTAGAC
Found at i:39814900 original size:9 final size:9
Alignment explanation
Indices: 39814886--39814923 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
39814876 TTTTTTCTCC
39814886 AAAAATCCT
1 AAAAATCCT
*
39814895 AAAAATCTT
1 AAAAATCCT
39814904 AAAAA-CTCT
1 AAAAATC-CT
39814913 AAAAATCCT
1 AAAAATCCT
39814922 AA
1 AA
39814924 CCTGGGAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 1 0.04
9 23 0.92
10 1 0.04
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAAATCCT
Found at i:39816094 original size:19 final size:17
Alignment explanation
Indices: 39816060--39816092 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
39816050 ATTAAATATT
39816060 TTTTTAATCAAATATAC
1 TTTTTAATCAAATATAC
39816077 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
39816093 TATTAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTAATCAAATATAC
Found at i:39816336 original size:15 final size:15
Alignment explanation
Indices: 39816316--39816344 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39816306 AAGATTGTAG
39816316 CTTTAAATTGAATCC
1 CTTTAAATTGAATCC
39816331 CTTTAAATTGAATC
1 CTTTAAATTGAATC
39816345 GAGTTGTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (15 bp):
CTTTAAATTGAATCC
Found at i:39818196 original size:87 final size:87
Alignment explanation
Indices: 39818042--39818201 Score: 198
Period size: 87 Copynumber: 1.8 Consensus size: 87
39818032 ACACTGAGTT
* * *
39818042 GTGGGTAAACCACATAAGTTGCAAGTTAATACGCTGCTAGATAGTTGTGAATGCAAAACATATTT
1 GTGGGTAAACCACATAAGTTGCAAGTTAATACGCTGCCAAATAGTTGTGAATACAAAACATATTT
*
39818107 GCATATAAGAGCTGCTAGATGG
66 GCAAATAAGAGCTGCTAGATGG
* * * * * *
39818129 GTGGGTGAACCACCA-ATGTTGCAAGTTAATACGGTGCCAAATGGTTGTGAATACACAATATGA-
1 GTGGGTAAACCA-CATAAGTTGCAAGTTAATACGCTGCCAAATAGTTGTGAATACAAAACAT-AT
39818192 TTGCAAATAA
64 TTGCAAATAA
39818202 AAGTTGTCGG
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
87 58 0.95
88 3 0.05
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (87 bp):
GTGGGTAAACCACATAAGTTGCAAGTTAATACGCTGCCAAATAGTTGTGAATACAAAACATATTT
GCAAATAAGAGCTGCTAGATGG
Found at i:39819788 original size:20 final size:19
Alignment explanation
Indices: 39819756--39819793 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
39819746 CAAAACCCCT
39819756 TTCCAAACTATACAAGCTTC
1 TTCCAAACTATAC-AGCTTC
39819776 TTCCAAAGC-ATACAGCTT
1 TTCCAAA-CTATACAGCTT
39819794 TTTGGATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 11 0.65
21 1 0.06
ACGTcount: A:0.34, C:0.29, G:0.08, T:0.29
Consensus pattern (19 bp):
TTCCAAACTATACAGCTTC
Found at i:39820865 original size:19 final size:20
Alignment explanation
Indices: 39820833--39820873 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
39820823 TGAGATTCAG
*
39820833 ATATATATTTTTTTGATGGA
1 ATATATATTTTTTTAATGGA
39820853 ATATATA-TTTTTTAATGGA
1 ATATATATTTTTTTAATGGA
39820872 AT
1 AT
39820874 TTTATTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (20 bp):
ATATATATTTTTTTAATGGA
Found at i:39825949 original size:17 final size:18
Alignment explanation
Indices: 39825927--39825960 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39825917 TCATTCGATT
*
39825927 ACAGATCAAAA-TCATAG
1 ACAGATAAAAATTCATAG
39825944 ACAGATAAAAATTCATA
1 ACAGATAAAAATTCATA
39825961 CTGTAGTCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.56, C:0.15, G:0.09, T:0.21
Consensus pattern (18 bp):
ACAGATAAAAATTCATAG
Found at i:39852932 original size:24 final size:24
Alignment explanation
Indices: 39852900--39852950 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
39852890 CTGGTTAAGG
*
39852900 TTCATTGTCCGCTTTTAGGGATCT
1 TTCATTGTCCGCTTCTAGGGATCT
39852924 TTCATTGTCCGCTTCTAGGGATCT
1 TTCATTGTCCGCTTCTAGGGATCT
39852948 TTC
1 TTC
39852951 TTGAATAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.45
Consensus pattern (24 bp):
TTCATTGTCCGCTTCTAGGGATCT
Found at i:39855520 original size:6 final size:6
Alignment explanation
Indices: 39855511--39855535 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
39855501 AAAAAAAAAG
39855511 ACTAAA ACTAAA ACTAAA ACTAAA A
1 ACTAAA ACTAAA ACTAAA ACTAAA A
39855536 AGAAAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
ACTAAA
Found at i:39857245 original size:43 final size:43
Alignment explanation
Indices: 39857184--39857269 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
39857174 TTCGACTAAG
39857184 CTAGTCTAAATTTCAGTTTCATGAAGAACTAGCTTAGGCTTAT
1 CTAGTCTAAATTTCAGTTTCATGAAGAACTAGCTTAGGCTTAT
*
39857227 CTAGTCTAAATTTTAGTTTCATGAAGAACTAGCTTAGGCTTAT
1 CTAGTCTAAATTTCAGTTTCATGAAGAACTAGCTTAGGCTTAT
39857270 GTCTCTGGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.38
Consensus pattern (43 bp):
CTAGTCTAAATTTCAGTTTCATGAAGAACTAGCTTAGGCTTAT
Found at i:39860910 original size:6 final size:6
Alignment explanation
Indices: 39860901--39860938 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
39860891 AACCATAACC
39860901 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TT
1 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TT
39860939 ACATTGTTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTCCT
Found at i:39870031 original size:13 final size:13
Alignment explanation
Indices: 39870013--39870038 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39870003 GGGGTCACAC
39870013 GGCCGTGTGGTCA
1 GGCCGTGTGGTCA
39870026 GGCCGTGTGGTCA
1 GGCCGTGTGGTCA
39870039 AGCCATGTAA
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:0.08, C:0.23, G:0.46, T:0.23
Consensus pattern (13 bp):
GGCCGTGTGGTCA
Found at i:39870592 original size:18 final size:18
Alignment explanation
Indices: 39870571--39870608 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
39870561 CCAAATATAC
39870571 ATTCTAAATCAATCATCA
1 ATTCTAAATCAATCATCA
39870589 ATTCTAAATCAATCATCA
1 ATTCTAAATCAATCATCA
39870607 AT
1 AT
39870609 ATACCTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (18 bp):
ATTCTAAATCAATCATCA
Found at i:39872375 original size:10 final size:10
Alignment explanation
Indices: 39872360--39872391 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
39872350 TTATTTACAA
39872360 AATTAACCTT
1 AATTAACCTT
39872370 AATTAACCTT
1 AATTAACCTT
39872380 AATTAACCTT
1 AATTAACCTT
39872390 AA
1 AA
39872392 AAATTACACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (10 bp):
AATTAACCTT
Found at i:39874413 original size:19 final size:19
Alignment explanation
Indices: 39874389--39874454 Score: 87
Period size: 19 Copynumber: 3.3 Consensus size: 19
39874379 GTAGTAGAAA
39874389 TTTATTTTCTAGAATAAAT
1 TTTATTTTCTAGAATAAAT
*
39874408 TTTATTTTCTGGAATAAAT
1 TTTATTTTCTAGAATAAAT
*
39874427 TCTATTTTCTATGAATAACAAT
1 TTTATTTTCTA-GAAT-A-AAT
39874449 TTTATT
1 TTTATT
39874455 AGTTTCTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 27 0.68
20 4 0.10
21 1 0.03
22 8 0.20
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.53
Consensus pattern (19 bp):
TTTATTTTCTAGAATAAAT
Found at i:39878627 original size:15 final size:15
Alignment explanation
Indices: 39878604--39878633 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39878594 ACGATAACAT
*
39878604 AGGTTAAGACCCATG
1 AGGTAAAGACCCATG
39878619 AGGTAAAGACCCATG
1 AGGTAAAGACCCATG
39878634 GTAGCTTGGT
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:0.37, C:0.20, G:0.27, T:0.17
Consensus pattern (15 bp):
AGGTAAAGACCCATG
Found at i:39878935 original size:48 final size:48
Alignment explanation
Indices: 39878882--39879047 Score: 125
Period size: 56 Copynumber: 3.1 Consensus size: 48
39878872 ACTGAATGAA
*
39878882 TGTATGTAAAACCATGTGGTTAAGACCTATGGAATTATATGAAATGTT
1 TGTATGTAAAACCATGTGGTTAAGACCCATGGAATTATATGAAATGTT
* * **
39878930 TGTATGAATGTATGTAAGACCATGAGGTTAAAACCCATGGCAAGATCTTATATGACTGAATGAA
1 TG--T--ATGTA---AA-ACCATGTGGTTAAGACCCATGG--A-A--TTATATGA---AATGTT
* *
39878994 TGTATGTAAGACCATGTGGTTAAGACCCATGGCATTATATGAAATGTT
1 TGTATGTAAAACCATGTGGTTAAGACCCATGGAATTATATGAAATGTT
39879042 TGTATG
1 TGTATG
39879048 AATGTTCATG
Statistics
Matches: 91, Mismatches: 11, Indels: 32
0.68 0.08 0.24
Matches are distributed among these distances:
48 12 0.13
50 1 0.01
51 8 0.09
52 5 0.05
53 1 0.01
55 2 0.02
56 39 0.43
57 1 0.01
58 1 0.01
59 1 0.01
60 5 0.05
61 8 0.09
62 1 0.01
64 6 0.07
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (48 bp):
TGTATGTAAAACCATGTGGTTAAGACCCATGGAATTATATGAAATGTT
Done.