Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, whole genome shotgun sequence
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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 101 of 113
Found at i:20172842 original size:11 final size:10
Alignment explanation
Indices: 20172797--20172844 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
20172787 GTCATAACTA
*
20172797 TTTTTTCTTC
1 TTTTTTTTTC
* *
20172807 TTTCTCTTCTC
1 TTT-TTTTTTC
20172818 TTTTTTTTTC
1 TTTTTTTTTC
*
20172828 TTTTTTTTTA
1 TTTTTTTTTC
20172838 TTTTTTT
1 TTTTTTT
20172845 GACATGCTCC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
10 24 0.77
11 7 0.23
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:20173687 original size:18 final size:17
Alignment explanation
Indices: 20173673--20173717 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
20173663 TTTTTTTCTT
20173673 CTTTTTTTGTTTTTTCC
1 CTTTTTTTGTTTTTTCC
*
20173690 CTTTTTTTTGCCTTATTTCC
1 C-TTTTTTTG--TTTTTTCC
20173710 CTTTTTTT
1 CTTTTTTT
20173718 CAGAATACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 1 0.04
18 8 0.33
19 7 0.29
20 8 0.33
ACGTcount: A:0.02, C:0.20, G:0.04, T:0.73
Consensus pattern (17 bp):
CTTTTTTTGTTTTTTCC
Found at i:20173696 original size:19 final size:19
Alignment explanation
Indices: 20173674--20173717 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
20173664 TTTTTTCTTC
*
20173674 TTTTTTTG-TTTTTTCCCT
1 TTTTTTTGCTTATTTCCCT
20173692 TTTTTTTGCCTTATTTCCCT
1 TTTTTTTG-CTTATTTCCCT
20173712 TTTTTT
1 TTTTTT
20173718 CAGAATACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
20 15 0.65
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (19 bp):
TTTTTTTGCTTATTTCCCT
Found at i:20177327 original size:201 final size:199
Alignment explanation
Indices: 20176981--20177483 Score: 618
Period size: 200 Copynumber: 2.5 Consensus size: 199
20176971 TGAGAACTCC
* * *
20176981 ATGAAAAAAAGTCATTAAAAGTTATAATCGTCATAAAATAAATGATAAAATTGATATATTAGTGA
1 ATGAAAAAAAGTCATTAAAGGCTATAATCGTCACAAAATAAATGATAAAATTGATATATTAGTGA
* * * * * * **
20177046 TAAAAGGTAAATCGTCACGATATTGGTGACATAATTATTATCATAAATGATTATAAGATAATGTC
66 TGAAAGGTAAATCATCAAG-TATTGGTGACACAATTATCATCACAAATGATTATAAGATAACATC
* * * **
20177111 AAATGAGACAATAAAATCAAATGTTACCTTATTCTTTTTTTTTTGTGACGA-TAGTTTTTGTCAG
130 AAATCAGACAATAAAATCAAATGTTACCTTATGCTTTATTTTTTGTGAC-ATTAGTTTTCATCAG
20177175 CTATTT
194 CTATTT
* * *
20177181 ATGAAAAAAAATCATTGAAGGCTATAATCGTCACAAAATAAATGATAAAATCTTATATATTAGTG
1 ATGAAAAAAAGTCATTAAAGGCTATAATCGTCACAAAATAAATGATAAAAT-TGATATATTAGTG
* * *
20177246 ATGTAAGGTAAATCATCATAGTATTGGTGATACAATTATCATCACAAATGATTGTAAGATAACAT
65 ATGAAAGGTAAATCATCA-AGTATTGGTGACACAATTATCATCACAAATGATTATAAGATAACAT
* * **
20177311 CAAA-CATGATAATAAAATCAAATGTTACGTTATGCTTTATTTTTTGTGACATTAGTTTTCATTG
129 CAAATCA-GACAATAAAATCAAATGTTACCTTATGCTTTATTTTTTGTGACATTAGTTTTCATCA
20177375 GCTATTT
193 GCTATTT
* * *
20177382 ATG-AAAAAAGTCATTAAAGGCTATGATCATCACAAAATAAATTATAAAATATGATATATTAGTG
1 ATGAAAAAAAGTCATTAAAGGCTATAATCGTCACAAAATAAATGATAAAAT-TGATATATTAGTG
* * *
20177446 ATGGAAA-GTAAATCTTTACAGTATTGGTGACATAATTA
65 AT-GAAAGGTAAATCATCA-AGTATTGGTGACACAATTA
20177484 ACGTCATTAA
Statistics
Matches: 259, Mismatches: 39, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
200 130 0.50
201 128 0.49
202 1 0.00
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (199 bp):
ATGAAAAAAAGTCATTAAAGGCTATAATCGTCACAAAATAAATGATAAAATTGATATATTAGTGA
TGAAAGGTAAATCATCAAGTATTGGTGACACAATTATCATCACAAATGATTATAAGATAACATCA
AATCAGACAATAAAATCAAATGTTACCTTATGCTTTATTTTTTGTGACATTAGTTTTCATCAGCT
ATTT
Found at i:20180933 original size:9 final size:8
Alignment explanation
Indices: 20180902--20180939 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
20180892 TTAACAAAAA
20180902 TTTTAAA-
1 TTTTAAAT
*
20180909 TTTGAAAT
1 TTTTAAAT
20180917 TTTTAAAT
1 TTTTAAAT
*
20180925 TTTTAAAA
1 TTTTAAAT
20180933 TTTTAAA
1 TTTTAAA
20180940 CAAAATGTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (8 bp):
TTTTAAAT
Found at i:20181736 original size:17 final size:17
Alignment explanation
Indices: 20181716--20181762 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
20181706 TTAAGATTAT
20181716 TTTTTATTTACAAAAAA
1 TTTTTATTTACAAAAAA
20181733 TTTTT-TTTA-ACAAAAA
1 TTTTTATTTACA-AAAAA
* *
20181749 TTTTAAATTACAAA
1 TTTTTATTTACAAA
20181763 TTTTTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 1 0.04
16 13 0.52
17 10 0.40
18 1 0.04
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTTTATTTACAAAAAA
Found at i:20182782 original size:235 final size:235
Alignment explanation
Indices: 20182242--20182908 Score: 706
Period size: 235 Copynumber: 2.8 Consensus size: 235
20182232 CCACCAAATT
* * * ** *
20182242 GTTTGTGATATTTATGTTATCGTTATATAACATCATATATTGGCATGATGAAATTGCAATGTCAT
1 GTTTGTGACATTTATGTTATCGTTATATAACACCATATATTGACATGACAAAATTGC-ATATCAT
* * * * *
20182307 TAATAATTAACTCAAGTGTTCAATTTGTGACAAAAATTAATAATGTCACCTAAAATCTATTAGAA
65 TAATAA-TAACTAAAGTGTTCAATTTGTAACAAAAATTAATAACGTCATCTAAAATCTATCA-AA
* * *
20182372 AAAATTCGA-CGCAT--ATAAAATTTTAAATTGGTAACAAAATTATAAAGTCATCTAAAATTAAA
128 AAAATTC-ATC-CATAGATAAAATTTTAAATTGATGACAAAATTATAAAGTCACCTAAAATT-AA
*
20182434 AAAAAATCACAAAAAATTTTTCCACCAAATAAATTTAAAGGTAAAA
190 AAAAAATCACAAAAAAATTTTCCACCAAATAAATTTAAAGGTAAAA
* *** * * * *
20182480 -TTTGGCGACATTTATGTTATCACCACATAACACCATACATTAACATGACAAAATTGCAAAGTCA
1 GTTT-GTGACATTTATGTTATCGTTATATAACACCATATATTGACATGACAAAATTGCATA-TCA
20182544 TTAATAGATAACTAAAGTGTTCAATTTGTAACAAAAATTAATAACGTCATCTAAAATCTATCAAA
64 TTAATA-ATAACTAAAGTGTTCAATTTGTAACAAAAATTAATAACGTCATCTAAAATCTATCAAA
* *
20182609 AAAATTC-TCCATAGATAAAATTTTAAATCGATGACAAAATTATAACA-TCACCTAAAGTT-AAA
128 AAAATTCATCCATAGATAAAATTTTAAATTGATGACAAAATTATAA-AGTCACCTAAAATTAAAA
** * * ***
20182671 AACGTCACAAAAAAATTTTCCACTAAATGAATTTGGTGGTAAAA
192 AAAATCACAAAAAAATTTTCCACCAAATAAATTTAAAGGTAAAA
* * * * *
20182715 GTTTATGACATTTATGTTGTCGTTGTATAGCACCATATATTGACATAACAAAATTGCAGTATCAT
1 GTTTGTGACATTTATGTTATCGTTATATAACACCATATATTGACATGACAAAATTGCA-TATCAT
* * * * * *
20182780 TAATACTTAATTAAAGTGTTTAATTTGTAATAAAACTTAATAACGTCATCTAAAATTTATCAAAA
65 TAATA-ATAACTAAAGTGTTCAATTTGTAACAAAAATTAATAACGTCATCTAAAATCTATC-AAA
* * * * **
20182845 AAAATTCAT-CATAGAT-AAATTTTAGATTGTTGATAAAATTATAATGTCAAATAAAA-TAAAAA
128 AAAATTCATCCATAGATAAAATTTTAAATTGATGACAAAATTATAAAGTCACCTAAAATTAAAAA
20182907 AA
193 AA
20182909 TGTTAAAAAA
Statistics
Matches: 355, Mismatches: 61, Indels: 29
0.80 0.14 0.07
Matches are distributed among these distances:
234 1 0.00
235 178 0.50
236 22 0.06
237 52 0.15
238 101 0.28
239 1 0.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (235 bp):
GTTTGTGACATTTATGTTATCGTTATATAACACCATATATTGACATGACAAAATTGCATATCATT
AATAATAACTAAAGTGTTCAATTTGTAACAAAAATTAATAACGTCATCTAAAATCTATCAAAAAA
ATTCATCCATAGATAAAATTTTAAATTGATGACAAAATTATAAAGTCACCTAAAATTAAAAAAAA
TCACAAAAAAATTTTCCACCAAATAAATTTAAAGGTAAAA
Found at i:20184478 original size:102 final size:102
Alignment explanation
Indices: 20184352--20184542 Score: 267
Period size: 102 Copynumber: 1.9 Consensus size: 102
20184342 TTACTTTGAG
* * * * * *
20184352 AAAATTCATTAAATCTTCTAATAGTTTGGTAAGATTTAATTTAAGATTTTGATT-CTCTAATAGT
1 AAAATTCATTAAATCCTCCAATAGTTTGGTAAGACTTAATTCAAGA-TTTAATTCCTCCAATAGT
*
20184416 GTGGTAGGGTTAAAAATGTATTATTTTATTTTATTTAA
65 GTGGTAGGATTAAAAATGTATTATTTTATTTTATTTAA
* *
20184454 AAAATTCATTAAGTCCTCCAATAGTTTGGTAAGACTTAATTCAAGATTTAATTCCTCCAATAGTT
1 AAAATTCATTAAATCCTCCAATAGTTTGGTAAGACTTAATTCAAGATTTAATTCCTCCAATAGTG
* *
20184519 TGGTAGGATTTAAAATTTATTATT
66 TGGTAGGATTAAAAATGTATTATT
20184543 AAAAAAATTA
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
101 6 0.08
102 71 0.92
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.44
Consensus pattern (102 bp):
AAAATTCATTAAATCCTCCAATAGTTTGGTAAGACTTAATTCAAGATTTAATTCCTCCAATAGTG
TGGTAGGATTAAAAATGTATTATTTTATTTTATTTAA
Found at i:20187214 original size:20 final size:19
Alignment explanation
Indices: 20187148--20187214 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 19
20187138 TTTTCTCTTC
* *
20187148 TTATTTTTTTTAATTTTTAA
1 TTATTATTTTAAATTTTT-A
*
20187168 TTAATT-TTTTAAATTATTA
1 TT-ATTATTTTAAATTTTTA
20187187 -TATATATTTTAAATATTTTA
1 TTAT-TATTTTAAAT-TTTTA
20187207 TTATTATT
1 TTATTATT
20187215 ATTATTAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
17 2 0.05
18 2 0.05
19 9 0.23
20 20 0.51
21 6 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTATTTTAAATTTTTA
Found at i:20187783 original size:103 final size:101
Alignment explanation
Indices: 20187662--20187868 Score: 315
Period size: 103 Copynumber: 2.0 Consensus size: 101
20187652 ACAAGTAAGA
* *
20187662 AATAAAGAGCTAGGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAACGACGATTTT
1 AATAAAGAGATAAGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAACGACGATTTT
* * *
20187727 AAATTAAAAGAGATCGAGATTGAATCATGAATCAGAG
66 AAATTAAAA-AGATCGAGATTAAACCACGAATCAGAG
* *
20187764 AATAAAGAGATCAAGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAACTATGATTT
1 AATAAAGAGAT-AAGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAACGACGATTT
* *
20187829 TAAATTAAAAAGATTGAGATTAAACCGCGAATCAGAG
65 TAAATTAAAAAGATCGAGATTAAACCACGAATCAGAG
20187866 AAT
1 AAT
20187869 TTTAACTTGG
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
102 35 0.37
103 60 0.63
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21
Consensus pattern (101 bp):
AATAAAGAGATAAGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAACGACGATTTT
AAATTAAAAAGATCGAGATTAAACCACGAATCAGAG
Found at i:20187796 original size:34 final size:34
Alignment explanation
Indices: 20187733--20187802 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 34
20187723 TTTTAAATTA
* * * *
20187733 AAAGAGATCGAGATTGAATCATGAATCAGAGAAT
1 AAAGAGATCAAGATTAAACCACGAATCAGAGAAT
* *
20187767 AAAGAGATCAAGATTAAACCACGAGTCAGAGGAT
1 AAAGAGATCAAGATTAAACCACGAATCAGAGAAT
20187801 AA
1 AA
20187803 CAACAATCGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.49, C:0.11, G:0.23, T:0.17
Consensus pattern (34 bp):
AAAGAGATCAAGATTAAACCACGAATCAGAGAAT
Found at i:20187849 original size:68 final size:68
Alignment explanation
Indices: 20187766--20187988 Score: 202
Period size: 68 Copynumber: 3.3 Consensus size: 68
20187756 AATCAGAGAA
*
20187766 TAAAGAGATCAAGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAACTATGATTTTA
1 TAAAGAGATCGAGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAACTATGATTTTA
20187831 AAT
66 AAT
* * * * * *** * * * **
20187834 TAAAAAGATTGAGATTAAACCGCGAATCAGAGAATTTTAAC--TTG-GATTGAA-TCATAAGTAA
1 TAAAGAGATCGAGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAACT-ATGA-TTT
* *
20187895 GAAAA
64 TAAAT
* * ** *
20187900 TAAAGGGACCGAGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAACTGCGACTTTA
1 TAAAGAGATCGAGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAACTATGATTTTA
20187965 AAT
66 AAT
*
20187968 TAAAGAGATCGAGATTGAACC
1 TAAAGAGATCGAGATTAAACC
20187989 GCAAATTGGA
Statistics
Matches: 110, Mismatches: 39, Indels: 12
0.68 0.24 0.07
Matches are distributed among these distances:
64 1 0.01
65 9 0.08
66 37 0.34
68 55 0.50
69 7 0.06
70 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.22
Consensus pattern (68 bp):
TAAAGAGATCGAGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAACTATGATTTTA
AAT
Found at i:20187930 original size:66 final size:66
Alignment explanation
Indices: 20187844--20188055 Score: 178
Period size: 66 Copynumber: 3.2 Consensus size: 66
20187834 TAAAAAGATT
*
20187844 GAGATTAAACCGCGAATCAGAGAATTTTAACTTGGATTGAATCATAAGTAAGAAAATAAAGGGAC
1 GAGATTAAACCGCGAATCAGAGAATATTAACTTGGATTGAATCATAAGTAAGAAAATAAAGGGAC
20187909 C
66 C
* * * ** * * ** ** *
20187910 GAGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATT-AAAC-TGCG-ACTTTAAATTAAA
1 GAGATTAAACCGCGAATCAGAGAATATTAAC--TTG-GATTGAATCATAAGTA--AGAAAATAAA
* *
20187972 GAGATC
61 GGGACC
* * ** *
20187978 GAGATTGAACCGCAAATTGGAGAATGTTAACTTGGATTGAATCATAAGTAAGAAAATAAAGGGAC
1 GAGATTAAACCGCGAATCAGAGAATATTAACTTGGATTGAATCATAAGTAAGAAAATAAAGGGAC
20188043 C
66 C
20188044 GAGATTAAACCG
1 GAGATTAAACCG
20188056 TGAGTCAAAG
Statistics
Matches: 103, Mismatches: 35, Indels: 16
0.67 0.23 0.10
Matches are distributed among these distances:
65 4 0.04
66 53 0.51
67 4 0.04
68 38 0.37
69 4 0.04
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (66 bp):
GAGATTAAACCGCGAATCAGAGAATATTAACTTGGATTGAATCATAAGTAAGAAAATAAAGGGAC
C
Found at i:20187989 original size:134 final size:134
Alignment explanation
Indices: 20187744--20188129 Score: 576
Period size: 134 Copynumber: 2.9 Consensus size: 134
20187734 AAGAGATCGA
* * * * *
20187744 GATTGAATCATGAA-TCAGAGAATAAAGAGATCAAGATTAAACCACGAGTCAGAGGATAACAACA
1 GATTGAATCAT-AAGTAAGAAAATAAAGGGACCGAGATTAAACCACGAGTCAGAGGATAACAACA
* * * * * * *
20187808 ATCGAGATTAAACTATGATTTTAAATTAAAAAGATTGAGATTAAACCGCGAATCAGAGAATTTTA
65 ATCGAGATTAAACTACGACTTTAAATTAAAGAGATCGAGATTGAACCGCAAATCAGAGAATGTTA
20187873 ACTTG
130 ACTTG
20187878 GATTGAATCATAAGTAAGAAAATAAAGGGACCGAGATTAAACCACGAGTCAGAGGATAACAACAA
1 GATTGAATCATAAGTAAGAAAATAAAGGGACCGAGATTAAACCACGAGTCAGAGGATAACAACAA
* **
20187943 TCGAGATTAAACTGCGACTTTAAATTAAAGAGATCGAGATTGAACCGCAAATTGGAGAATGTTAA
66 TCGAGATTAAACTACGACTTTAAATTAAAGAGATCGAGATTGAACCGCAAATCAGAGAATGTTAA
20188008 CTTG
131 CTTG
** * *
20188012 GATTGAATCATAAGTAAGAAAATAAAGGGACCGAGATTAAACCGTGAGTCAAAGGCTAACAACAA
1 GATTGAATCATAAGTAAGAAAATAAAGGGACCGAGATTAAACCACGAGTCAGAGGATAACAACAA
*
20188077 TCGAGATTAAACTACGACTTTGAATTAAAGAGATCGAGATTGAACCGCAAATC
66 TCGAGATTAAACTACGACTTTAAATTAAAGAGATCGAGATTGAACCGCAAATC
20188130 GAAGAATAAA
Statistics
Matches: 229, Mismatches: 22, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
133 2 0.01
134 227 0.99
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.22
Consensus pattern (134 bp):
GATTGAATCATAAGTAAGAAAATAAAGGGACCGAGATTAAACCACGAGTCAGAGGATAACAACAA
TCGAGATTAAACTACGACTTTAAATTAAAGAGATCGAGATTGAACCGCAAATCAGAGAATGTTAA
CTTG
Found at i:20188929 original size:18 final size:18
Alignment explanation
Indices: 20188908--20188961 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
20188898 GCACATGTAA
20188908 TAATACATATAAAGCAAG
1 TAATACATATAAAGCAAG
*
20188926 TAAT--A-A-AAACCAA-
1 TAATACATATAAAGCAAG
20188939 TAATACATATAAAGCAAG
1 TAATACATATAAAGCAAG
20188957 TAATA
1 TAATA
20188962 AAAACCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
13 4 0.14
14 6 0.21
15 2 0.07
16 2 0.07
17 6 0.21
18 9 0.31
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.22
Consensus pattern (18 bp):
TAATACATATAAAGCAAG
Found at i:20188944 original size:31 final size:31
Alignment explanation
Indices: 20188906--20188969 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
20188896 ATGCACATGT
20188906 AATAATACATATAAAGCAAGTAATAAAAACC
1 AATAATACATATAAAGCAAGTAATAAAAACC
20188937 AATAATACATATAAAGCAAGTAATAAAAACC
1 AATAATACATATAAAGCAAGTAATAAAAACC
20188968 AA
1 AA
20188970 AAAACTATCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (31 bp):
AATAATACATATAAAGCAAGTAATAAAAACC
Found at i:20189645 original size:2 final size:2
Alignment explanation
Indices: 20189638--20189664 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20189628 TTTAAATTAG
20189638 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
20189665 GACACACTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20191366 original size:21 final size:20
Alignment explanation
Indices: 20191334--20191372 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
20191324 AATTCATTTT
* *
20191334 TTTTTTTATTTTCGTTTTGA
1 TTTTTTGATTTTAGTTTTGA
20191354 TTTTTTGATTTTTAGTTTT
1 TTTTTTGA-TTTTAGTTTT
20191373 TTTCTTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.10, C:0.03, G:0.10, T:0.77
Consensus pattern (20 bp):
TTTTTTGATTTTAGTTTTGA
Found at i:20192204 original size:2 final size:2
Alignment explanation
Indices: 20192197--20192224 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20192187 TAGATTCATC
20192197 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
20192225 CACTCTATTT
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):
TA
Found at i:20194128 original size:63 final size:62
Alignment explanation
Indices: 20193977--20194121 Score: 168
Period size: 62 Copynumber: 2.4 Consensus size: 62
20193967 GTTTGGTAAG
* * * ** * *
20193977 ATTTTACTTTGGTGCAAATTTCCCAATAGTTTGGTGAGATTTTTTTTAAAATCATTTATAAA
1 ATTTTACTTTGATGTAAAATTCTAAATAGTTTGGTAAGATTTTTTTGAAAATCATTTATAAA
** * *
20194039 ATTTTGTTTTGATGTAGAATTCTAAATAGTTTGGTAAGATTTTATTTGAAAATTATTTATAAA
1 ATTTTACTTTGATGTAAAATTCTAAATAGTTTGGTAAGATTTT-TTTGAAAATCATTTATAAA
20194102 ATTTTACTTTGA-G-AAAATTC
1 ATTTTACTTTGATGTAAAATTC
20194122 ATTAAATCTT
Statistics
Matches: 68, Mismatches: 14, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
61 6 0.09
62 35 0.51
63 27 0.40
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (62 bp):
ATTTTACTTTGATGTAAAATTCTAAATAGTTTGGTAAGATTTTTTTGAAAATCATTTATAAA
Found at i:20194642 original size:12 final size:11
Alignment explanation
Indices: 20194617--20194641 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20194607 TTTTGGTAGG
20194617 TTTCCTTTTTT
1 TTTCCTTTTTT
20194628 TTTCCTTTTTT
1 TTTCCTTTTTT
20194639 TTT
1 TTT
20194642 TTGTATGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTCCTTTTTT
Found at i:20195643 original size:84 final size:83
Alignment explanation
Indices: 20195458--20195672 Score: 236
Period size: 84 Copynumber: 2.5 Consensus size: 83
20195448 GAGTTCTTAT
* * * * *
20195458 AAATCTTGACTTTAAAATAAATTCAGCTCGAAAGACTTACAAATCTTTACCCAGAGGACTTAGAG
1 AAATCTCGACTTTAAAATAAATTCAGCTC-AAAGACTTATAAATC-TTACCCAAAGGACTCAAAG
*
20195523 ATTACGCGCGGAGGCTTTAC
64 ATTACACGCGGAGGCTTTAC
* * * * * *
20195543 AAATCCCGA-TCTTAAAATAGATTCAACTCACAAGACTTATGAATCTTGCCCAAATGACTCAAAG
1 AAATCTCGACT-TTAAAATAAATTCAGCTCA-AAGACTTATAAATCTTACCCAAAGGACTCAAAG
**
20195607 ATTACACTTGGAGG-TGTTAC
64 ATTACACGCGGAGGCT-TTAC
20195627 AAATCTCGACTTTAAAATAAATTCAGCTCAGAAGACTTATAAATCT
1 AAATCTCGACTTTAAAATAAATTCAGCTCA-AAGACTTATAAATCT
20195673 CGACTCTAAA
Statistics
Matches: 107, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
83 1 0.01
84 70 0.65
85 36 0.34
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (83 bp):
AAATCTCGACTTTAAAATAAATTCAGCTCAAAGACTTATAAATCTTACCCAAAGGACTCAAAGAT
TACACGCGGAGGCTTTAC
Found at i:20195767 original size:31 final size:31
Alignment explanation
Indices: 20195729--20195788 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
20195719 GAAGACTTCG
** *
20195729 AGATTATGCATGGAGGTTTTACAAATCTTGA
1 AGATTATGCACAGAGGTCTTACAAATCTTGA
*
20195760 AGATTATGCCCAGAGGTCTTACAAATCTT
1 AGATTATGCACAGAGGTCTTACAAATCTT
20195789 AACTCTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (31 bp):
AGATTATGCACAGAGGTCTTACAAATCTTGA
Found at i:20195906 original size:84 final size:84
Alignment explanation
Indices: 20195755--20195909 Score: 231
Period size: 84 Copynumber: 1.8 Consensus size: 84
20195745 TTTTACAAAT
* * * * *
20195755 CTTGAAGATTATGCCCAGAGGTCTTACAAATCTTAACTCTAAAATAGATTCAGCTTGAAAGATTT
1 CTTGAAGATTATACCCAGAGGTCTGACAAATCTCAACTCTAAAATAGATTCAACTTGAAAGACTT
20195820 ATGAATATTGACTAAAAGA
66 ATGAATATTGACTAAAAGA
* *
20195839 CTTGGAGATTATACCC-GAAGGTCTGATAAATCTCAACTCTAAAATAGATTCAACTTGAAAGACT
1 CTTGAAGATTATACCCAG-AGGTCTGACAAATCTCAACTCTAAAATAGATTCAACTTGAAAGACT
20195903 TATGAAT
65 TATGAAT
20195910 CTTACCCAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
83 1 0.02
84 62 0.98
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (84 bp):
CTTGAAGATTATACCCAGAGGTCTGACAAATCTCAACTCTAAAATAGATTCAACTTGAAAGACTT
ATGAATATTGACTAAAAGA
Found at i:20197259 original size:10 final size:10
Alignment explanation
Indices: 20197238--20197284 Score: 62
Period size: 10 Copynumber: 4.7 Consensus size: 10
20197228 CAAAGATGCC
20197238 TTTTTCTC-T
1 TTTTTCTCTT
20197247 TTTTTCTCTT
1 TTTTTCTCTT
20197257 TTTTTCTTCTT
1 TTTTTC-TCTT
20197268 TTCTTT-TCTT
1 TT-TTTCTCTT
20197278 TTTTTCT
1 TTTTTCT
20197285 TTTGCATGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 11 0.32
10 14 0.41
11 6 0.18
12 3 0.09
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTCTCTT
Found at i:20197269 original size:18 final size:18
Alignment explanation
Indices: 20197237--20197287 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
20197227 TCAAAGATGC
*
20197237 CTTTTTCTCTT-TTTTCT
1 CTTTTTTTCTTCTTTTCT
20197254 CTTTTTTTCTTCTTTTCT
1 CTTTTTTTCTTCTTTTCT
*
20197272 -TTTCTTTTTTTCTTTT
1 CTTT-TTTTCTTCTTTT
20197288 GCATGAGCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 13 0.43
18 17 0.57
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
CTTTTTTTCTTCTTTTCT
Found at i:20197274 original size:13 final size:13
Alignment explanation
Indices: 20197244--20197287 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
20197234 TGCCTTTTTC
20197244 TCTTTT-TTCTCTT
1 TCTTTTCTTCT-TT
20197257 T-TTTTCTTCTTT
1 TCTTTTCTTCTTT
*
20197269 TCTTTTCTTTTTT
1 TCTTTTCTTCTTT
20197282 TCTTTT
1 TCTTTT
20197288 GCATGAGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 7 0.25
13 21 0.75
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TCTTTTCTTCTTT
Found at i:20197279 original size:21 final size:20
Alignment explanation
Indices: 20197238--20197285 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
20197228 CAAAGATGCC
20197238 TTTTTC-TCTTTTTTCTCTT
1 TTTTTCTTCTTTTTTCTCTT
*
20197257 TTTTTCTTCTTTTCTTTTCTT
1 TTTTTCTTCTTTT-TTCTCTT
20197278 TTTTTCTT
1 TTTTTCTT
20197286 TTGCATGAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 6 0.23
20 6 0.23
21 14 0.54
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTTCTTCTTTTTTCTCTT
Found at i:20202229 original size:17 final size:18
Alignment explanation
Indices: 20202209--20202254 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
20202199 AGACTAAAGC
*
20202209 ATAAAAAAGATAAATAA-
1 ATAAAAAAGACAAATAAG
*
20202226 ATAAATAAGACAAATAAG
1 ATAAAAAAGACAAATAAG
20202244 ATATAAAAAGA
1 ATA-AAAAAGA
20202255 AATGTTGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 15 0.62
18 3 0.12
19 6 0.25
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.17
Consensus pattern (18 bp):
ATAAAAAAGACAAATAAG
Found at i:20202240 original size:9 final size:9
Alignment explanation
Indices: 20202209--20202246 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
20202199 AGACTAAAGC
*
20202209 ATAAAAAAG
1 ATAAATAAG
20202218 ATAAATAA-
1 ATAAATAAG
20202226 ATAAATAAG
1 ATAAATAAG
*
20202235 ACAAATAAG
1 ATAAATAAG
20202244 ATA
1 ATA
20202247 TAAAAAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (9 bp):
ATAAATAAG
Found at i:20202547 original size:21 final size:21
Alignment explanation
Indices: 20202514--20202553 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
20202504 ACAACTTAAC
20202514 TTTTTTTATCCTTT-TTTTCG
1 TTTTTTTATCCTTTATTTTCG
*
20202534 TTTTTTTCTCCCTTTATTTT
1 TTTTTTTAT-CCTTTATTTT
20202554 TTATTAGGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 5 0.29
22 4 0.24
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.75
Consensus pattern (21 bp):
TTTTTTTATCCTTTATTTTCG
Found at i:20203191 original size:21 final size:21
Alignment explanation
Indices: 20203161--20203212 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
20203151 CTTATTGAGC
20203161 TTTCTTTTTTGTTTTT-GTTTT
1 TTTC-TTTTTGTTTTTGGTTTT
20203182 TTTCTCTTTTGTTTTTGGTTTT
1 TTTCT-TTTTGTTTTTGGTTTT
*
20203204 CTTCTTTTT
1 TTTCTTTTT
20203213 CAATTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 1 0.04
21 18 0.64
22 9 0.32
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.81
Consensus pattern (21 bp):
TTTCTTTTTGTTTTTGGTTTT
Found at i:20204580 original size:18 final size:17
Alignment explanation
Indices: 20204548--20204586 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
20204538 AAATGGGTTA
20204548 AAAATAAAATAAAATTAG
1 AAAATAAAATAAAA-TAG
20204566 AAAATAAAA-ATAAATAG
1 AAAATAAAATA-AAATAG
20204583 AAAA
1 AAAA
20204587 GGAAAAACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (17 bp):
AAAATAAAATAAAATAG
Found at i:20204592 original size:18 final size:19
Alignment explanation
Indices: 20204553--20204593 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
20204543 GGTTAAAAAT
*
20204553 AAAATAAAATTAGAAAATA
1 AAAATAAAATTAGAAAAGA
20204572 AAAAT-AAA-TAGAAAAGGA
1 AAAATAAAATTAGAAAA-GA
20204590 AAAA
1 AAAA
20204594 CCTGCGATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 7 0.35
18 8 0.40
19 5 0.25
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.15
Consensus pattern (19 bp):
AAAATAAAATTAGAAAAGA
Found at i:20207536 original size:2 final size:2
Alignment explanation
Indices: 20207525--20207559 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
20207515 GAAAGCTGTA
20207525 AT AT AT -T 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
20207560 TTAAAATTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:20208402 original size:24 final size:24
Alignment explanation
Indices: 20208375--20208420 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
20208365 ATAAAATCTT
*
20208375 GATATATATAA-TTTTGCTAAATAA
1 GATATATA-AACTTTTGATAAATAA
*
20208399 GATATTTAAACTTTTGATAAAT
1 GATATATAAACTTTTGATAAAT
20208421 GAAGTTACCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (24 bp):
GATATATAAACTTTTGATAAATAA
Found at i:20212395 original size:52 final size:52
Alignment explanation
Indices: 20212314--20212470 Score: 183
Period size: 52 Copynumber: 3.0 Consensus size: 52
20212304 TATAACCATA
* * * *
20212314 CAAACTTACCCATTAAGAATCCCTCTCCTTTTAGAATTCTTCTCCTGTAAGT
1 CAAACATACCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCCTGCAAGT
* *
20212366 CAAACATGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACATACCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCCTGCAAGT
* * * **
20212418 CGAACTTACCTATTAAGAATCCTCTTT-CTCTT-GAAATTCTTCTTTTGCAAGT
1 CAAACATACCTATTAAGAATCC-CTTTCCTTTTAG-AATTCTTCTCCTGCAAGT
20212470 C
1 C
20212471 TTCTTGTCCA
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
51 1 0.01
52 87 0.95
53 4 0.04
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.39
Consensus pattern (52 bp):
CAAACATACCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCCTGCAAGT
Found at i:20213534 original size:52 final size:51
Alignment explanation
Indices: 20213388--20213544 Score: 188
Period size: 52 Copynumber: 3.0 Consensus size: 51
20213378 TATAACCATA
* * * * *
20213388 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCACCTGTAAGT
1 CAAACTTGCCTATTAAGAATCCCT-TTCTCTTAGAATTCTTCTCTTGCAAGT
* *
20213440 CAAACATGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTTT-CTCTTAGAATTCTTCTCTTGCAAGT
* * * *
20213492 TAAACTTACCTATTAAGAATCCTCTTTCTCTTGGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATCC-CTTTCTCTTAGAATTCTTCTCTTGCAAGT
20213544 C
1 C
20213545 TTCTTGTCTA
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
51 1 0.01
52 84 0.94
53 4 0.04
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATCCCTTTCTCTTAGAATTCTTCTCTTGCAAGT
Found at i:20213585 original size:11 final size:11
Alignment explanation
Indices: 20213569--20213610 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
20213559 GCAATATCTG
20213569 ACAAATCTCAA
1 ACAAATCTCAA
*
20213580 ACAAATCTCTA
1 ACAAATCTCAA
20213591 ACAAATCTCAA
1 ACAAATCTCAA
20213602 ACAAATCTC
1 ACAAATCTC
20213611 TTATGAGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:20213594 original size:22 final size:22
Alignment explanation
Indices: 20213569--20213611 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
20213559 GCAATATCTG
20213569 ACAAATCTCAAACAAATCTCTA
1 ACAAATCTCAAACAAATCTCTA
20213591 ACAAATCTCAAACAAATCTCT
1 ACAAATCTCAAACAAATCTCT
20213612 TATGAGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (22 bp):
ACAAATCTCAAACAAATCTCTA
Found at i:20213766 original size:52 final size:52
Alignment explanation
Indices: 20213704--20213848 Score: 152
Period size: 52 Copynumber: 2.8 Consensus size: 52
20213694 TGACTGCACC
* * *
20213704 TTAAGAATCCCTCTCCTCTTAGAATTTTTCT-TCTGTAAGTCAAACATGCCTA
1 TTAAGAATCCCTCTCCTCTTAGAATTCTTCTCT-TGCAAGTCAAACATACCTA
* * * *
20213756 TTAAGAATCCCTTTCTTTTTAGAATTCTTCTCTTGCAAGTCAAACTTACCTA
1 TTAAGAATCCCTCTCCTCTTAGAATTCTTCTCTTGCAAGTCAAACATACCTA
* * *
20213808 TTAAGAAT-CCTCTTTCTCTT-GAAATTCTTTTTTTGCAAGTC
1 TTAAGAATCCCTC-TCCTCTTAG-AATTCTTCTCTTGCAAGTC
20213849 TTCTTGTCCA
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
51 4 0.05
52 72 0.94
53 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.43
Consensus pattern (52 bp):
TTAAGAATCCCTCTCCTCTTAGAATTCTTCTCTTGCAAGTCAAACATACCTA
Found at i:20213889 original size:11 final size:11
Alignment explanation
Indices: 20213873--20213914 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
20213863 GCAATATCTG
20213873 ACAAATCTCAA
1 ACAAATCTCAA
*
20213884 ACAAATCTCTA
1 ACAAATCTCAA
20213895 ACAAATCTCAA
1 ACAAATCTCAA
20213906 ACAAATCTC
1 ACAAATCTC
20213915 TTATGAGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:20213898 original size:22 final size:22
Alignment explanation
Indices: 20213873--20213915 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
20213863 GCAATATCTG
20213873 ACAAATCTCAAACAAATCTCTA
1 ACAAATCTCAAACAAATCTCTA
20213895 ACAAATCTCAAACAAATCTCT
1 ACAAATCTCAAACAAATCTCT
20213916 TATGAGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (22 bp):
ACAAATCTCAAACAAATCTCTA
Found at i:20214842 original size:21 final size:20
Alignment explanation
Indices: 20214818--20214857 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
20214808 TATATCTAAG
20214818 ATAGACTTAGGCATTATAAAA
1 ATAGACTTAGGCATT-TAAAA
20214839 ATAGACTTAGGCATTTAAA
1 ATAGACTTAGGCATTTAAA
20214858 GAGTATATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (20 bp):
ATAGACTTAGGCATTTAAAA
Found at i:20214878 original size:53 final size:56
Alignment explanation
Indices: 20214798--20214909 Score: 185
Period size: 53 Copynumber: 2.1 Consensus size: 56
20214788 AATCTATCTT
20214798 ATTTAAAGAGTATATCTAAGATAGACTTAGGCA-T-TAT-AAAAATAGACTTAGGC
1 ATTTAAAGAGTATATCTAAGATAGACTTAGGCAGTATATCAAAAATAGACTTAGGC
* *
20214851 ATTTAAAGAGTATATCTAAGATAGACTTAGGCAGTATATCTAAGATAGACTTAGGC
1 ATTTAAAGAGTATATCTAAGATAGACTTAGGCAGTATATCAAAAATAGACTTAGGC
20214907 ATT
1 ATT
20214910 CTTCTGTTTG
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
53 33 0.61
54 1 0.02
55 3 0.06
56 17 0.31
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (56 bp):
ATTTAAAGAGTATATCTAAGATAGACTTAGGCAGTATATCAAAAATAGACTTAGGC
Found at i:20214891 original size:24 final size:24
Alignment explanation
Indices: 20214859--20214907 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
20214849 GCATTTAAAG
20214859 AGTATATCTAAGATAGACTTAGGC
1 AGTATATCTAAGATAGACTTAGGC
20214883 AGTATATCTAAGATAGACTTAGGC
1 AGTATATCTAAGATAGACTTAGGC
20214907 A
1 A
20214908 TTCTTCTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (24 bp):
AGTATATCTAAGATAGACTTAGGC
Found at i:20215145 original size:31 final size:30
Alignment explanation
Indices: 20215110--20215167 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 30
20215100 GGTAGCTGAT
20215110 CGAAAAATTCAAACTTGGCCTGAAAATTCAC
1 CGAAAAATTCAAACTTGGCC-GAAAATTCAC
*
20215141 CGAAAAATTTAAACTTGGCCGAAAATT
1 CGAAAAATTCAAACTTGGCCGAAAATT
20215168 TCAATCGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (30 bp):
CGAAAAATTCAAACTTGGCCGAAAATTCAC
Found at i:20215564 original size:20 final size:20
Alignment explanation
Indices: 20215510--20215571 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
20215500 AATCAAATAA
*
20215510 AAAAATGTTAATAGATAATT
1 AAAAATGTTAATAGATAAAT
**
20215530 AAAAA-AATAATTAGATAAAT
1 AAAAATGTTAA-TAGATAAAT
20215550 AAAAATGTTAATAGATAAAT
1 AAAAATGTTAATAGATAAAT
20215570 AA
1 AA
20215572 TAATAATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 3 0.09
20 29 0.83
21 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (20 bp):
AAAAATGTTAATAGATAAAT
Found at i:20215571 original size:4 final size:4
Alignment explanation
Indices: 20215519--20215667 Score: 52
Period size: 4 Copynumber: 39.0 Consensus size: 4
20215509 AAAAAATGTT
* * * * * * * *
20215519 AATA GATA ATTA AAAA AATA ATTA GATA AATA AA-A ATGTT AATA GATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA AATA
* *
20215567 AAT- AAT- AAT- AAT- AAT- AAT- AAT- AATA AATA TATA AATA GATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
* * *
20215608 AGT- AAT- AATA AAAA AATA TATATT AATA AATA GTAAT- AATA AATA
1 AATA AATA AATA AATA AATA -A-ATA AATA AATA --AATA AATA AATA
20215653 AAT- AATA AATA AATA
1 AATA AATA AATA AATA
20215668 CAAAAAATAC
Statistics
Matches: 109, Mismatches: 26, Indels: 20
0.70 0.17 0.13
Matches are distributed among these distances:
3 34 0.31
4 67 0.61
5 3 0.03
6 5 0.05
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (4 bp):
AATA
Found at i:20215575 original size:3 final size:3
Alignment explanation
Indices: 20215567--20215660 Score: 73
Period size: 3 Copynumber: 28.7 Consensus size: 3
20215557 TTAATAGATA
20215567 AAT AAT AAT AAT AAT AAT AAT AAT AAAT ATAT AAAT AGAT AAGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT A-AT -AAT A-AT AA-T AAT
* * *
20215614 AAT AA- AAA AAT ATAT ATT AAT AAAT AGT AAT AAT AAAT AAAT AAT AA
1 AAT AAT AAT AAT A-AT AAT AAT -AAT AAT AAT AAT -AAT -AAT AAT AA
20215661 ATAAATACAA
Statistics
Matches: 77, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
2 2 0.03
3 48 0.62
4 26 0.34
5 1 0.01
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:20215580 original size:41 final size:38
Alignment explanation
Indices: 20215505--20215618 Score: 124
Period size: 41 Copynumber: 2.9 Consensus size: 38
20215495 AATCAAATCA
* *
20215505 AATAA-AAAAATGTTAATAGATAATTAA-AAAAATAATT
1 AATAATAAAAATGTTAATAGATAAATAATAATAATAA-T
20215542 AGATAAATAAAAATGTTAATAGATAAATAATAATAATAAT
1 A-AT-AATAAAAATGTTAATAGATAAATAATAATAATAAT
* *
20215582 AATAATAATAAATATATAAATAGATAAGTAATAATAA
1 AATAATAA-AAATGT-T-AATAGATAAATAATAATAA
20215619 AAAAATATAT
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
37 1 0.02
38 7 0.11
39 9 0.14
40 24 0.36
41 25 0.38
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (38 bp):
AATAATAAAAATGTTAATAGATAAATAATAATAATAAT
Found at i:20215581 original size:20 final size:20
Alignment explanation
Indices: 20215518--20215660 Score: 96
Period size: 20 Copynumber: 7.0 Consensus size: 20
20215508 AAAAAAATGT
* *
20215518 TAATAGATAATTAA-AAAAA
1 TAATAGATAAATAATAATAA
* **
20215537 TAATTAGATAAATAAAAATGT
1 TAA-TAGATAAATAATAATAA
20215558 TAATAGATAAATAATAATAA
1 TAATAGATAAATAATAATAA
20215578 TAATA-AT-AATAATAAATATA
1 TAATAGATAAATAAT-AATA-A
*
20215598 TAAATAGATAAGTAATAATAA
1 T-AATAGATAAATAATAATAA
* * * * *
20215619 AAAAATATATATTAATAAATAG
1 TAATAGATA-AATAAT-AATAA
20215641 TAATA-ATAAATAAATAATAA
1 TAATAGATAAAT-AATAATAA
20215661 ATAAATACAA
Statistics
Matches: 97, Mismatches: 17, Indels: 19
0.73 0.13 0.14
Matches are distributed among these distances:
18 6 0.06
19 9 0.09
20 43 0.44
21 21 0.22
22 13 0.13
23 5 0.05
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (20 bp):
TAATAGATAAATAATAATAA
Found at i:20215690 original size:27 final size:28
Alignment explanation
Indices: 20215652--20215710 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
20215642 AATAATAAAT
* *
20215652 AAATAATAAATAAATACAAAA-AATACA
1 AAATAATAAATAAAAACAAAATAAAACA
20215679 AAATACAT-AATAAAAACAAAATAAAACA
1 AAATA-ATAAATAAAAACAAAATAAAACA
20215707 AAAT
1 AAAT
20215711 GAAATGGGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.17
Consensus pattern (28 bp):
AAATAATAAATAAAAACAAAATAAAACA
Found at i:20215699 original size:18 final size:16
Alignment explanation
Indices: 20215663--20215701 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
20215653 AATAATAAAT
*
20215663 AAATACAAAAAATACA
1 AAATACAAAAAAAACA
20215679 AAATACATAATAAAAACA
1 AAATACA-AA-AAAAACA
20215697 AAATA
1 AAATA
20215702 AAACAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 2 0.10
18 11 0.55
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.15
Consensus pattern (16 bp):
AAATACAAAAAAAACA
Found at i:20215956 original size:45 final size:44
Alignment explanation
Indices: 20215892--20216181 Score: 286
Period size: 45 Copynumber: 6.6 Consensus size: 44
20215882 AAATTTTGAT
* *
20215892 CAAAGTTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAACATAAA
1 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAA-ATAAA
*
20215937 CAAAGCTCCTCTAATCAGAGGCTCAAAGACTTTGAAAATAATAAA
1 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAA-AATAAA
* *
20215982 CAAAGCTCCTTTAATGAGAGGCTCAACGACTTTGAAAATAAATAAA
1 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTG-AAA-AAATAAA
* *** *
20216028 CAAAGCTCCTCTAATCAGAGGCTTAACGACTTTTGGGGAAGT-AA
1 CAAAGCTCCTCTAATCAGAGGCTCAACGAC-TTTGAAAAAATAAA
** * * * * *
20216072 -ATTGCTCGTCTAATCAGAGGCTCTATGACTTTTG-GAAAGTAAA
1 CAAAGCTCCTCTAATCAGAGGCTCAACGAC-TTTGAAAAAATAAA
** * * *
20216115 -TTA-CTCCTCTAATTAAAGGCTCTACGACTTTG-AAAAATAAA
1 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAAATAAA
20216156 CAAAGCTCCTCTAATCAGAGGCTCAA
1 CAAAGCTCCTCTAATCAGAGGCTCAA
20216182 TAACTTTTGA
Statistics
Matches: 205, Mismatches: 33, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
41 11 0.05
42 27 0.13
43 49 0.24
44 2 0.01
45 74 0.36
46 37 0.18
47 5 0.02
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.25
Consensus pattern (44 bp):
CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAAATAAA
Found at i:20216142 original size:85 final size:84
Alignment explanation
Indices: 20215942--20216282 Score: 237
Period size: 85 Copynumber: 4.0 Consensus size: 84
20215932 ATAAACAAAG
* * * * *
20215942 CTCCTCTAATCAGAGGCTCAAAGACTTTGAAAATAATAAACAAAGCTCCTTTAATGAGAGGCTCA
1 CTCCTCTAATCAAAGGCTTAACGACTTTG-AAA-AATAAACAAAGCTCCTCTAATCAGAGGCTCA
** *
20216007 ACGAC-TTTGAAAATAAATAAACAAA
64 ATAACTTTTGAAAATAAAT-----TA
* ** * ** *
20216032 GCTCCTCTAATCAGAGGCTTAACGACTTTTGGGGAAGT-AA-ATTGCTCGTCTAATCAGAGGCTC
1 -CTCCTCTAATCAAAGGCTTAACGAC-TTT-GAAAAATAAACAAAGCTCCTCTAATCAGAGGCTC
* * *
20216095 TATGACTTTTGGAAAGTAAATTA
63 AATAACTTTT-GAAAATAAATTA
*
20216118 CTCCTCTAATTAAAGGCTCT-ACGACTTTGAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAA
1 CTCCTCTAATCAAAGGCT-TAACGACTTTGAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAA
*
20216182 TAACTTTTGAAAATAAATTG
65 TAACTTTTGAAAATAAATTA
* * * * * * * **
20216202 CTCCTCTAAACAGAGGCATGACAACTTTGAAGAAT--AGATTGCTCCTCTAATCAGAGGCATC-A
1 CTCCTCTAATCAAAGGCTTAACGACTTTGAAAAATAAACAAAGCTCCTCTAATCAGAGGC-TCAA
* *
20216264 CAACTTTGGAAAATAAATT
65 TAACTTTTGAAAATAAATT
20216283 GTTCCTTGAC
Statistics
Matches: 204, Mismatches: 37, Indels: 27
0.76 0.14 0.10
Matches are distributed among these distances:
82 38 0.19
83 7 0.03
84 42 0.21
85 49 0.24
86 2 0.01
89 22 0.11
90 5 0.02
91 34 0.17
92 4 0.02
93 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (84 bp):
CTCCTCTAATCAAAGGCTTAACGACTTTGAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAAT
AACTTTTGAAAATAAATTA
Found at i:20216217 original size:41 final size:41
Alignment explanation
Indices: 20216032--20216288 Score: 207
Period size: 41 Copynumber: 6.1 Consensus size: 41
20216022 AATAAACAAA
* * * *
20216032 GCTCCTCTAATCAGAGGCTTAACGACTTTTGGGGAAGTAAATT
1 GCTCCTCTAATCAGAGGCTCAACAACTTTT--GAAAATAAATT
* * ** *
20216075 GCTCGTCTAATCAGAGGCTCTATGACTTTTGGAAAGTAAATT
1 GCTCCTCTAATCAGAGGCTCAACAACTTTT-GAAAATAAATT
* * * * * **
20216117 ACTCCTCTAATTAAAGGCTCTACGAC-TTTGAAAAATAAACAAA
1 GCTCCTCTAATCAGAGGCTCAACAACTTTTG-AAAAT-AA-ATT
*
20216160 GCTCCTCTAATCAGAGGCTCAATAACTTTTGAAAATAAATT
1 GCTCCTCTAATCAGAGGCTCAACAACTTTTGAAAATAAATT
* * *
20216201 GCTCCTCTAAACAGAGGCAT-GACAAC-TTTGAAGAATAGATT
1 GCTCCTCTAATCAGAGGC-TCAACAACTTTTGAA-AATAAATT
*
20216242 GCTCCTCTAATCAGAGGCATC-ACAACTTTGGAAAATAAATT
1 GCTCCTCTAATCAGAGGC-TCAACAACTTTTGAAAATAAATT
*
20216283 GTTCCT
1 GCTCCT
20216289 TGACAATCAT
Statistics
Matches: 177, Mismatches: 29, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
40 7 0.04
41 72 0.41
42 42 0.24
43 52 0.29
44 4 0.02
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (41 bp):
GCTCCTCTAATCAGAGGCTCAACAACTTTTGAAAATAAATT
Found at i:20217309 original size:9 final size:9
Alignment explanation
Indices: 20217295--20217356 Score: 58
Period size: 9 Copynumber: 7.1 Consensus size: 9
20217285 TTTTCATTCA
20217295 CTTTTTTTT
1 CTTTTTTTT
20217304 CTTTTTTTT
1 CTTTTTTTT
*
20217313 C--ATTTTT
1 CTTTTTTTT
*
20217320 CATTTTTTT
1 CTTTTTTTT
*
20217329 CATTTTATTT
1 C-TTTTTTTT
*
20217339 -TTTCTTTT
1 CTTTTTTTT
20217347 CTTTTTTTT
1 CTTTTTTTT
20217356 C
1 C
20217357 AAGCATAGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
7 6 0.14
8 6 0.14
9 24 0.57
10 6 0.14
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:20217318 original size:16 final size:16
Alignment explanation
Indices: 20217299--20217352 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
20217289 CATTCACTTT
20217299 TTTTTCTTTTTTTTCA
1 TTTTTCTTTTTTTTCA
*
20217315 TTTTTCATTTTTTTCA
1 TTTTTCTTTTTTTTCA
*
20217331 TTTTATTTTTTCTTTTC-
1 TTTT-TCTTTT-TTTTCA
20217348 TTTTT
1 TTTTT
20217353 TTTCAAGCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 20 0.61
17 8 0.24
18 5 0.15
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTCTTTTTTTTCA
Found at i:20224594 original size:15 final size:15
Alignment explanation
Indices: 20224570--20224600 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20224560 TGTTAAGTGT
*
20224570 AATGAGTGAGAATGC
1 AATGAATGAGAATGC
20224585 AATGAATGAGAATGC
1 AATGAATGAGAATGC
20224600 A
1 A
20224601 TGTATGCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.29, T:0.19
Consensus pattern (15 bp):
AATGAATGAGAATGC
Found at i:20227943 original size:74 final size:74
Alignment explanation
Indices: 20227822--20227965 Score: 211
Period size: 74 Copynumber: 1.9 Consensus size: 74
20227812 TCAACTTTTC
* * * * *
20227822 CTCAAAAATTCATTTTTGAAAACTTATTTTTAAGTAAAATTGATACTTTCAACTTTTTCCCAAAA
1 CTCAAAAATTCATTTTAGAAAACTTATTTTCAAGAAAAAATGATACTTTCAACTTTTCCCCAAAA
20227887 ATATTCTTT
66 ATATTCTTT
20227896 CTCAAAAATAT-ATTTTAGAAAGA-TTATTTTCAAGAAAAAATGATACTTTCAACTTTTCCCCAA
1 CTCAAAAAT-TCATTTTAGAAA-ACTTATTTTCAAGAAAAAATGATACTTTCAACTTTTCCCCAA
20227959 AAATATT
64 AAATATT
20227966 TTTTAGAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
74 61 0.97
75 2 0.03
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (74 bp):
CTCAAAAATTCATTTTAGAAAACTTATTTTCAAGAAAAAATGATACTTTCAACTTTTCCCCAAAA
ATATTCTTT
Found at i:20228050 original size:57 final size:58
Alignment explanation
Indices: 20227896--20228201 Score: 442
Period size: 57 Copynumber: 5.3 Consensus size: 58
20227886 AATATTCTTT
* * * * *
20227896 CTCAAAAATATATTTTAGAAAGATTATTTTCAAGAAAAAATGATACTTTCAACTTTTC
1 CTCAAAAATATTTTTTAAAAAGCTTATTTTCAAGGAAAATTGATACTTTCAACTTTTC
*
20227954 CCCAAAAATATTTTTTAGAAATA-CTTATTTTCAAGGAAAATTGATACTTTCAACTTTT-
1 CTCAAAAATATTTTTTA-AAA-AGCTTATTTTCAAGGAAAATTGATACTTTCAACTTTTC
* *
20228012 TTCAAAAATATTTTTTAAAAAGCTTATTTTCAAGGAAAATTAATACTTTCAACTTTTC
1 CTCAAAAATATTTTTTAAAAAGCTTATTTTCAAGGAAAATTGATACTTTCAACTTTTC
*
20228070 CTCAAAAAT-TTTTTTAGAAAAACTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTC
1 CTCAAAAATATTTTTTA-AAAAGCTTATTTTCAAGGAAAATTGATACTTTCAAC-TTTTC
*
20228129 C-CAAAAATA-TTTTTAGAAAGCTTATTTTCAAGGAAAATTGATACTTTCAACTTTTC
1 CTCAAAAATATTTTTTAAAAAGCTTATTTTCAAGGAAAATTGATACTTTCAACTTTTC
20228185 CTCAAAAATATATTTTT
1 CTCAAAAATAT-TTTTT
20228202 TTGAATTTTA
Statistics
Matches: 224, Mismatches: 14, Indels: 19
0.87 0.05 0.07
Matches are distributed among these distances:
56 7 0.03
57 86 0.38
58 85 0.38
59 45 0.20
60 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (58 bp):
CTCAAAAATATTTTTTAAAAAGCTTATTTTCAAGGAAAATTGATACTTTCAACTTTTC
Found at i:20228142 original size:115 final size:116
Alignment explanation
Indices: 20227893--20228201 Score: 505
Period size: 115 Copynumber: 2.7 Consensus size: 116
20227883 AAAAATATTC
* * * *
20227893 TTTCTCAAAAATATATTTTAGAAAGATTATTTTCAAGAAAAAATGATACTTTCAACTTTTCCCCA
1 TTTCTCAAAAATAT-TTTTAGAAAGCTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCA
*
20227958 AAAATATTTTTTAGAAATACTTATTTTCAAGGAAAATTGATACTTTCAACTT
65 AAAATATTTTTTAGAAAAACTTATTTTCAAGGAAAATTGATACTTTCAACTT
* *
20228010 TTT-TCAAAAATATTTTTTAAAAAGCTTATTTTCAAGGAAAATTAATACTTTCAACTTTTCCTCA
1 TTTCTCAAAAATA-TTTTTAGAAAGCTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCA
20228074 AAAAT-TTTTTTAGAAAAACTTATTTTCAAGGAAAATTGATACTTTCAACTT
65 AAAATATTTTTTAGAAAAACTTATTTTCAAGGAAAATTGATACTTTCAACTT
*
20228125 TTTCCCAAAAATATTTTTAGAAAGCTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAA
1 TTTCTCAAAAATATTTTTAGAAAGCTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAA
20228190 AAATATATTTTT
66 AAATAT-TTTTT
20228202 TTGAATTTTA
Statistics
Matches: 178, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
115 102 0.57
116 67 0.38
117 9 0.05
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (116 bp):
TTTCTCAAAAATATTTTTAGAAAGCTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAA
AAATATTTTTTAGAAAAACTTATTTTCAAGGAAAATTGATACTTTCAACTT
Found at i:20228223 original size:57 final size:58
Alignment explanation
Indices: 20227896--20228201 Score: 458
Period size: 58 Copynumber: 5.3 Consensus size: 58
20227886 AATATTCTTT
* * * *
20227896 CTCAAAAATATATTTTAGAAAGATTATTTTCAAGAAAAAATGATACTTTCAACTTTTC
1 CTCAAAAATATTTTTTAGAAAGCTTATTTTCAAGGAAAATTGATACTTTCAACTTTTC
* *
20227954 CCCAAAAATATTTTTTAGAAATACTTATTTTCAAGGAAAATTGATACTTTCAACTTTT-
1 CTCAAAAATATTTTTTAGAAA-GCTTATTTTCAAGGAAAATTGATACTTTCAACTTTTC
* * *
20228012 TTCAAAAATATTTTTTAAAAAGCTTATTTTCAAGGAAAATTAATACTTTCAACTTTTC
1 CTCAAAAATATTTTTTAGAAAGCTTATTTTCAAGGAAAATTGATACTTTCAACTTTTC
*
20228070 CTCAAAAAT-TTTTTTAGAAAAACTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTC
1 CTCAAAAATATTTTTTAG-AAAGCTTATTTTCAAGGAAAATTGATACTTTCAAC-TTTTC
20228129 C-CAAAAATA-TTTTTAGAAAGCTTATTTTCAAGGAAAATTGATACTTTCAACTTTTC
1 CTCAAAAATATTTTTTAGAAAGCTTATTTTCAAGGAAAATTGATACTTTCAACTTTTC
20228185 CTCAAAAATATATTTTT
1 CTCAAAAATAT-TTTTT
20228202 TTGAATTTTA
Statistics
Matches: 224, Mismatches: 16, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
56 6 0.03
57 83 0.37
58 92 0.41
59 43 0.19
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (58 bp):
CTCAAAAATATTTTTTAGAAAGCTTATTTTCAAGGAAAATTGATACTTTCAACTTTTC
Found at i:20228235 original size:6 final size:6
Alignment explanation
Indices: 20228224--20228265 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
20228214 TAAAGAAAAT
20228224 AATAAA AATAAA AATAAA AATAAA AATAAA AAT-AA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA A
20228266 TGAGATAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:20228323 original size:4 final size:4
Alignment explanation
Indices: 20228306--20228337 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
20228296 TAATCTAATC
20228306 AATA AAT- AAT- AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AA
20228338 AACCTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 6 0.22
4 21 0.78
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:20228728 original size:12 final size:12
Alignment explanation
Indices: 20228711--20228747 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
20228701 TGGGTAGCTG
20228711 ACCGAAAAATTC
1 ACCGAAAAATTC
20228723 ACCGAAAAATTC
1 ACCGAAAAATTC
*
20228735 ATCGAAAAATTC
1 ACCGAAAAATTC
20228747 A
1 A
20228748 AACTTGGTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.51, C:0.22, G:0.08, T:0.19
Consensus pattern (12 bp):
ACCGAAAAATTC
Found at i:20229124 original size:18 final size:19
Alignment explanation
Indices: 20229103--20229171 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 19
20229093 ATCAAATCAA
20229103 ATAA-AAAAATGTTAATAG
1 ATAATAAAAATGTTAATAG
***
20229121 ATAATTAAAAGAAAATAATTAG
1 ATAA-TAAAA-ATGTTAA-TAG
20229143 ATAAATAAAAATGTTAATAG
1 AT-AATAAAAATGTTAATAG
20229163 ATATATAAA
1 ATA-ATAAA
20229172 TAGATAAGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
18 4 0.10
19 1 0.03
20 14 0.36
21 8 0.21
22 10 0.26
23 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (19 bp):
ATAATAAAAATGTTAATAG
Found at i:20229129 original size:22 final size:21
Alignment explanation
Indices: 20229102--20229171 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
20229092 AATCAAATCA
20229102 AATAAAAAAATGTTAATAGAT
1 AATAAAAAAATGTTAATAGAT
*
20229123 AATTAAAAGAAA--ATAATTAGAT
1 AA-TAAAA-AAATGTTAA-TAGAT
*
20229145 AA-ATAAAAATGTTAATAGAT
1 AATAAAAAAATGTTAATAGAT
20229165 ATATAAA
1 A-ATAAA
20229172 TAGATAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
19 3 0.08
20 9 0.24
21 9 0.24
22 14 0.37
23 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.29
Consensus pattern (21 bp):
AATAAAAAAATGTTAATAGAT
Found at i:20229132 original size:42 final size:42
Alignment explanation
Indices: 20229085--20229165 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 42
20229075 AATAAGAAGA
20229085 AAAAGAAAATCAAATCAAAT-AA-AAAAATGTTAATAGATAATT
1 AAAAGAAAAT--AATCAAATAAATAAAAATGTTAATAGATAATT
* *
20229127 AAAAGAAAATAATTAGATAAATAAAAATGTTAATAGATA
1 AAAAGAAAATAATCAAATAAATAAAAATGTTAATAGATA
20229166 TATAAATAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 6 0.17
41 2 0.06
42 27 0.77
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (42 bp):
AAAAGAAAATAATCAAATAAATAAAAATGTTAATAGATAATT
Found at i:20229221 original size:17 final size:17
Alignment explanation
Indices: 20229167--20229225 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
20229157 TAATAGATAT
*
20229167 ATAAATAGATAAGTAATA
1 ATAAATAAAT-AGTAATA
20229185 ATAAA-AAATA-T-AT-
1 ATAAATAAATAGTAATA
*
20229198 ATTAATAAATAGTAATA
1 ATAAATAAATAGTAATA
20229215 ATAAATAAATA
1 ATAAATAAATA
20229226 CAAAAAATAC
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
13 4 0.12
14 7 0.21
15 2 0.06
16 3 0.09
17 13 0.38
18 5 0.15
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (17 bp):
ATAAATAAATAGTAATA
Found at i:20230061 original size:10 final size:10
Alignment explanation
Indices: 20230040--20230069 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
20230030 AAACATATAA
20230040 ATAAATAAGAT
1 ATAAA-AAGAT
20230051 ATAAAAAGAT
1 ATAAAAAGAT
20230061 ATAAAAAGA
1 ATAAAAAGA
20230070 AATGAAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.74
11 5 0.26
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (10 bp):
ATAAAAAGAT
Found at i:20230063 original size:25 final size:22
Alignment explanation
Indices: 20230014--20230065 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 22
20230004 TTAAAATAAA
*
20230014 ATAAATAAAAAGAGTAAAACAT
1 ATAAATAAAAAGAATAAAACAT
*
20230036 ATAAATAAATAAGATATAAAAAGAT
1 ATAAATAAA-AAGA-AT-AAAACAT
20230061 ATAAA
1 ATAAA
20230066 AAGAAATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 9 0.36
23 4 0.16
24 1 0.04
25 11 0.44
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.21
Consensus pattern (22 bp):
ATAAATAAAAAGAATAAAACAT
Found at i:20230310 original size:22 final size:22
Alignment explanation
Indices: 20230282--20230332 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
20230272 AAGGACGACA
*
20230282 CCCAAAGGTTTTGATA-ATCATG
1 CCCAAAGGTCTT-ATAGATCATG
20230304 CCCAAAGGTCTTATAGATCATG
1 CCCAAAGGTCTTATAGATCATG
*
20230326 TCCAAAG
1 CCCAAAG
20230333 AGCTTGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (22 bp):
CCCAAAGGTCTTATAGATCATG
Found at i:20230588 original size:84 final size:84
Alignment explanation
Indices: 20230444--20230800 Score: 346
Period size: 84 Copynumber: 4.3 Consensus size: 84
20230434 AAAGATCATA
* * *
20230444 CCCAAAGGTCTTAGAGATTATGCTC-GGAGTTCTTACAAATCTTGACTCTAAAATAAATTCAACT
1 CCCAAAGGACTTAGAGATTATGCTCAGAAG-TCTTACAAATCTCGACTCTAAAATAAATTCAACT
*
20230508 CGAAAGACTTACAAATCTT-
65 CGAAAGACTTACGAATCTTG
*
20230527 CCCTAAAGGACTTAGAGATTATGCTCGGAAGTCTTACAAATCTCGA-TCTTAAAATAAATTCAAC
1 CCC-AAAGGACTTAGAGATTATGCTCAGAAGTCTTACAAATCTCGACTC-TAAAATAAATTCAAC
*
20230591 TCGCAAGACTTACGAATCTTG
64 TCGAAAGACTTACGAATCTTG
* * ** * * * * *
20230612 CCCAAATGACTCAGAGATTACACTTAGAAGTGTTACAAATCTTGACTTTAAAATAAATTCAGCTC
1 CCCAAAGGACTTAGAGATTATGCTCAGAAGTCTTACAAATCTCGACTCTAAAATAAATTCAACTC
* * *
20230677 AAAAAACTTATGAATCTTG
66 GAAAGACTTACGAATCTTG
* * * * * ** * * *
20230696 TCC-AATGACATATAAATTATAATCAGAGGTCTTATAAATCTCGACTCTAAAATAAATTCAAGTC
1 CCCAAAGGACTTAGAGATTATGCTCAGAAGTCTTACAAATCTCGACTCTAAAATAAATTCAACTC
*
20230760 -AGAAGACTTACGAATCTTA
66 GA-AAGACTTACGAATCTTG
*** *
20230779 CTTGAAGGACTTGGAGATTATG
1 CCCAAAGGACTTAGAGATTATG
20230801 TGTAGAGGTT
Statistics
Matches: 221, Mismatches: 46, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
82 1 0.00
83 66 0.30
84 147 0.67
85 7 0.03
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (84 bp):
CCCAAAGGACTTAGAGATTATGCTCAGAAGTCTTACAAATCTCGACTCTAAAATAAATTCAACTC
GAAAGACTTACGAATCTTG
Found at i:20230774 original size:167 final size:167
Alignment explanation
Indices: 20230476--20230777 Score: 394
Period size: 167 Copynumber: 1.8 Consensus size: 167
20230466 CTCGGAGTTC
* * *
20230476 TTACAAATCTTGACTCTAAAATAAATTCAACTCGAAAGACTTACAAATCTTCCCTAAAGGACTTA
1 TTACAAATCTTGACTCTAAAATAAATTCAACTCAAAAAACTTACAAATCTTCCC-AAAGGACATA
* ** *
20230541 GAGATTATGCTCGGAAGTCTTACAAATCTCGATCTTAAAATAAATTCAACTCGCAAGACTTACGA
65 GAAATTATAATCAGAAGTCTTACAAATCTCGATCTTAAAATAAATTCAACTCGCAAGACTTACGA
20230606 ATCTTGCCCAAATGACTCAGAGATTACACTTAGAAGTG
130 ATCTTGCCCAAATGACTCAGAGATTACACTTAGAAGTG
* * ** * *
20230644 TTACAAATCTTGACTTTAAAATAAATTCAGCTCAAAAAACTTATGAATCTTGTCC-AATGACATA
1 TTACAAATCTTGACTCTAAAATAAATTCAACTCAAAAAACTTACAAATCTT-CCCAAAGGACATA
* * * *
20230708 TAAATTATAATCAGAGGTCTTATAAATCTCGA-CTCTAAAATAAATTCAAGTCAG-AAGACTTAC
65 GAAATTATAATCAGAAGTCTTACAAATCTCGATCT-TAAAATAAATTCAACTC-GCAAGACTTAC
20230771 GAATCTT
128 GAATCTT
20230778 ACTTGAAGGA
Statistics
Matches: 114, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
166 2 0.02
167 64 0.56
168 46 0.40
169 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.30
Consensus pattern (167 bp):
TTACAAATCTTGACTCTAAAATAAATTCAACTCAAAAAACTTACAAATCTTCCCAAAGGACATAG
AAATTATAATCAGAAGTCTTACAAATCTCGATCTTAAAATAAATTCAACTCGCAAGACTTACGAA
TCTTGCCCAAATGACTCAGAGATTACACTTAGAAGTG
Found at i:20230826 original size:31 final size:31
Alignment explanation
Indices: 20230788--20230852 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
20230778 ACTTGAAGGA
** *
20230788 CTTGGAGATTATGTGTAGAGGTTTTACAAAT
1 CTTGGAGATTATGCCTAGAGGTCTTACAAAT
20230819 CTTGGAGATTATGCCTAGAGGTCTTACAAAT
1 CTTGGAGATTATGCCTAGAGGTCTTACAAAT
20230850 CTT
1 CTT
20230853 AACTCTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (31 bp):
CTTGGAGATTATGCCTAGAGGTCTTACAAAT
Found at i:20232333 original size:16 final size:15
Alignment explanation
Indices: 20232314--20232351 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
20232304 CTCTTTTCTC
20232314 TCTTTTTTTCTTCTTT
1 TCTTTTTTTC-TCTTT
*
20232330 TCTTTTCTTCTCTTT
1 TCTTTTTTTCTCTTT
20232345 T-TTTTTT
1 TCTTTTTT
20232352 CTTTTGCATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 5 0.25
15 6 0.30
16 9 0.45
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TCTTTTTTTCTCTTT
Found at i:20232335 original size:25 final size:26
Alignment explanation
Indices: 20232305--20232356 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
20232295 ATGCATTTTC
20232305 TCTTTTC-TCTCTTTTTTTCTTCTTT
1 TCTTTTCTTCTCTTTTTTTCTTCTTT
*
20232330 TCTTTTCTTCTCTTTTTTTTTTCTTT
1 TCTTTTCTTCTCTTTTTTTCTTCTTT
20232356 T
1 T
20232357 GCATGAGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (26 bp):
TCTTTTCTTCTCTTTTTTTCTTCTTT
Found at i:20232337 original size:13 final size:13
Alignment explanation
Indices: 20232307--20232356 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
20232297 GCATTTTCTC
20232307 TTTTC-TCTCTTT
1 TTTTCTTCTCTTT
20232319 TTTTCTTCT-TTT
1 TTTTCTTCTCTTT
20232331 CTTTTCTTCTCTTT
1 -TTTTCTTCTCTTT
20232345 TTTT-TT-TCTTT
1 TTTTCTTCTCTTT
20232356 T
1 T
20232357 GCATGAGCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.17
12 10 0.29
13 16 0.46
14 3 0.09
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTCTTCTCTTT
Found at i:20232894 original size:20 final size:20
Alignment explanation
Indices: 20232839--20232895 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 20
20232829 AAAGGATAAA
20232839 ATTTCTTTATTTATTTGAAAAG
1 ATTT-TTTATTTA-TTGAAAAG
20232861 ACCTTTTTT-TTTATTGAAAAG
1 A--TTTTTTATTTATTGAAAAG
*
20232882 ATTTTTTAATTATT
1 ATTTTTTATTTATT
20232896 TTTTATTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
19 6 0.19
20 5 0.16
21 9 0.29
22 5 0.16
23 3 0.10
24 3 0.10
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.58
Consensus pattern (20 bp):
ATTTTTTATTTATTGAAAAG
Found at i:20233045 original size:5 final size:5
Alignment explanation
Indices: 20233037--20233080 Score: 52
Period size: 5 Copynumber: 8.2 Consensus size: 5
20233027 AAATGGGTTA
*
20233037 AAAAT AAAAT AAAAT AAAAT AAAATT AGAAAAT AAAAA AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAA-T --AAAAT AAAAT AAAAT A
20233081 GAAAAGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 28 0.82
6 1 0.03
7 1 0.03
8 4 0.12
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:20233082 original size:17 final size:17
Alignment explanation
Indices: 20233035--20233092 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
20233025 AAAAATGGGT
20233035 TAAAAATAAAAT--AAAA
1 TAAAAA-AAAATAGAAAA
*
20233051 TAAAATAAAATTAGAAAA
1 TAAAA-AAAAATAGAAAA
20233069 TAAAAAAAAATAGAAAA
1 TAAAAAAAAATAGAAAA
*
20233086 GAAAAAA
1 TAAAAAA
20233093 CCTGCGATCA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
16 9 0.25
17 18 0.50
18 9 0.25
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (17 bp):
TAAAAAAAAATAGAAAA
Found at i:20233091 original size:23 final size:22
Alignment explanation
Indices: 20233042--20233090 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
20233032 GGTTAAAAAT
*
20233042 AAAATAAAATAAAATAAAATTAG
1 AAAATAAAAAAAAATAAAA-TAG
20233065 AAAATAAAAAAAAATAGAAA-AG
1 AAAATAAAAAAAAATA-AAATAG
20233087 AAAA
1 AAAA
20233091 AACCTGCGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 6 0.25
23 15 0.62
24 3 0.12
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (22 bp):
AAAATAAAAAAAAATAAAATAG
Found at i:20236861 original size:2 final size:2
Alignment explanation
Indices: 20236854--20236884 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20236844 AATACGATTC
20236854 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20236885 CACACACACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20237875 original size:1 final size:1
Alignment explanation
Indices: 20237869--20237893 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
20237859 TTAGTTTTAG
20237869 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
20237894 GTGGTTGCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:20239449 original size:2 final size:2
Alignment explanation
Indices: 20239442--20239472 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20239432 AATTAGATTG
20239442 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20239473 CACTATCTGC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20241361 original size:63 final size:63
Alignment explanation
Indices: 20241233--20241354 Score: 167
Period size: 63 Copynumber: 2.0 Consensus size: 63
20241223 CAAGTCTCCC
** ** *
20241233 AATAGTTTTTTGAGATTTTATATGAAAATCATTTATAAAATTTTGTTTTGATGTAGAATTCTA
1 AATAGTTTGGTGAGATTTTATATGAAAATCATTTATAAAATTTTACTTTGATGTAAAATTCTA
* *
20241296 AATAGTTTGGTGAGATTTTATTTGAAAATTATTTATAAAATTTTACTTTGA-G-AAAATTC
1 AATAGTTTGGTGAGATTTTATATGAAAATCATTTATAAAATTTTACTTTGATGTAAAATTC
20241355 ATTAAATCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
61 6 0.12
62 1 0.02
63 45 0.87
ACGTcount: A:0.36, C:0.03, G:0.13, T:0.48
Consensus pattern (63 bp):
AATAGTTTGGTGAGATTTTATATGAAAATCATTTATAAAATTTTACTTTGATGTAAAATTCTA
Found at i:20242252 original size:22 final size:24
Alignment explanation
Indices: 20242218--20242262 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
20242208 GATAAAAATT
20242218 TAAAACAAAATAAATAAA-AAGAG
1 TAAAACAAAATAAATAAATAAGAG
*
20242241 TAAAAC-ATATAAATAAATAAGA
1 TAAAACAAAATAAATAAATAAGA
20242263 CAAAAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.18
Consensus pattern (24 bp):
TAAAACAAAATAAATAAATAAGAG
Found at i:20242753 original size:84 final size:84
Alignment explanation
Indices: 20242654--20243032 Score: 342
Period size: 84 Copynumber: 4.5 Consensus size: 84
20242644 AAGATCATGT
* *
20242654 CCAAAGGTCTTAGAGATTATGCTCGGAGTTCTTACAAATCTTGACTCTAAAATAAATTCAGCTCG
1 CCAAAGGACTTAGAGATTATGCTCGGAGGTCTTACAAATCTTGACTCTAAAATAAATTCAGCTCG
20242719 AAAGACTTTCAAATCTTTC
66 AAAGACTTTCAAATCTTTC
* * *
20242738 CCAAAGGACTTAGAGATTACGCTCGGAGGTCTTACAAAT-TTCGA-TCTTAAAATAGATTCAACT
1 CCAAAGGACTTAGAGATTATGCTCGGAGGTCTTACAAATCTT-GACTC-TAAAATAAATTCAGCT
* * * *
20242801 CGCAAGACTTACGAATCTTGC
64 CGAAAGACTTTCAAATCTTTC
* * ** * * * * *
20242822 CCAAATGACTAAGAGATTACACTTGAAAGTGTTACAAATCTTGACTTTAAAATAAATTCAGCTC-
1 CCAAAGGACTTAGAGATTATGCTCGGAGGTCTTACAAATCTTGACTCTAAAATAAATTCAGCTCG
*
20242886 AGAAGACTTAT-GAATCTTGT-
66 A-AAGACTT-TCAAATCTT-TC
* * * * ** *
20242906 CCAAA-GACATAGAGATTATACTCAGAGGTCTTATAAATCTCAACTCTAAAATAGATTCAAG-TC
1 CCAAAGGACTTAGAGATTATGCTCGGAGGTCTTACAAATCTTGACTCTAAAATAAATTC-AGCTC
* * *
20242969 AAAAGACTTGCAAATCTTAC
65 GAAAGACTTTCAAATCTTTC
* * * *
20242989 TCGAAGGACTTGGAGATTATG-TGCGGAGGTTTTACAAATCTTGA
1 CCAAAGGACTTAGAGATTATGCT-CGGAGGTCTTACAAATCTTGA
20243033 AGATTATGCC
Statistics
Matches: 234, Mismatches: 48, Indels: 26
0.76 0.16 0.08
Matches are distributed among these distances:
83 63 0.27
84 168 0.72
85 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (84 bp):
CCAAAGGACTTAGAGATTATGCTCGGAGGTCTTACAAATCTTGACTCTAAAATAAATTCAGCTCG
AAAGACTTTCAAATCTTTC
Found at i:20243026 original size:167 final size:166
Alignment explanation
Indices: 20242654--20243032 Score: 399
Period size: 167 Copynumber: 2.3 Consensus size: 166
20242644 AAGATCATGT
*
20242654 CCAAAGGTCTTAGAGATTATGCTCGGAGTTCTTACAAATCTTGACTCTAAAATAAATTCAGCTCG
1 CCAAAGGACTTAGAGATTATG-TCGGAGTT-TTACAAATCTTGACTCTAAAATAAATTCAGCTCG
* * * * *
20242719 AAAGACTTTCAAATCTTTCCCAAAGGACTTAGAGATTACGCTCGGAGGTCTTACAAATTTCGATC
64 AAAGACTTTCAAATCTTTCCCAAAGGACATAGAGATTACACTCAGAGGTCTTACAAATCTCAATC
** * *
20242784 TTAAAATAGATTCAACTCGCAAGACTTACGAATCTTGC
129 TTAAAATAGATTCAACTCAAAAGACTTACAAATCTTAC
* * ** * * * *
20242822 CCAAATGACTAAGAGATTACACTTGAAAGTGTTACAAATCTTGACTTTAAAATAAATTCAGCTC-
1 CCAAAGGACTTAGAGATTA-TGTCG-GAGTTTTACAAATCTTGACTCTAAAATAAATTCAGCTCG
* * *
20242886 AGAAGACTTAT-GAATCTTGT-CCAAA-GACATAGAGATTATACTCAGAGGTCTTATAAATCTCA
64 A-AAGACTT-TCAAATCTT-TCCCAAAGGACATAGAGATTACACTCAGAGGTCTTACAAATCTCA
* *
20242948 A-CTCTAAAATAGATTCAAGTCAAAAGACTTGCAAATCTTAC
126 ATCT-TAAAATAGATTCAACTCAAAAGACTTACAAATCTTAC
* * *
20242989 TCGAAGGACTTGGAGATTATGTGCGGAGGTTTTACAAATCTTGA
1 CCAAAGGACTTAGAGATTATGT-CGGA-GTTTTACAAATCTTGA
20243033 AGATTATGCC
Statistics
Matches: 170, Mismatches: 33, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
166 4 0.02
167 93 0.55
168 68 0.40
169 5 0.03
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (166 bp):
CCAAAGGACTTAGAGATTATGTCGGAGTTTTACAAATCTTGACTCTAAAATAAATTCAGCTCGAA
AGACTTTCAAATCTTTCCCAAAGGACATAGAGATTACACTCAGAGGTCTTACAAATCTCAATCTT
AAAATAGATTCAACTCAAAAGACTTACAAATCTTAC
Found at i:20244550 original size:15 final size:16
Alignment explanation
Indices: 20244532--20244575 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
20244522 TTTTCTCTCT
20244532 TTTTTTCTTCTTTT-A
1 TTTTTTCTTCTTTTCA
20244547 TTTTCTTC-TCTTTTCA
1 TTTT-TTCTTCTTTTCA
20244563 TTTTTT-TTCTTTT
1 TTTTTTCTTCTTTT
20244576 GCATGAGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 18 0.69
16 8 0.31
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTCTTCTTTTCA
Found at i:20244550 original size:16 final size:16
Alignment explanation
Indices: 20244531--20244575 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
20244521 CTTTTCTCTC
20244531 TTTTTTTCTTCTTTT-A
1 TTTTTTTC-TCTTTTCA
*
20244547 TTTTCTTCTCTTTTCA
1 TTTTTTTCTCTTTTCA
20244563 TTTTTTT-TCTTTT
1 TTTTTTTCTCTTTT
20244576 GCATGAGCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTTCTCTTTTCA
Found at i:20244552 original size:13 final size:13
Alignment explanation
Indices: 20244522--20244560 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
20244512 GCCTTTGCTC
20244522 TTTTC-TCTCTTT
1 TTTTCTTCTCTTT
20244534 TTTTCTTCT-TTT
1 TTTTCTTCTCTTT
20244546 ATTTTCTTCTCTTT
1 -TTTTCTTCTCTTT
20244560 T
1 T
20244561 CATTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 8 0.33
13 13 0.54
14 3 0.12
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTCTTCTCTTT
Found at i:20249518 original size:17 final size:17
Alignment explanation
Indices: 20249485--20249543 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
20249475 CTAGATAAGT
*
20249485 AAAAGACTAAA-ACATAA
1 AAAAGA-TAAATAAATAA
20249502 AAAAGATAAATAAATAA
1 AAAAGATAAATAAATAA
*
20249519 ATAAA-ACAAATAAGATATA
1 A-AAAGATAAATAA-ATA-A
20249538 AAAAGA
1 AAAAGA
20249544 AAAGTTGGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
16 4 0.11
17 19 0.54
18 9 0.26
19 3 0.09
ACGTcount: A:0.73, C:0.05, G:0.07, T:0.15
Consensus pattern (17 bp):
AAAAGATAAATAAATAA
Found at i:20250515 original size:21 final size:21
Alignment explanation
Indices: 20250476--20250515 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20250466 ATTGAGCTTT
*
20250476 TCTTTTTTGTTTTTGTTTTTC
1 TCTTTTTTGTTTTTATTTTTC
20250497 TCTTTTTT-TTGTTTATTTT
1 TCTTTTTTGTT-TTTATTTT
20250516 GTTTTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.03, C:0.07, G:0.07, T:0.82
Consensus pattern (21 bp):
TCTTTTTTGTTTTTATTTTTC
Found at i:20251698 original size:20 final size:21
Alignment explanation
Indices: 20251665--20251703 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
20251655 GATAAAAATT
20251665 CTTTATTTATTTGAAAAGACC
1 CTTTATTTATTTGAAAAGACC
*
20251686 CTTTTTTTA-TTGAAAAGA
1 CTTTATTTATTTGAAAAGA
20251704 GTTTTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (21 bp):
CTTTATTTATTTGAAAAGACC
Found at i:20251888 original size:19 final size:18
Alignment explanation
Indices: 20251859--20251904 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
20251849 GGTTAAAAAT
20251859 AAAAT-AAAATAAAATTAG
1 AAAATAAAAATAAAA-TAG
20251877 AAAATAAAAATAAAATAG
1 AAAATAAAAATAAAATAG
*
20251895 AAAAGAAAAA
1 AAAATAAAAA
20251905 ACCTGCGATC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (18 bp):
AAAATAAAAATAAAATAG
Found at i:20251904 original size:24 final size:23
Alignment explanation
Indices: 20251853--20251904 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 23
20251843 AAAATGGGTT
20251853 AAAAATAAAATAAAATAAAATTAG
1 AAAAATAAAATAAAATAAAA-TAG
20251877 -AAAATAAAAATAAAATAGAAA-AG
1 AAAAAT-AAAATAAAATA-AAATAG
20251900 AAAAA
1 AAAAA
20251905 ACCTGCGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
23 7 0.28
24 15 0.60
25 3 0.12
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (23 bp):
AAAAATAAAATAAAATAAAATAG
Found at i:20251905 original size:19 final size:19
Alignment explanation
Indices: 20251859--20251905 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
20251849 GGTTAAAAAT
*
20251859 AAAATAAAATAAAATTAGA
1 AAAAAAAAATAAAATTAGA
*
20251878 AAATAAAAATAAAA-TAGA
1 AAAAAAAAATAAAATTAGA
20251896 AAAGAAAAAA
1 AAA-AAAAAA
20251906 CCTGCGATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (19 bp):
AAAAAAAAATAAAATTAGA
Found at i:20252960 original size:60 final size:60
Alignment explanation
Indices: 20252832--20253043 Score: 308
Period size: 60 Copynumber: 3.5 Consensus size: 60
20252822 TTTTGTGCAG
* *
20252832 GGAAAATTGATACTTTCAACTTTTTCC-CAAAAA---TATTTTTTTGAAACTTTGATTTCCAA
1 GGAAAATTGATACTTTCAAC-TTTTCCTCAAAAACCCT-TTTTTTTGAAAATTT-ATTTCTAA
20252891 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTTGAAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTTGAAAATTTATTTCTAA
* *
20252951 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCC-CTTTTTTGAAAATTTATTTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTTGAAAATTTA-TTTCTAA
*
20253011 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA
20253044 TATTTTTTTT
Statistics
Matches: 143, Mismatches: 5, Indels: 9
0.91 0.03 0.06
Matches are distributed among these distances:
58 6 0.04
59 41 0.29
60 81 0.57
61 14 0.10
62 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (60 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTTGAAAATTTATTTCTAA
Found at i:20255631 original size:8 final size:8
Alignment explanation
Indices: 20255602--20255659 Score: 64
Period size: 9 Copynumber: 6.9 Consensus size: 8
20255592 ATATATGCAA
*
20255602 ATTTTGTT
1 ATTTTTTT
20255610 ATTTTCTTGT
1 ATTTT-TT-T
20255620 -TTTTTTT
1 ATTTTTTT
20255627 ATTTTTTTT
1 A-TTTTTTT
20255636 ATTTTTTTT
1 A-TTTTTTT
20255645 ATTTTTTT
1 ATTTTTTT
20255653 ATTTTTT
1 ATTTTTT
20255660 AAAATTTGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
7 1 0.02
8 21 0.47
9 22 0.49
10 1 0.02
ACGTcount: A:0.10, C:0.02, G:0.03, T:0.84
Consensus pattern (8 bp):
ATTTTTTT
Found at i:20255631 original size:9 final size:9
Alignment explanation
Indices: 20255619--20255659 Score: 75
Period size: 9 Copynumber: 4.7 Consensus size: 9
20255609 TATTTTCTTG
20255619 TTTTTTTTA
1 TTTTTTTTA
20255628 TTTTTTTTA
1 TTTTTTTTA
20255637 TTTTTTTTA
1 TTTTTTTTA
20255646 -TTTTTTTA
1 TTTTTTTTA
20255654 TTTTTT
1 TTTTTT
20255660 AAAATTTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 8 0.26
9 23 0.74
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:20255632 original size:18 final size:17
Alignment explanation
Indices: 20255603--20255659 Score: 78
Period size: 17 Copynumber: 3.3 Consensus size: 17
20255593 TATATGCAAA
* * *
20255603 TTTTGTTATTTTCTTGT
1 TTTTTTTATTTTTTTAT
20255620 TTTTTTTATTTTTTTTAT
1 TTTTTTTA-TTTTTTTAT
20255638 TTTTTTTATTTTTTTAT
1 TTTTTTTATTTTTTTAT
20255655 TTTTT
1 TTTTT
20255660 AAAATTTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
17 21 0.58
18 15 0.42
ACGTcount: A:0.09, C:0.02, G:0.04, T:0.86
Consensus pattern (17 bp):
TTTTTTTATTTTTTTAT
Found at i:20255766 original size:9 final size:9
Alignment explanation
Indices: 20255739--20255787 Score: 54
Period size: 7 Copynumber: 5.9 Consensus size: 9
20255729 ATAGAGGCAA
20255739 CTTTTTTTG
1 CTTTTTTTG
20255748 --TTTTTT-
1 CTTTTTTTG
20255754 -TTTTTTTG
1 CTTTTTTTG
20255762 C-TTTTTTG
1 CTTTTTTTG
20255770 CTTTTTTTG
1 CTTTTTTTG
20255779 CCTTTTTTT
1 -CTTTTTTT
20255788 TTTAAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
7 12 0.34
8 8 0.23
9 7 0.20
10 8 0.23
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.82
Consensus pattern (9 bp):
CTTTTTTTG
Found at i:20255768 original size:17 final size:18
Alignment explanation
Indices: 20255748--20255790 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
20255738 ACTTTTTTTG
20255748 TTTTTTTTTTTTTG-CTT
1 TTTTTTTTTTTTTGCCTT
**
20255765 TTTTGCTTTTTTTGCCTT
1 TTTTTTTTTTTTTGCCTT
20255783 TTTTTTTT
1 TTTTTTTT
20255791 AAAAAAATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (18 bp):
TTTTTTTTTTTTTGCCTT
Found at i:20255784 original size:8 final size:8
Alignment explanation
Indices: 20255741--20255786 Score: 51
Period size: 9 Copynumber: 5.8 Consensus size: 8
20255731 AGAGGCAACT
20255741 TTTTTTG-
1 TTTTTTGC
*
20255748 TTTTTT-T
1 TTTTTTGC
20255755 TTTTTTGC
1 TTTTTTGC
20255763 TTTTTTGC
1 TTTTTTGC
20255771 TTTTTTTGCC
1 -TTTTTTG-C
20255781 TTTTTT
1 TTTTTT
20255787 TTTTAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 12 0.35
8 8 0.24
9 13 0.38
10 1 0.03
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.83
Consensus pattern (8 bp):
TTTTTTGC
Found at i:20255824 original size:132 final size:136
Alignment explanation
Indices: 20255509--20255869 Score: 462
Period size: 132 Copynumber: 2.7 Consensus size: 136
20255499 TTTTTTCTTT
* * * *
20255509 TTTTTTTTTTAAAAAAATCTTGATCAAAGCTCCTCTAAACAGAGGTTCAATGATTTTGAAAAACA
1 TTTTTTTTTTAAAAAAA---TGATCAAAGCTCCTCTAAGCAGAGGCTCAATGACTTTGAGAAACA
* * ** *
20255574 TAAACAAAGCTCCTCTAAATATATGCAAATTTTGTTATTTTCTTGTTTTTTTTATTTTTTTTATT
63 TAAACAAAGCTCCTCTAAATAGAGGCAAATTTTGTTATTTTCTTGTTTTTTTTAGCTTTTTTACT
**
20255639 TTTTTTATT
128 TTTTTTACC
* ** *
20255648 TTTTTATTTTTTAAAATTTGATCAAAGCTCCTCTAAGCAAAGGCTCAATGACTTTGAGAAACATA
1 TTTTT-TTTTTAAAAAAATGATCAAAGCTCCTCTAAGCAGAGGCTCAATGACTTTGAGAAACATA
* *
20255713 AACAAAGCTCCTCTAAATAGAGGCAACTTTT-TT-TGTTT-TT-TTTTTTTT-GCTTTTTTGCTT
65 AACAAAGCTCCTCTAAATAGAGGCAAATTTTGTTAT-TTTCTTGTTTTTTTTAGCTTTTTTACTT
*
20255773 TTTTTGCC
129 TTTTTACC
20255781 TTTTTTTTTTAAAAAAATGATCAAAGCTCCTCTAAGCAGAGGCTCAATGACTTTGAGAAACATAA
1 TTTTTTTTTTAAAAAAATGATCAAAGCTCCTCTAAGCAGAGGCTCAATGACTTTGAGAAACATAA
* *
20255846 ACAAAGCTGCTCTAAACAGAGGCA
66 ACAAAGCTCCTCTAAATAGAGGCA
20255870 CCACGACTTT
Statistics
Matches: 196, Mismatches: 24, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
132 78 0.40
133 18 0.09
134 8 0.04
135 3 0.02
136 5 0.03
137 70 0.36
139 5 0.03
140 9 0.05
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (136 bp):
TTTTTTTTTTAAAAAAATGATCAAAGCTCCTCTAAGCAGAGGCTCAATGACTTTGAGAAACATAA
ACAAAGCTCCTCTAAATAGAGGCAAATTTTGTTATTTTCTTGTTTTTTTTAGCTTTTTTACTTTT
TTTACC
Found at i:20255878 original size:45 final size:42
Alignment explanation
Indices: 20255802--20255925 Score: 142
Period size: 41 Copynumber: 2.9 Consensus size: 42
20255792 AAAAAATGAT
* * * *
20255802 CAAAGCTCCTCTAAGCAGAGGCTCAATGACTTTGAGAAACATAAA
1 CAAAGCTCCTCTAAACAGAGGCACCACGACTTTG-GAAA-AT-AA
* *
20255847 CAAAGCTGCTCTAAACAGAGGCACCACGACTTTGGAAAGTAA
1 CAAAGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAA
**
20255889 -ATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAA
1 CAAAGCTCCTCTAAACAGAGGCACCACGACTTTGGAAA
20255926 TGTAAATTGC
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 34 0.49
42 2 0.03
43 1 0.01
44 4 0.06
45 29 0.41
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (42 bp):
CAAAGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAA
Found at i:20255909 original size:41 final size:42
Alignment explanation
Indices: 20255855--20255939 Score: 163
Period size: 41 Copynumber: 2.0 Consensus size: 42
20255845 AACAAAGCTG
20255855 CTCTAAACAGAGGCACCACGACTTTGGAAA-GTAAATTGCTC
1 CTCTAAACAGAGGCACCACGACTTTGGAAATGTAAATTGCTC
20255896 CTCTAAACAGAGGCACCACGACTTTGGAAATGTAAATTGCTC
1 CTCTAAACAGAGGCACCACGACTTTGGAAATGTAAATTGCTC
20255938 CT
1 CT
20255940 TAACAATCAT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 30 0.70
42 13 0.30
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (42 bp):
CTCTAAACAGAGGCACCACGACTTTGGAAATGTAAATTGCTC
Found at i:20257185 original size:15 final size:16
Alignment explanation
Indices: 20257167--20257196 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20257157 TCAATTTGAA
20257167 TCTC-TTTTTTCATTT
1 TCTCATTTTTTCATTT
20257182 TCTCATTTTTTCATT
1 TCTCATTTTTTCATT
20257197 CATTCTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.70
Consensus pattern (16 bp):
TCTCATTTTTTCATTT
Found at i:20257218 original size:14 final size:13
Alignment explanation
Indices: 20257199--20257255 Score: 62
Period size: 13 Copynumber: 4.2 Consensus size: 13
20257189 TTTTCATTCA
20257199 TTCTTTCTTCTTTT
1 TTCTTTCTT-TTTT
20257213 TTCTTTCTTTTTT
1 TTCTTTCTTTTTT
20257226 TTCCTTT-TTTTTT
1 TT-CTTTCTTTTTT
*
20257239 TTCATCATCTTTTTT
1 TTC-T-TTCTTTTTT
20257254 TT
1 TT
20257256 TTCTCATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
12 1 0.03
13 15 0.39
14 14 0.37
15 8 0.21
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.79
Consensus pattern (13 bp):
TTCTTTCTTTTTT
Found at i:20257262 original size:16 final size:15
Alignment explanation
Indices: 20257220--20257266 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 15
20257210 TTTTTCTTTC
20257220 TTTTTTTTC-C-TTT
1 TTTTTTTTCTCATTT
20257233 TTTTTTTTCATCATCTT
1 TTTTTTTTC-TCAT-TT
20257250 TTTTTTTTCTCATTT
1 TTTTTTTTCTCATTT
20257265 TT
1 TT
20257267 CATCCATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 9 0.30
15 5 0.17
16 5 0.17
17 11 0.37
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTTTCTCATTT
Found at i:20261298 original size:60 final size:60
Alignment explanation
Indices: 20261134--20261304 Score: 220
Period size: 60 Copynumber: 2.8 Consensus size: 60
20261124 TTTTGTGCAG
* *
20261134 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAATATTTTTTTTTAGAAATTTTAATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTTCCC-AAAAATA-TTTTTTTT-GAAAATTTAATTTTCAA
**** * *
20261197 GGAAAATTGATACTTTCAAC-TTTTCCTCAAAAACCCCTTTTTTGAAAATTTATTTTTTAA
1 GGAAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTTTGAAAATTTAATTTTCAA
20261257 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTT-AAAAT
1 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTTGAAAAT
20261305 CTTTTTATCT
Statistics
Matches: 94, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
59 5 0.05
60 46 0.49
61 12 0.13
62 10 0.11
63 21 0.22
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (60 bp):
GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTTGAAAATTTAATTTTCAA
Found at i:20266152 original size:2 final size:2
Alignment explanation
Indices: 20266141--20266177 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
20266131 GAAAGCTGTA
20266141 AT AT AT -T 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
20266178 TTTTAAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:20271004 original size:52 final size:52
Alignment explanation
Indices: 20270918--20271074 Score: 208
Period size: 52 Copynumber: 3.0 Consensus size: 52
20270908 TATAACCATA
* * *
20270918 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* * *
20270970 CAAACATGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* * **
20271022 CAAACTTACCTATTAAGAATCCTCTTT-CTCTTGGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATCC-CTTTCCTCTTAGAATTCTTCTCCTGCAAGT
20271074 C
1 C
20271075 TTCTTGTCCA
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
52 89 0.96
53 4 0.04
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.38
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:20271109 original size:21 final size:22
Alignment explanation
Indices: 20271091--20271137 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
20271081 TCCATCAAGC
*
20271091 AATATCTGACAAATCTCAAACA
1 AATATCTAACAAATCTCAAACA
* *
20271113 AATCTCTAACAAATCTCAAAGA
1 AATATCTAACAAATCTCAAACA
20271135 AAT
1 AAT
20271138 CTCTTATGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.21, G:0.04, T:0.23
Consensus pattern (22 bp):
AATATCTAACAAATCTCAAACA
Found at i:20271115 original size:11 final size:11
Alignment explanation
Indices: 20271099--20271140 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
20271089 GCAATATCTG
20271099 ACAAATCTCAA
1 ACAAATCTCAA
*
20271110 ACAAATCTCTA
1 ACAAATCTCAA
20271121 ACAAATCTCAA
1 ACAAATCTCAA
*
20271132 AGAAATCTC
1 ACAAATCTC
20271141 TTATGGGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.50, C:0.26, G:0.02, T:0.21
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:20271124 original size:22 final size:22
Alignment explanation
Indices: 20271099--20271141 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
20271089 GCAATATCTG
20271099 ACAAATCTCAAACAAATCTCTA
1 ACAAATCTCAAACAAATCTCTA
*
20271121 ACAAATCTCAAAGAAATCTCT
1 ACAAATCTCAAACAAATCTCT
20271142 TATGGGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.26, G:0.02, T:0.23
Consensus pattern (22 bp):
ACAAATCTCAAACAAATCTCTA
Found at i:20272154 original size:52 final size:51
Alignment explanation
Indices: 20272013--20272169 Score: 179
Period size: 52 Copynumber: 3.0 Consensus size: 51
20272003 TATAACCATA
* * * *
20272013 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCCCT-TTCTCTTAGAATTCTTCTCTTGCAAGT
* *
20272065 CAAACATGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTTT-CTCTTAGAATTCTTCTCTTGCAAGT
* * * * * *
20272117 TAAACTTACCTATTAAGAATCTTCTTTCTCTTGGAATTATTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATC-CCTTTCTCTTAGAATTCTTCTCTTGCAAGT
20272169 C
1 C
20272170 TTCTTGTCCA
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
51 1 0.01
52 83 0.94
53 4 0.05
ACGTcount: A:0.26, C:0.25, G:0.10, T:0.39
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATCCCTTTCTCTTAGAATTCTTCTCTTGCAAGT
Done.