Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, 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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 120 of 121
Found at i:20881811 original size:40 final size:40
Alignment explanation
Indices: 20881568--20881823 Score: 212
Period size: 40 Copynumber: 6.2 Consensus size: 40
20881558 GAGGAGCTTT
* * *
20881568 ATTTATTTTTTCAAAGTCATTGAGCCTCTGTTTAGAGGAGT
1 ATTTA-TTTTTCAAAGTTATTGAGCCTCTATTTAGAGGAGC
* * * * *
20881609 GTTTATTTTTTCAAAGTTGTTGAGCCTCTATATAGATGAGG
1 ATTTA-TTTTTCAAAGTTATTGAGCCTCTATTTAGAGGAGC
* * * * *
20881650 ATTTA-TTTTCTAAAGTTGTTGAACATTTGTTTAGAGGAGCCCC
1 ATTTATTTTTC-AAAGTTATTGAGCCTCTATTTAGAGGAG---C
*
20881693 A-TTATTTTTTCAAAGTTATTGAGCCTTTATTTAGAGGAGC
1 ATTTA-TTTTTCAAAGTTATTGAGCCTCTATTTAGAGGAGC
* * * *
20881733 TTTATTTAATTTTTCAAAGTTGTTGAGCTTTTGTTTAGAGGAGC
1 ---ATTT-ATTTTTCAAAGTTATTGAGCCTCTATTTAGAGGAGC
*
20881777 ATTTATTTTTCAAAGTTATTGAGCCTCTACTTAGAGGAG-
1 ATTTATTTTTCAAAGTTATTGAGCCTCTATTTAGAGGAGC
*
20881816 TTTTATTT
1 ATTTATTT
20881824 ATTTTTCTAA
Statistics
Matches: 176, Mismatches: 28, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
39 12 0.07
40 53 0.30
41 42 0.24
42 3 0.02
43 26 0.15
44 39 0.22
45 1 0.01
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.46
Consensus pattern (40 bp):
ATTTATTTTTCAAAGTTATTGAGCCTCTATTTAGAGGAGC
Found at i:20881829 original size:127 final size:125
Alignment explanation
Indices: 20881557--20881846 Score: 309
Period size: 127 Copynumber: 2.3 Consensus size: 125
20881547 GCTTCTGTTC
* * * * *
20881557 AGAGGAGCTTTATTTATTTTTTCAAAGTCATTGAGCCTCTGTTTAGAGGAGTGTTTATTTTTTCA
1 AGAGGAGCTTTATTTATTTTTTCAAAGTTATTGAGCCTTTATTTAGAGGAGTATTTAATTTTTCA
* * * * **
20881622 AAGTTGTTGAGCCTCTATATAGATGAGGATTTATTTTCTAAAGTTGTTGAACATTTGTTT
66 AAGTTGTTGAGCCTCTATATAGAGGAGCATTTATTTTCTAAAGTTATTGAACATCTACTT
***
20881682 AGAGGAGCCCCA-TTATTTTTTCAAAGTTATTGAGCCTTTATTTAGAGGAGCTTTATTTAATTTT
1 AGAGGAGCTTTATTTATTTTTTCAAAGTTATTGAGCCTTTATTTAGAGGAG---TATTTAATTTT
* * * * * *
20881746 TCAAAGTTGTTGAGCTTTTGTTTAGAGGAGCATTTATTTT-TCAAAGTTATTGAGCCTCTACTT
63 TCAAAGTTGTTGAGCCTCTATATAGAGGAGCATTTATTTTCT-AAAGTTATTGAACATCTACTT
* * *
20881809 AGAGGAGTTTTATTTA-TTTTTCTAAGTT-GTGAGCCTTT
1 AGAGGAGCTTTATTTATTTTTTCAAAGTTATTGAGCCTTT
20881847 GCTTAGGGGA
Statistics
Matches: 134, Mismatches: 26, Indels: 9
0.79 0.15 0.05
Matches are distributed among these distances:
124 35 0.26
125 9 0.07
126 10 0.07
127 77 0.57
128 3 0.02
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.46
Consensus pattern (125 bp):
AGAGGAGCTTTATTTATTTTTTCAAAGTTATTGAGCCTTTATTTAGAGGAGTATTTAATTTTTCA
AAGTTGTTGAGCCTCTATATAGAGGAGCATTTATTTTCTAAAGTTATTGAACATCTACTT
Found at i:20881909 original size:9 final size:9
Alignment explanation
Indices: 20881895--20881927 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
20881885 TCTGATTATT
20881895 AAAAAACAA
1 AAAAAACAA
20881904 AAAAAACAA
1 AAAAAACAA
20881913 AAAAAACAA
1 AAAAAACAA
20881922 AAAAAA
1 AAAAAA
20881928 AGTGCTGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAACAA
Found at i:20886980 original size:6 final size:6
Alignment explanation
Indices: 20886966--20886997 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
20886956 TTGAATCCTT
*
20886966 GAATTG GAATAG GAATAG GAATAG GAATAG GA
1 GAATAG GAATAG GAATAG GAATAG GAATAG GA
20886998 GAGGGCAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.34, T:0.19
Consensus pattern (6 bp):
GAATAG
Found at i:20887366 original size:14 final size:15
Alignment explanation
Indices: 20887336--20887383 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
20887326 ATTCATTTAA
20887336 ATTTGTTTAAGATTT
1 ATTTGTTTAAGATTT
20887351 ATTTGTTTAA-ATTT
1 ATTTGTTTAAGATTT
* * *
20887365 ATTTGATTATGGTTT
1 ATTTGTTTAAGATTT
20887380 ATTT
1 ATTT
20887384 ATTATTAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (15 bp):
ATTTGTTTAAGATTT
Found at i:20888806 original size:61 final size:57
Alignment explanation
Indices: 20888717--20888878 Score: 153
Period size: 61 Copynumber: 2.7 Consensus size: 57
20888707 GTTTTTTTTT
* * *
20888717 TTTAAATTTTTGTTTGCAAGAAAAATTGATACTTTCAATTTTTTCTCAAAATAAATATCC
1 TTTAAATTTTTATTT-CAAGGAAAATTGATACTTTCAATTTTTGCTCAAAA-AAATAT-C
* * * * *
20888777 TTTAAATATTTTATCTTCAAGGAAAATTGATATTTTTAACTTTTGCTCAAAAAAATGTT
1 TTTAAAT-TTTTAT-TTCAAGGAAAATTGATACTTTCAATTTTTGCTCAAAAAAATATC
* * * **
20888836 TTTTAGTTCTTATTTTTTAGGAAAATTGATACTTTCAATTTTT
1 TTTAAATTTTTA-TTTCAAGGAAAATTGATACTTTCAATTTTT
20888879 CTTAAAACAT
Statistics
Matches: 83, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
58 28 0.34
59 6 0.07
60 12 0.14
61 35 0.42
62 2 0.02
ACGTcount: A:0.34, C:0.09, G:0.08, T:0.49
Consensus pattern (57 bp):
TTTAAATTTTTATTTCAAGGAAAATTGATACTTTCAATTTTTGCTCAAAAAAATATC
Found at i:20891155 original size:17 final size:16
Alignment explanation
Indices: 20891101--20891148 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 16
20891091 GAAGAGTCGT
20891101 AAGATTTTCAGATTCGC
1 AAGA-TTTCAGATTCGC
*
20891118 AAGAATTCGAGATTCGC
1 AAGATTTC-AGATTCGC
20891135 AAGACTTTCAGATT
1 AAGA-TTTCAGATT
20891149 TGTAAGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 3 0.11
17 21 0.78
18 3 0.11
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (16 bp):
AAGATTTCAGATTCGC
Found at i:20891164 original size:34 final size:34
Alignment explanation
Indices: 20891077--20891165 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 34
20891067 TAAGAATAAG
* * * * *
20891077 GATTCTCAAGAATTGAAGAGTCGTAAGATTTTCA
1 GATTCGCAAGAATTGGAGATTCGCAAGACTTTCA
*
20891111 GATTCGCAAGAATTCGAGATTCGCAAGACTTTCA
1 GATTCGCAAGAATTGGAGATTCGCAAGACTTTCA
* *
20891145 GATTTGTAAGAATTGGAGATT
1 GATTCGCAAGAATTGGAGATT
20891166 TGTGAAAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.31
Consensus pattern (34 bp):
GATTCGCAAGAATTGGAGATTCGCAAGACTTTCA
Found at i:20891200 original size:15 final size:17
Alignment explanation
Indices: 20891144--20891259 Score: 87
Period size: 17 Copynumber: 6.9 Consensus size: 17
20891134 CAAGACTTTC
* * *
20891144 AGATTTGTAAGAATTGG
1 AGATTTGCAAAAATTAG
*
20891161 AGATTTGTGAAAAATTAG
1 AGATTTG-CAAAAATTAG
20891179 AGATTTGCAAAAATT-G
1 AGATTTGCAAAAATTAG
20891195 -GATTTGCAAAAATTAG
1 AGATTTGCAAAAATTAG
* * **
20891211 AGA-TTGACAAGACTTTT
1 AGATTTG-CAAAAATTAG
**
20891228 AGATTTGCAAAAA-GGG
1 AGATTTGCAAAAATTAG
*
20891244 AAATTTGCAAAAATTA
1 AGATTTGCAAAAATTA
20891260 AAGGTTCGTA
Statistics
Matches: 77, Mismatches: 16, Indels: 12
0.73 0.15 0.11
Matches are distributed among these distances:
15 14 0.18
16 17 0.22
17 29 0.38
18 17 0.22
ACGTcount: A:0.43, C:0.05, G:0.21, T:0.31
Consensus pattern (17 bp):
AGATTTGCAAAAATTAG
Found at i:20891315 original size:25 final size:25
Alignment explanation
Indices: 20891287--20891341 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
20891277 TAGATTCACT
*
20891287 AGATTTT-CAGATTCGA-AAGAATTTA
1 AGATTTTGC-GATTC-ACAAGAATTGA
20891312 AGATTTTGCGATTCACAAGAATTGA
1 AGATTTTGCGATTCACAAGAATTGA
20891337 AGATT
1 AGATT
20891342 CATAAAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 1 0.04
25 25 0.93
26 1 0.04
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (25 bp):
AGATTTTGCGATTCACAAGAATTGA
Found at i:20896791 original size:56 final size:56
Alignment explanation
Indices: 20896659--20896831 Score: 186
Period size: 56 Copynumber: 3.0 Consensus size: 56
20896649 TAATGATTTT
** * *
20896659 ATTT-AAAGAAAAATTGATACTTTCAACTTTTTCCCCAAATACATATTTTTTAAAATTTTTA
1 ATTTCAAA-AAAAATTGATACTTTCAACTTTTT-CTTAAA-AC--ATTTTTGAAAA-TTTCA
* * *
20896720 TTTTCAAGAAAAATTGATACTCTCAACTTTTTCTTAAAACATTTTTGAAAATTTCA
1 ATTTCAAAAAAAATTGATACTTTCAACTTTTTCTTAAAACATTTTTGAAAATTTCA
* *
20896776 ATTTCAAAAAAAATTGATACTTTCAAGTTTTCCTTAAAACATTTTTTGAAATATTT
1 ATTTCAAAAAAAATTGATACTTTCAACTTTTTCTTAAAACA-TTTTTGAAA-ATTT
20896832 TTTATTTATT
Statistics
Matches: 97, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
56 40 0.41
57 19 0.20
58 4 0.04
59 2 0.02
60 4 0.04
61 26 0.27
62 2 0.02
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.44
Consensus pattern (56 bp):
ATTTCAAAAAAAATTGATACTTTCAACTTTTTCTTAAAACATTTTTGAAAATTTCA
Found at i:20901441 original size:20 final size:19
Alignment explanation
Indices: 20901399--20901444 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
20901389 CACGTGGCAC
* **
20901399 TTTTTCACTTTTTTTTTGT
1 TTTTTAACTTTTTTTTTAA
20901418 TTTTTAACTTTTTTTTATAA
1 TTTTTAACTTTTTTTT-TAA
20901438 TTTTTAA
1 TTTTTAA
20901445 TATTTAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTTAACTTTTTTTTTAA
Found at i:20901887 original size:18 final size:18
Alignment explanation
Indices: 20901859--20901903 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
20901849 ATTGTTTTTT
20901859 CTTTTTA-AATATTTATAA
1 CTTTTTATAATATTT-TAA
20901877 -TTTTTATAATATTTTAA
1 CTTTTTATAATATTTTAA
20901894 CTTTTT-TAAT
1 CTTTTTATAAT
20901904 GTGGAATCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (18 bp):
CTTTTTATAATATTTTAA
Found at i:20901901 original size:19 final size:17
Alignment explanation
Indices: 20901860--20901899 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
20901850 TTGTTTTTTC
20901860 TTTTTAAATATTTATAA
1 TTTTTAAATATTTATAA
20901877 TTTTTATAATATTT-TAA
1 TTTTTA-AATATTTATAA
20901894 CTTTTT
1 -TTTTT
20901900 TAATGTGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTAAATATTTATAA
Found at i:20903848 original size:20 final size:18
Alignment explanation
Indices: 20903793--20903849 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 18
20903783 CCTCAATGAG
20903793 CTTTTTTTTTTTTTTTTC
1 CTTTTTTTTTTTTTTTTC
* *
20903811 ATTTTTTCTCTTTCTTTTTC
1 CTTTTTT-T-TTTTTTTTTC
20903831 CTTTTTTGTGTTTTTTTTT
1 CTTTTTT-T-TTTTTTTTT
20903850 TTAATTTTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
18 6 0.19
19 1 0.03
20 24 0.77
ACGTcount: A:0.02, C:0.12, G:0.04, T:0.82
Consensus pattern (18 bp):
CTTTTTTTTTTTTTTTTC
Found at i:20904285 original size:13 final size:15
Alignment explanation
Indices: 20904269--20904300 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
20904259 TTTAAAAATT
20904269 TTTTCCTT-TTTT-A
1 TTTTCCTTATTTTAA
20904282 TTTTCCTTATTTTAA
1 TTTTCCTTATTTTAA
20904297 TTTT
1 TTTT
20904301 TTAAGGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 4 0.24
15 5 0.29
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTCCTTATTTTAA
Found at i:20904397 original size:14 final size:14
Alignment explanation
Indices: 20904370--20904400 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
20904360 TATTCACATG
20904370 TTATTTTCATTTTT
1 TTATTTTCATTTTT
20904384 TTATCTTTCATTTTT
1 TTAT-TTTCATTTTT
20904399 TT
1 TT
20904401 TGTTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (14 bp):
TTATTTTCATTTTT
Found at i:20918967 original size:13 final size:13
Alignment explanation
Indices: 20918948--20918987 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
20918938 ATTTACTTAA
20918948 ATATATTAAAATT
1 ATATATTAAAATT
* *
20918961 TTATATTAAAATA
1 ATATATTAAAATT
*
20918974 ATATATAAAAATT
1 ATATATTAAAATT
20918987 A
1 A
20918988 AAAAAATTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATATTAAAATT
Found at i:20918988 original size:32 final size:31
Alignment explanation
Indices: 20918915--20918990 Score: 77
Period size: 32 Copynumber: 2.4 Consensus size: 31
20918905 ATTTTTAAAA
*
20918915 ATAAAAA-TAAAATTTTTATCAAAATTTACT
1 ATAAAAATTAAAATTTTTATCAAAATATACT
*
20918945 -TAAATATATTAAAATTTTATATTAAAATAATA-T
1 ATAAA-A-ATTAAAATTTT-TATCAAAAT-ATACT
20918978 ATAAAAATTAAAA
1 ATAAAAATTAAAA
20918991 AAATTAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
29 4 0.11
30 1 0.03
31 1 0.03
32 16 0.42
33 10 0.26
34 6 0.16
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (31 bp):
ATAAAAATTAAAATTTTTATCAAAATATACT
Found at i:20922978 original size:2 final size:2
Alignment explanation
Indices: 20922971--20922996 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20922961 ACTATACATG
20922971 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
20922997 AAACTGTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20927440 original size:42 final size:42
Alignment explanation
Indices: 20927393--20927481 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 42
20927383 AGAAGAAAAG
*
20927393 CTTAAATAAGTTAGAAGTGCTGGTAGAAAGGGTAACCACAAA
1 CTTAAATAAGTTAGAAGTACTGGTAGAAAGGGTAACCACAAA
* *
20927435 CTTAAATAAGTTAGAAGTACTGGTCGAAAGGGTAACTACAAA
1 CTTAAATAAGTTAGAAGTACTGGTAGAAAGGGTAACCACAAA
20927477 CTTAA
1 CTTAA
20927482 GTAGATTTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (42 bp):
CTTAAATAAGTTAGAAGTACTGGTAGAAAGGGTAACCACAAA
Found at i:20929274 original size:142 final size:138
Alignment explanation
Indices: 20929121--20929382 Score: 319
Period size: 138 Copynumber: 1.9 Consensus size: 138
20929111 CTTGATCACC
* * **
20929121 TTAAGTCTAACACTACTCCTAATCAAAAGCTTTTTTTTTTTTTTTGTATGTAATTGAGCTTGTGT
1 TTAAGTCTAACACTACTCCTAATCAAAAGC----ATTTTTTATTTGTATGTAATTGAGCTTGCCT
* * * *
20929186 AGTCTGACAATAATTAAATTATTAAA-AGCTAACATCTCTATTCTGTTGTCTACTATTCATATAC
62 AGCCTGACAATAATTAAAATA-TAAAGAACTAAAATCTCTATTCTGTTGTCTACTATTCATATAC
20929250 ACCCTAATTACCT
126 ACCCTAATTACCT
* ** *
20929263 TTAAGTCTAACACTAGTCCTAATTGAAAGCATTTTTTATTTGTATGTAATTGAGCTTGCCTTGCC
1 TTAAGTCTAACACTACTCCTAATCAAAAGCATTTTTTATTTGTATGTAATTGAGCTTGCCTAGCC
* * * * *
20929328 TGACATTAATTAAAATATAAAGAATTAAAATCTTTGTTCTGTTGTCTATTATTCA
66 TGACAATAATTAAAATATAAAGAACTAAAATCTCTATTCTGTTGTCTACTATTCA
20929383 ATGCAAAAGG
Statistics
Matches: 102, Mismatches: 17, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
137 4 0.04
138 71 0.70
142 27 0.26
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.43
Consensus pattern (138 bp):
TTAAGTCTAACACTACTCCTAATCAAAAGCATTTTTTATTTGTATGTAATTGAGCTTGCCTAGCC
TGACAATAATTAAAATATAAAGAACTAAAATCTCTATTCTGTTGTCTACTATTCATATACACCCT
AATTACCT
Found at i:20934960 original size:13 final size:13
Alignment explanation
Indices: 20934942--20934969 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
20934932 AGACTAAAGC
20934942 GAAGAGTGAATGA
1 GAAGAGTGAATGA
20934955 GAAGAGTGAATGA
1 GAAGAGTGAATGA
20934968 GA
1 GA
20934970 TATACACAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.39, T:0.14
Consensus pattern (13 bp):
GAAGAGTGAATGA
Found at i:20935470 original size:12 final size:12
Alignment explanation
Indices: 20935453--20935483 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
20935443 CCTCTTAGGT
20935453 GGTAGCTGGCTA
1 GGTAGCTGGCTA
20935465 GGTAGCTGGCTA
1 GGTAGCTGGCTA
*
20935477 GGCAGCT
1 GGTAGCT
20935484 TTGTGGGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.19, G:0.42, T:0.23
Consensus pattern (12 bp):
GGTAGCTGGCTA
Found at i:20938484 original size:16 final size:16
Alignment explanation
Indices: 20938445--20938487 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
20938435 AGATAAATGT
*
20938445 AAATTTTGAAACTTTA
1 AAATTTTTAAACTTTA
20938461 AAATTTTTAAACTTTA
1 AAATTTTTAAACTTTA
20938477 AAATTTTTAAA
1 AAATTTTTAAA
20938488 AATTAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (16 bp):
AAATTTTTAAACTTTA
Found at i:20938493 original size:16 final size:16
Alignment explanation
Indices: 20938458--20938494 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
20938448 TTTTGAAACT
**
20938458 TTAAAATTTTTAAACT
1 TTAAAATTTTTAAAAA
20938474 TTAAAATTTTTAAAAA
1 TTAAAATTTTTAAAAA
20938490 TTAAA
1 TTAAA
20938495 TAATTGATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAAAATTTTTAAAAA
Found at i:20939752 original size:5 final size:5
Alignment explanation
Indices: 20939742--20939768 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
20939732 GCTACTTAAT
20939742 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
20939769 ACACAAGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:20943962 original size:30 final size:30
Alignment explanation
Indices: 20943914--20944002 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
20943904 TTGTGTGAAT
* *
20943914 AATTGATTTAGGTACAAATTAAAGATTAAG
1 AATTTATTTAAGTACAAATTAAAGATTAAG
* *
20943944 AATTTATTTGAA-TACAAATTAGAGCTTAAG
1 AATTTATTT-AAGTACAAATTAAAGATTAAG
* * *
20943974 CATTTATTTAAGTGCACATTAAAGATTAA
1 AATTTATTTAAGTACAAATTAAAGATTAA
20944003 TAGGTTATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
29 2 0.04
30 45 0.94
31 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (30 bp):
AATTTATTTAAGTACAAATTAAAGATTAAG
Found at i:20945181 original size:29 final size:29
Alignment explanation
Indices: 20945138--20945202 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
20945128 GAAAAAAATA
*
20945138 TCTATTTAAAGATAGATTTTTCATTAAACC
1 TCTA-TTAAAGATAGATTTTTCATCAAACC
20945168 TCTATTAAAGATAGATTTTTCATCAAACC
1 TCTATTAAAGATAGATTTTTCATCAAACC
20945197 TCTATT
1 TCTATT
20945203 TTAATTGTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 30 0.88
30 4 0.12
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.43
Consensus pattern (29 bp):
TCTATTAAAGATAGATTTTTCATCAAACC
Found at i:20945423 original size:30 final size:29
Alignment explanation
Indices: 20945339--20945425 Score: 81
Period size: 26 Copynumber: 3.1 Consensus size: 29
20945329 AATAAGTTTA
*
20945339 ATAATAAAAAATTATTTAAATTAAAATTT
1 ATAATAAAAAATCATTTAAATTAAAATTT
* * * * *
20945368 AT--TAAAAATTGA-ATAAATGAGAATTT
1 ATAATAAAAAATCATTTAAATTAAAATTT
*
20945394 AGTAATAAAAAGTCATTTAAATTAAAATTT
1 A-TAATAAAAAATCATTTAAATTAAAATTT
20945424 AT
1 AT
20945426 TAAAAATATT
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
26 12 0.27
27 9 0.20
29 11 0.25
30 12 0.27
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (29 bp):
ATAATAAAAAATCATTTAAATTAAAATTT
Found at i:20945728 original size:151 final size:153
Alignment explanation
Indices: 20945569--20945860 Score: 430
Period size: 151 Copynumber: 1.9 Consensus size: 153
20945559 TCTAAAACTA
* * *
20945569 TTAAAAGTGAA-CGATATAAATATCCTTACAAATTTTAAGAAATAACAAATTTACCTTTAAATTT
1 TTAAAAGTGAATCG-CATAAATATCCCTACAAATTTTAAAAAATAACAAATTTACCTTTAAATTT
* * *
20945633 CTAGCATTT-TTTATTTATGTAGTAAAGATTATTTTCCATTAAATATATATA-A-TTTATTAGTC
65 CTAGCATTTATTTATTTATGTAATAAAAATTATTTGCCATTAAATATATA-ACATTTTATTAGTC
20945695 AATTATTTAAATTAATCCAAAAGTG
129 AATTATTTAAATTAATCCAAAAGTG
**
20945720 TTAAAAGTGAATCGCATAAATATCCCTATGAATTTTAAAAAATAACAAATTTACCTTTAAATTTC
1 TTAAAAGTGAATCGCATAAATATCCCTACAAATTTTAAAAAATAACAAATTTACCTTTAAATTTC
* * * *
20945785 TAGCATTTATTTATTTATTTAATAAAAATTATTTGCCATTAAATATATAACATTTTATTTGTTAG
66 TAGCATTTATTTATTTATGTAATAAAAATTATTTGCCATTAAATATATAACATTTTATTAGTCAA
20945850 TTATTTAAATT
131 TTATTTAAATT
20945861 TAAATCAATT
Statistics
Matches: 125, Mismatches: 12, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
151 66 0.53
152 39 0.31
153 20 0.16
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (153 bp):
TTAAAAGTGAATCGCATAAATATCCCTACAAATTTTAAAAAATAACAAATTTACCTTTAAATTTC
TAGCATTTATTTATTTATGTAATAAAAATTATTTGCCATTAAATATATAACATTTTATTAGTCAA
TTATTTAAATTAATCCAAAAGTG
Found at i:20946354 original size:20 final size:24
Alignment explanation
Indices: 20946311--20946355 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
20946301 GATCAATTAA
20946311 AATTAAAGTTCATACAAAATTATT
1 AATTAAAGTTCATACAAAATTATT
20946335 AATTAAA-TT-AT-CAAAA-TATT
1 AATTAAAGTTCATACAAAATTATT
20946355 A
1 A
20946356 TTGAGAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.24
21 5 0.24
22 2 0.10
23 2 0.10
24 7 0.33
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (24 bp):
AATTAAAGTTCATACAAAATTATT
Found at i:20948333 original size:22 final size:22
Alignment explanation
Indices: 20948303--20948350 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
20948293 TAAATTATGG
*
20948303 ATAATTTAATAGGAAA-ACAATA
1 ATAACTTAATAGGAAATA-AATA
*
20948325 ATAACTTAATAGTAAATAAATA
1 ATAACTTAATAGGAAATAAATA
20948347 ATAA
1 ATAA
20948351 TTTAGTCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.29
Consensus pattern (22 bp):
ATAACTTAATAGGAAATAAATA
Found at i:20948410 original size:22 final size:22
Alignment explanation
Indices: 20948384--20948444 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
20948374 ATAATGTATG
20948384 ATAACATAATAATAAAT-ACATA
1 ATAACATAATAATAAATAACA-A
* **
20948406 ATAACATAGTAGGAAATAACAA
1 ATAACATAATAATAAATAACAA
* *
20948428 ATAACTTAACAATAAAT
1 ATAACATAATAATAAAT
20948445 CATTTATACA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
22 27 0.90
23 3 0.10
ACGTcount: A:0.61, C:0.10, G:0.05, T:0.25
Consensus pattern (22 bp):
ATAACATAATAATAAATAACAA
Found at i:20948541 original size:44 final size:44
Alignment explanation
Indices: 20948479--20948590 Score: 118
Period size: 44 Copynumber: 2.5 Consensus size: 44
20948469 TAACACATAT
*
20948479 TAGTAAATTAA-AGATAACTTAATAAAAAATAAATGATAACTTAG
1 TAGTAAATTAATA-ATAACTTAATAAAAAATAAATGATAACTTAA
* * * ** * * *
20948523 TAGTTAATTATTAATAACTTAGTAATGAGTCAATGATATCTTAA
1 TAGTAAATTAATAATAACTTAATAAAAAATAAATGATAACTTAA
*
20948567 TAGTAAATTAATGATAACTTAATA
1 TAGTAAATTAATAATAACTTAATA
20948591 GTATATAAGA
Statistics
Matches: 54, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
44 53 0.98
45 1 0.02
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (44 bp):
TAGTAAATTAATAATAACTTAATAAAAAATAAATGATAACTTAA
Found at i:20948579 original size:22 final size:22
Alignment explanation
Indices: 20948479--20948593 Score: 104
Period size: 22 Copynumber: 5.2 Consensus size: 22
20948469 TAACACATAT
*
20948479 TAGTAAATTAAAGATAACTTAA
1 TAGTAAATTAATGATAACTTAA
** * *
20948501 TAAAAAATAAATGATAACTTAG
1 TAGTAAATTAATGATAACTTAA
* * * *
20948523 TAGTTAATTATTAATAACTTAG
1 TAGTAAATTAATGATAACTTAA
* * * * *
20948545 TAATGAGTCAATGATATCTTAA
1 TAGTAAATTAATGATAACTTAA
20948567 TAGTAAATTAATGATAACTTAA
1 TAGTAAATTAATGATAACTTAA
20948589 TAGTA
1 TAGTA
20948594 TATAAGATTC
Statistics
Matches: 69, Mismatches: 24, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 69 1.00
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (22 bp):
TAGTAAATTAATGATAACTTAA
Found at i:20948943 original size:22 final size:22
Alignment explanation
Indices: 20948918--20949582 Score: 125
Period size: 22 Copynumber: 30.2 Consensus size: 22
20948908 AGCTTAGTAA
*
20948918 TAAATCAATGATAATTTAATAG
1 TAAATCAATGATAACTTAATAG
*
20948940 TAAAT-AATTTATAAC-TAAGTAG
1 TAAATCAA-TGATAACTTAA-TAG
* * * *
20948962 TAATTAAT-AATTAAAAATTAAAAG
1 T-A--AATCAATGATAACTTAATAG
*
20948986 TAAATCAAT-ATAACTTAATAA
1 TAAATCAATGATAACTTAATAG
* *
20949007 T-AATC-ATCAGTAAATTAATAG
1 TAAATCAATGA-TAACTTAATAG
* * * * *
20949028 TTAATTAGTAATAATTTAATATAG
1 TAAATCAATGATAACTT-A-ATAG
* *
20949052 TAAATTAAAGATATAACTTAATAG
1 TAAATCAATG--ATAACTTAATAG
* * * * *
20949076 TATATCAATTATTATTTAGTAG
1 TAAATCAATGATAACTTAATAG
* * *
20949098 TAAATTAGTAATAA-TATAATAG
1 TAAATCAATGATAACT-TAATAG
* * *
20949120 TCAAAGC-ATAATAACTTAATAA
1 T-AAATCAATGATAACTTAATAG
* * *
20949142 TAAATCAATTATAA-TATAGTTG
1 TAAATCAATGATAACT-TAATAG
* * * *
20949164 TAAATGC-ATAATAACATAGTTG
1 TAAAT-CAATGATAACTTAATAG
* *
20949186 TAAATTAATGATGAA-TTCATA-
1 TAAATCAATGAT-AACTTAATAG
20949207 -AAA--AATGATAACTTAATAG
1 TAAATCAATGATAACTTAATAG
* * * * * * *
20949226 TTAATTATTAATAATTTAGTGG
1 TAAATCAATGATAACTTAATAG
* *
20949248 TAAATCAATGAAAACTTAGTAG
1 TAAATCAATGATAACTTAATAG
* * * *
20949270 TAAATTAGTGATAGCATAATAG
1 TAAATCAATGATAACTTAATAG
** * **
20949292 TAAATTTA-GTTTAGTTTAATAG
1 TAAATCAATG-ATAACTTAATAG
* * * * *
20949314 TAATTAAATTATAAATTTAGTAG
1 TAAATCAATGAT-AACTTAATAG
* **
20949337 TAAATC-ATAAATAACTT-AGCG
1 TAAATCAAT-GATAACTTAATAG
* *
20949358 ATAAATCAATTATAATTTAATAG
1 -TAAATCAATGATAACTTAATAG
* * *
20949381 CT-AATCACT-AAAACTCAATAG
1 -TAAATCAATGATAACTTAATAG
**
20949402 TAAATCAATGATAACAAAATAG
1 TAAATCAATGATAACTTAATAG
* ** * *
20949424 CAAATGTATAAT-AGTATAATAG
1 TAAATCAATGATAACT-TAATAG
* * *
20949446 TAAATCATTAATAACTTAGTAG
1 TAAATCAATGATAACTTAATAG
* * * * *
20949468 TAAATTATTAATACCTTAGTAG
1 TAAATCAATGATAACTTAATAG
* * *
20949490 TAAATCACTAATAACATAATAG
1 TAAATCAATGATAACTTAATAG
* *
20949512 TAAAAT-AATGATAACTTAGTTG
1 T-AAATCAATGATAACTTAATAG
* * * *
20949534 TAAATTAGTGATAATTTAGTTA-
1 TAAATCAATGATAACTTA-ATAG
* *
20949556 TAAATCAATGATAATTTAATTG
1 TAAATCAATGATAACTTAATAG
20949578 TAAAT
1 TAAAT
20949583 TAGTTAGTTA
Statistics
Matches: 464, Mismatches: 135, Indels: 88
0.68 0.20 0.13
Matches are distributed among these distances:
17 2 0.00
18 11 0.02
19 2 0.00
20 11 0.02
21 56 0.12
22 301 0.65
23 38 0.08
24 28 0.06
25 9 0.02
26 6 0.01
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (22 bp):
TAAATCAATGATAACTTAATAG
Found at i:20949553 original size:66 final size:66
Alignment explanation
Indices: 20949439--20949562 Score: 153
Period size: 66 Copynumber: 1.9 Consensus size: 66
20949429 GTATAATAGT
* * *
20949439 ATAATAGTAAATCATTAATAACTTAGTAGTAAATTATTAATACCTTAG-TAGTAAATCACTAATA
1 ATAATAGTAAATCAATAATAACTTAGTAGTAAATTAGTAATAACTTAGTTA-TAAATCACTAATA
20949503 AC
65 AC
* * * *
20949505 ATAATAGTAAAAT-AATGATAACTTAGTTGTAAATTAGTGATAATTTAGTTATAAATCA
1 ATAATAGT-AAATCAATAATAACTTAGTAGTAAATTAGTAATAACTTAGTTATAAATCA
20949563 ATGATAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
66 43 0.88
67 6 0.12
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.36
Consensus pattern (66 bp):
ATAATAGTAAATCAATAATAACTTAGTAGTAAATTAGTAATAACTTAGTTATAAATCACTAATAA
C
Found at i:20949608 original size:22 final size:22
Alignment explanation
Indices: 20949590--20949689 Score: 121
Period size: 22 Copynumber: 4.5 Consensus size: 22
20949580 AATTAGTTAG
20949590 TTATTAATAACTTTATAGTAAA
1 TTATTAATAACTTTATAGTAAA
* *
20949612 TCACTAATAACTTTATAGTAAA
1 TTATTAATAACTTTATAGTAAA
* * *
20949634 TCAGTAATAA-TATTATAATAAA
1 TTATTAATAACT-TTATAGTAAA
*
20949656 TTATTAATAACTTAATAGTAAA
1 TTATTAATAACTTTATAGTAAA
*
20949678 TTATCAATAACT
1 TTATTAATAACT
20949690 AAGTAATACA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
21 1 0.01
22 65 0.97
23 1 0.01
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (22 bp):
TTATTAATAACTTTATAGTAAA
Found at i:20949697 original size:44 final size:44
Alignment explanation
Indices: 20949616--20949767 Score: 123
Period size: 44 Copynumber: 3.5 Consensus size: 44
20949606 AGTAAATCAC
* *
20949616 TAATAACTTTATAGTAAATCAGT-AATAA-TATTA-TAATAAATTAT
1 TAATAACTTAATAGTAAATTA-TCAATAACTA--AGTAATAAATTAT
* *
20949660 TAATAACTTAATAGTAAATTATCAATAACTAAGTAATACATCAT
1 TAATAACTTAATAGTAAATTATCAATAACTAAGTAATAAATTAT
* * * * * * *
20949704 TTATAGCTTAGTAGTAAATAATCTATAACTTAGTGATAAATTA-
1 TAATAACTTAATAGTAAATTATCAATAACTAAGTAATAAATTAT
* * *
20949747 TGATAATTTAGTAGTAAATTA
1 TAATAACTTAATAGTAAATTA
20949768 GTGATAAGAT
Statistics
Matches: 88, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
43 19 0.22
44 67 0.76
45 2 0.02
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.39
Consensus pattern (44 bp):
TAATAACTTAATAGTAAATTATCAATAACTAAGTAATAAATTAT
Found at i:20949757 original size:21 final size:22
Alignment explanation
Indices: 20949710--20949785 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
20949700 TCATTTATAG
* *
20949710 CTTAGTAGTAAA-TAATCTATAA
1 CTTAGTAGTAAATTAGT-GATAA
20949732 CTTAGT-GATAAATTA-TGATAA
1 CTTAGTAG-TAAATTAGTGATAA
*
20949753 TTTAGTAGTAAATTAGTGATAA
1 CTTAGTAGTAAATTAGTGATAA
**
20949775 GATAGTAGTAA
1 CTTAGTAGTAA
20949786 GTGAGTAGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
21 17 0.37
22 27 0.59
23 2 0.04
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (22 bp):
CTTAGTAGTAAATTAGTGATAA
Found at i:20950191 original size:22 final size:22
Alignment explanation
Indices: 20950160--20950212 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
20950150 TAAATTTAGC
20950160 AATAAATCACTAATAACGTAGT
1 AATAAATCACTAATAACGTAGT
* * *
20950182 AATAAGTCACTTATAACTTAGT
1 AATAAATCACTAATAACGTAGT
* *
20950204 TATATATCA
1 AATAAATCA
20950213 ATGATAATTC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.34
Consensus pattern (22 bp):
AATAAATCACTAATAACGTAGT
Found at i:20950263 original size:22 final size:22
Alignment explanation
Indices: 20950238--20950364 Score: 98
Period size: 22 Copynumber: 5.8 Consensus size: 22
20950228 TAAATCATCG
*
20950238 ATAACTTCATAGTAAATTAATT
1 ATAACTTAATAGTAAATTAATT
* * *
20950260 ATAACTTTATAATAAATT-ATCA
1 ATAACTTAATAGTAAATTAAT-T
* * *
20950282 ATAACTTAATACTAAA-TCATCA
1 ATAACTTAATAGTAAATTAAT-T
* * *
20950304 ATAATTTAGTAGTAAATTATTT
1 ATAACTTAATAGTAAATTAATT
20950326 ATAACTTAATAGTAAA-TAATT
1 ATAACTTAATAGTAAATTAATT
* *
20950347 AATAAGTTAATAATAAAT
1 -ATAACTTAATAGTAAAT
20950365 CACTGATAAC
Statistics
Matches: 84, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
21 7 0.08
22 75 0.89
23 2 0.02
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (22 bp):
ATAACTTAATAGTAAATTAATT
Found at i:20950276 original size:44 final size:42
Alignment explanation
Indices: 20950228--20950374 Score: 125
Period size: 44 Copynumber: 3.4 Consensus size: 42
20950218 AATTCTGTAG
*
20950228 TAAATCATCGATAACTTCATAGTAAATTAATTATAACTTTATAA
1 TAAATCATCGATAACTTAATAGTAAA-TAATTATAA-TTTATAA
* * * * * *
20950272 TAAATTATCAATAACTTAATACTAAATCATCAATAATTTAGTAG
1 TAAATCATCGATAACTTAATAGTAAATAAT-TATAATTTA-TAA
* ** *
20950316 TAAATTATTTATAACTTAATAGTAAATAATTAATAAGTTAATAA
1 TAAATCATCGATAACTTAATAGTAAATAATT-ATAA-TTTATAA
20950360 TAAATCA-CTGATAAC
1 TAAATCATC-GATAAC
20950375 ATAGTAATAA
Statistics
Matches: 81, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
43 7 0.09
44 71 0.88
45 3 0.04
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.37
Consensus pattern (42 bp):
TAAATCATCGATAACTTAATAGTAAATAATTATAATTTATAA
Found at i:20950298 original size:66 final size:67
Alignment explanation
Indices: 20950228--20950374 Score: 183
Period size: 66 Copynumber: 2.2 Consensus size: 67
20950218 AATTCTGTAG
* *
20950228 TAAATCATCGATAACTTCA-TAGTAAATTAATTATAACTTTATAATAAATTATCAATAACTTAAT
1 TAAATCATCGATAACTTCAGTAGTAAATTAATTATAACTTAATAATAAATAATCAATAACTTAAT
*
20950292 AC
66 AA
* * * * * *
20950294 TAAATCATCAATAA-TTTAGTAGTAAATTATTTATAACTTAATAGTAAATAATTAATAAGTTAAT
1 TAAATCATCGATAACTTCAGTAGTAAATTAATTATAACTTAATAATAAATAATCAATAACTTAAT
20950358 AA
66 AA
20950360 TAAATCA-CTGATAAC
1 TAAATCATC-GATAAC
20950375 ATAGTAATAA
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
65 4 0.06
66 64 0.94
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.37
Consensus pattern (67 bp):
TAAATCATCGATAACTTCAGTAGTAAATTAATTATAACTTAATAATAAATAATCAATAACTTAAT
AA
Found at i:20950575 original size:22 final size:22
Alignment explanation
Indices: 20950571--20950642 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
20950561 TAATTTAGTT
20950571 GTAAATCAATGATAACTTATTA
1 GTAAATCAATGATAACTTATTA
* ** * *
20950593 GTAAATCAGTTTTAGCTTAGTA
1 GTAAATCAATGATAACTTATTA
* *
20950615 GTAAAGTCTA-GATAACTTAATA
1 GTAAA-TCAATGATAACTTATTA
20950637 GTAAAT
1 GTAAAT
20950643 TATTCATATT
Statistics
Matches: 38, Mismatches: 11, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
21 1 0.03
22 35 0.92
23 2 0.05
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (22 bp):
GTAAATCAATGATAACTTATTA
Found at i:20950598 original size:44 final size:44
Alignment explanation
Indices: 20950537--20950642 Score: 108
Period size: 44 Copynumber: 2.4 Consensus size: 44
20950527 ATAATTTATT
* * *
20950537 GATAACTAAAT-GCTAAATCACTTATAATTTAGTTGTAAA-TCAA
1 GATAACTTAATAG-TAAATCACTTATAACTTAGTAGTAAAGTCAA
* * * * *
20950580 TGATAACTTATTAGTAAATCAGTTTTAGCTTAGTAGTAAAGTCTA
1 -GATAACTTAATAGTAAATCACTTATAACTTAGTAGTAAAGTCAA
20950625 GATAACTTAATAGTAAAT
1 GATAACTTAATAGTAAAT
20950643 TATTCATATT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
44 47 0.92
45 4 0.08
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (44 bp):
GATAACTTAATAGTAAATCACTTATAACTTAGTAGTAAAGTCAA
Found at i:20950673 original size:22 final size:22
Alignment explanation
Indices: 20950631--20950673 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
20950621 TCTAGATAAC
* * *
20950631 TTAATAGTAAATTATTCATATT
1 TTAATAATAAATTAGTAATATT
20950653 TTAATAATAAATTAGTAATAT
1 TTAATAATAAATTAGTAATAT
20950674 AACTTAACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (22 bp):
TTAATAATAAATTAGTAATATT
Found at i:20952244 original size:18 final size:18
Alignment explanation
Indices: 20952223--20952260 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
20952213 TATAGTCAAA
* *
20952223 AAAAATTTTTAAAAAAAG
1 AAAAATATTAAAAAAAAG
20952241 AAAAATATTAAAAAAAAG
1 AAAAATATTAAAAAAAAG
20952259 AA
1 AA
20952261 TGAAGATAAT
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:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (18 bp):
AAAAATATTAAAAAAAAG
Found at i:20952525 original size:2 final size:2
Alignment explanation
Indices: 20952518--20952575 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
20952508 AATAAAACTA
* *
20952518 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20952560 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
20952576 TTGTCGGAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20966160 original size:22 final size:20
Alignment explanation
Indices: 20966121--20966161 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
20966111 GTATTTTTAT
*
20966121 AATATTTTGAAAATTAATTG
1 AATATTTTGAAAACTAATTG
20966141 AATATTTTAGTAAAACTAATT
1 AATATTTT-G-AAAACTAATT
20966162 TCATTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (20 bp):
AATATTTTGAAAACTAATTG
Found at i:20967158 original size:26 final size:25
Alignment explanation
Indices: 20967121--20967169 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
20967111 GGAAGAAGAA
20967121 GAAAAAAAAAAAAAAGGAAAAATGT
1 GAAAAAAAAAAAAAAGGAAAAATGT
* *
20967146 GAAAAAAGAAAAAGAAGGTAAAAT
1 GAAAAAA-AAAAAAAAGGAAAAAT
20967170 TTTAATTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.08
Consensus pattern (25 bp):
GAAAAAAAAAAAAAAGGAAAAATGT
Found at i:20967257 original size:21 final size:20
Alignment explanation
Indices: 20967219--20967257 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
20967209 GGTATTTTTG
*
20967219 AAAGAAAATTGATTTGGTGT
1 AAAGAAAATTGATGTGGTGT
*
20967239 AAAGAGAAATTTATGTGGT
1 AAAGA-AAATTGATGTGGT
20967258 ATATTTAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.41, C:0.00, G:0.26, T:0.33
Consensus pattern (20 bp):
AAAGAAAATTGATGTGGTGT
Found at i:20970059 original size:33 final size:35
Alignment explanation
Indices: 20969983--20970068 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 35
20969973 TTTTTATGAT
*
20969983 TTATTGATTTATTTA-TTATTATGTTTTTTGGTTGA
1 TTATTCATTTATTTATTTATTATGTTTTTT-GTTGA
*
20970018 TTATTCATTTATTTATTTA-T-TGTTTGTTT-TTTA
1 TTATTCATTTATTTATTTATTATGTTT-TTTGTTGA
20970051 TTATTCATTTATTTATTT
1 TTATTCATTTATTTATTT
20970069 GATTTTATCT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
33 21 0.45
34 5 0.11
35 18 0.38
36 3 0.06
ACGTcount: A:0.20, C:0.02, G:0.08, T:0.70
Consensus pattern (35 bp):
TTATTCATTTATTTATTTATTATGTTTTTTGTTGA
Found at i:20970702 original size:15 final size:17
Alignment explanation
Indices: 20970669--20970704 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
20970659 GAGATAGAGG
20970669 GAGAGGAAAAGGAAGAA
1 GAGAGGAAAAGGAAGAA
20970686 GAGA-GAAAAGGAA-AA
1 GAGAGGAAAAGGAAGAA
20970701 GAGA
1 GAGA
20970705 AATTTGAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 9 0.47
17 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (17 bp):
GAGAGGAAAAGGAAGAA
Found at i:20971011 original size:20 final size:20
Alignment explanation
Indices: 20970973--20971010 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20970963 TTTTTGGTAT
**
20970973 TTTTTTTATTAGTTATTTTA
1 TTTTTTTAAAAGTTATTTTA
20970993 TTTTTTTAAAAGTT-TTTT
1 TTTTTTTAAAAGTTATTTT
20971011 TGTATGATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTTTTTAAAAGTTATTTTA
Found at i:20971472 original size:44 final size:43
Alignment explanation
Indices: 20971398--20971494 Score: 137
Period size: 44 Copynumber: 2.3 Consensus size: 43
20971388 ATTTTTTTTC
20971398 AAAAA-AAAAAAAATTTAAATAGACCTAAATGGTGAAAAATTT
1 AAAAATAAAAAAAATTTAAATAGACCTAAATGGTGAAAAATTT
*
20971440 AGAAATAAAAAAAATTCTAAATTA-A-CTCAAATGGTGAAAAATTT
1 AAAAATAAAAAAAATT-TAAA-TAGACCT-AAATGGTGAAAAATTT
20971484 AAAAATAAAAA
1 AAAAATAAAAA
20971495 TAAAATAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
42 4 0.08
43 12 0.24
44 31 0.63
45 2 0.04
ACGTcount: A:0.63, C:0.05, G:0.08, T:0.24
Consensus pattern (43 bp):
AAAAATAAAAAAAATTTAAATAGACCTAAATGGTGAAAAATTT
Found at i:20971501 original size:11 final size:11
Alignment explanation
Indices: 20971485--20971509 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20971475 GAAAAATTTA
20971485 AAAATAAAAAT
1 AAAATAAAAAT
20971496 AAAATAAAAAT
1 AAAATAAAAAT
20971507 AAA
1 AAA
20971510 TTTTGAGGAT
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:20974675 original size:16 final size:16
Alignment explanation
Indices: 20974650--20974690 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
20974640 CATCCAACCA
20974650 TTATTT-CATA-CTTT
1 TTATTTCCATATCTTT
20974664 GTTATTTCCATATCTTT
1 -TTATTTCCATATCTTT
*
20974681 TTATTCCCAT
1 TTATTTCCAT
20974691 TCTCAAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 6 0.26
16 13 0.57
17 4 0.17
ACGTcount: A:0.20, C:0.20, G:0.02, T:0.59
Consensus pattern (16 bp):
TTATTTCCATATCTTT
Found at i:20975490 original size:19 final size:18
Alignment explanation
Indices: 20975466--20975503 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
20975456 AGATATCAAT
20975466 AATGAAAAATGAAAGAAAA
1 AATGAAAAATGAAA-AAAA
20975485 AATGAAAAATGAAAAAAA
1 AATGAAAAATGAAAAAAA
20975503 A
1 A
20975504 GGAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (18 bp):
AATGAAAAATGAAAAAAA
Found at i:20975493 original size:8 final size:8
Alignment explanation
Indices: 20975480--20975575 Score: 56
Period size: 8 Copynumber: 11.9 Consensus size: 8
20975470 AAAAATGAAA
20975480 GAAAAAAT
1 GAAAAAAT
20975488 G-AAAAAT
1 GAAAAAAT
*
20975495 GAAAAAAAAG
1 G--AAAAAAT
20975505 GAAAAAAAT
1 G-AAAAAAT
*
20975514 -AAAAAAG
1 GAAAAAAT
20975521 GAAAAAA-
1 GAAAAAAT
*
20975528 -AATAAAAG
1 GAA-AAAAT
*
20975536 GAAAAAAA
1 GAAAAAAT
*
20975544 GAGAAAAAA
1 GA-AAAAAT
*
20975553 GGAAAAAT
1 GAAAAAAT
*
20975561 GAAATAAT
1 GAAAAAAT
20975569 GAAAAAA
1 GAAAAAA
20975576 ATGTAAAAAG
Statistics
Matches: 71, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
6 2 0.03
7 17 0.24
8 30 0.42
9 16 0.23
10 6 0.08
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (8 bp):
GAAAAAAT
Found at i:20975508 original size:25 final size:24
Alignment explanation
Indices: 20975466--20975576 Score: 93
Period size: 26 Copynumber: 4.5 Consensus size: 24
20975456 AGATATCAAT
20975466 AATGAAAAATGAAAGAAAAAATGAAA
1 AATGAAAAA--AAAGAAAAAATGAAA
*
20975492 AATGAAAAAAAAGGAAAAAAATAAAA
1 AATGAAAAAAAA-G-AAAAAATGAAA
* *
20975518 AAGGAAAAAAAATAAAAGGAA--AAA
1 AATGAAAAAAAAGAAAA--AATGAAA
* *
20975542 AA-GAGAAAAAAGGAAAAATGAAA
1 AATGAAAAAAAAGAAAAAATGAAA
20975565 TAATGAAAAAAA
1 -AATGAAAAAAA
20975577 TGTAAAAAGA
Statistics
Matches: 70, Mismatches: 7, Indels: 17
0.74 0.07 0.18
Matches are distributed among these distances:
21 2 0.03
23 14 0.20
24 14 0.20
25 8 0.11
26 32 0.46
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (24 bp):
AATGAAAAAAAAGAAAAAATGAAA
Found at i:20975517 original size:15 final size:15
Alignment explanation
Indices: 20975481--20975559 Score: 86
Period size: 16 Copynumber: 4.9 Consensus size: 15
20975471 AAAATGAAAG
*
20975481 AAAAAATGAAAAATGAA
1 AAAAAAGGAAAAA--AA
20975498 AAAAAAGGAAAAAAA
1 AAAAAAGGAAAAAAA
20975513 TAAAAAAGGAAAAAAA
1 -AAAAAAGGAAAAAAA
*
20975529 ATAAAAGGAAAAAAAGA
1 AAAAAAGG-AAAAAA-A
20975546 GAAAAAAGGAAAAA
1 -AAAAAAGGAAAAA
20975560 TGAAATAATG
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
15 9 0.16
16 21 0.38
17 18 0.33
18 7 0.13
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (15 bp):
AAAAAAGGAAAAAAA
Found at i:20975564 original size:15 final size:15
Alignment explanation
Indices: 20975480--20975574 Score: 59
Period size: 15 Copynumber: 5.9 Consensus size: 15
20975470 AAAAATGAAA
*
20975480 GAAAAAATGAAAAAT
1 GAAAAAAGGAAAAAT
20975495 GAAAAAAAAGGAAAAAAAT
1 G--AAAAAAGG--AAAAAT
20975514 -AAAAAAGGAAAAA-
1 GAAAAAAGGAAAAAT
* *
20975527 AAATAAAAGGAAAAAAAGA
1 GAA-AAAAGG--AAAAA-T
20975546 GAAAAAAGGAAAAAT
1 GAAAAAAGGAAAAAT
* *
20975561 GAAATAATGAAAAA
1 GAAAAAAGGAAAAA
20975575 AATGTAAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 7 0.11
15 19 0.29
16 13 0.20
17 12 0.18
18 6 0.09
19 8 0.12
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (15 bp):
GAAAAAAGGAAAAAT
Found at i:20975573 original size:33 final size:32
Alignment explanation
Indices: 20975463--20975594 Score: 106
Period size: 33 Copynumber: 3.9 Consensus size: 32
20975453 GAGAGATATC
*
20975463 AATAATGAAAAATGAAAGAAAAAATGAAAAATGAA
1 AATAATGAAAAA--AAAGAAAAAAGGAAAAATG-A
* * * *
20975498 AAAAAAGGAAAAAAATAAAAAAGGAAAAA--A
1 AATAATGAAAAAAAAGAAAAAAGGAAAAATGA
*
20975528 AATAAAAGGAAAAAAAGAGAAAAAAGGAAAAATGA
1 AAT--AATGAAAAAAA-AGAAAAAAGGAAAAATGA
* *
20975563 AATAATGAAAAAAATGTAAAAAGAGAGAAAAT
1 AATAATGAAAAAAAAGAAAAAAG-GA-AAAAT
20975595 AAAGACTCAA
Statistics
Matches: 78, Mismatches: 12, Indels: 15
0.74 0.11 0.14
Matches are distributed among these distances:
30 3 0.04
32 16 0.21
33 41 0.53
34 5 0.06
35 13 0.17
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.10
Consensus pattern (32 bp):
AATAATGAAAAAAAAGAAAAAAGGAAAAATGA
Found at i:20975584 original size:25 final size:24
Alignment explanation
Indices: 20975477--20975576 Score: 89
Period size: 25 Copynumber: 4.1 Consensus size: 24
20975467 ATGAAAAATG
20975477 AAAGAAAAAATG-AAAAATGAAAAA
1 AAAGAAAAAATGAAAAAATG-AAAA
*
20975501 AAAGGAAAAAAAT-AAAAAAGGAAAA
1 AAA-G-AAAAAATGAAAAAATGAAAA
* * *
20975526 AAA-ATAAAAGGAAAAAAAGAGAAA
1 AAAGAAAAAATGAAAAAATGA-AAA
* *
20975550 AAAGGAAAAATGAAATAATGAAAA
1 AAAGAAAAAATGAAAAAATGAAAA
20975574 AAA
1 AAA
20975577 TGTAAAAAGA
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
22 5 0.08
23 8 0.13
24 15 0.25
25 20 0.33
26 13 0.21
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (24 bp):
AAAGAAAAAATGAAAAAATGAAAA
Found at i:20976311 original size:79 final size:79
Alignment explanation
Indices: 20976134--20976317 Score: 206
Period size: 79 Copynumber: 2.3 Consensus size: 79
20976124 TAGTTTACAT
* * * * * *
20976134 AACCTAGGAGTTGTGATGAAGTGATGAAAATGATATGGATCAGTGGACAAAATTTATGTTGAAAT
1 AACCTATGAGTTGTGATCAAATGATGAAAATGATATGGATCAGTAGACAAAATTTATGCTAAAAT
**
20976199 TGCTAGTGTTGAGA
66 TGCTAGTGCCGAGA
* * * * * * * **
20976213 AGCTTGTGAGATGCGATCAAATGATGAAAATGATGTGGATTAGTAGATGAAATTTATGCTAAAAT
1 AACCTATGAGTTGTGATCAAATGATGAAAATGATATGGATCAGTAGACAAAATTTATGCTAAAAT
20976278 TGCTAGTGCCGAGA
66 TGCTAGTGCCGAGA
*
20976292 AACCTATGAGTTGTAATCAAATGATG
1 AACCTATGAGTTGTGATCAAATGATG
20976318 TGGATCAGTT
Statistics
Matches: 82, Mismatches: 23, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
79 82 1.00
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (79 bp):
AACCTATGAGTTGTGATCAAATGATGAAAATGATATGGATCAGTAGACAAAATTTATGCTAAAAT
TGCTAGTGCCGAGA
Found at i:20976924 original size:98 final size:96
Alignment explanation
Indices: 20976806--20977092 Score: 258
Period size: 94 Copynumber: 3.0 Consensus size: 96
20976796 ACTAGAATGA
* * *
20976806 GAAGCTTTAAACTCTTGGATGCAAATCTCTAAATTTGTGAATGAGAACCTTTGAATTTTGATG-A
1 GAAGCTTTGAACTTTTGGATGCAAATCTCTAAATTTGTGAATGAGAACCTTTGAATTTAGATGTA
* * ** *
20976870 AAAATTTAAAAATTTTTTGAATATGAATCTTC
66 AAAATCT-AAAATTTATCAAATATGAATATTC
* * * *
20976902 GAAATGCTTTGAACTTTTGGATGCAAA-CCCCAAATTTGTCGAATGTGAACCTTTAAATTTAGAT
1 G-AA-GCTTTGAACTTTTGGATGCAAATCTCTAAATTTGT-GAATGAGAACCTTTGAATTTAGAT
* * *
20976966 GTAAAACTCTAAAATTTATCAAATGTGAATATTT
63 GTAAAAATCTAAAATTTATCAAATATGAATATTC
* * ** * * *
20977000 GAA-C-TCGGACTTTTGGATGTGAATCTTTAAATTTTTGAATGAGAACCTTTGAACTTAGATGTA
1 GAAGCTTTGAACTTTTGGATGCAAATCTCTAAATTTGTGAATGAGAACCTTTGAATTTAGATGTA
** * ** *
20977063 AAACCCTAATATTTATTGAATGTGAATATT
66 AAAATCTAAAATTTATCAAATATGAATATT
20977093 TGAACTCAAA
Statistics
Matches: 156, Mismatches: 30, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
94 65 0.42
95 9 0.06
96 1 0.01
97 14 0.09
98 61 0.39
99 6 0.04
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (96 bp):
GAAGCTTTGAACTTTTGGATGCAAATCTCTAAATTTGTGAATGAGAACCTTTGAATTTAGATGTA
AAAATCTAAAATTTATCAAATATGAATATTC
Found at i:20977391 original size:33 final size:33
Alignment explanation
Indices: 20977343--20977405 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
20977333 TCTTAAAATC
* *
20977343 TTACAAATTTGAATTCTTGTGAAGCCAAAATTT
1 TTACAAATCTGAATTCTTGAGAAGCCAAAATTT
* *
20977376 TTACGAATCTGAATTCTTGAGAAGCTAAAA
1 TTACAAATCTGAATTCTTGAGAAGCCAAAA
20977406 AATCTTGTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (33 bp):
TTACAAATCTGAATTCTTGAGAAGCCAAAATTT
Found at i:20979158 original size:24 final size:25
Alignment explanation
Indices: 20979101--20979158 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
20979091 TATCTAAAGA
20979101 TGAAAATTTTAAAAATTTCAAATGG
1 TGAAAATTTTAAAAATTTCAAATGG
* *
20979126 T-AAATTTTTATAAAA-TTCAGA-GG
1 TGAAAATTTTA-AAAATTTCAAATGG
20979149 TGAAAATTTT
1 TGAAAATTTT
20979159 CTCTAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 3 0.11
24 20 0.71
25 5 0.18
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.40
Consensus pattern (25 bp):
TGAAAATTTTAAAAATTTCAAATGG
Found at i:20979334 original size:27 final size:27
Alignment explanation
Indices: 20979302--20979364 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
20979292 TTCAAATGGT
20979302 AAATTTCTTAAGAAATCTCTAGGTGAA
1 AAATTTCTTAAGAAATCTCTAGGTGAA
* *
20979329 AAATTTCTTAAGAAATCTCTATGTGAG
1 AAATTTCTTAAGAAATCTCTAGGTGAA
20979356 AAATTTCTT
1 AAATTTCTT
20979365 TAAATTTGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (27 bp):
AAATTTCTTAAGAAATCTCTAGGTGAA
Found at i:20979499 original size:44 final size:44
Alignment explanation
Indices: 20979449--20979533 Score: 127
Period size: 44 Copynumber: 1.9 Consensus size: 44
20979439 AAAAAGTAAT
20979449 TTCTAAA-TAATCCCAAATGGTGAAAAATTTAGAAATAAAAAAAA
1 TTCTAAATTAA-CCCAAATGGTGAAAAATTTAGAAATAAAAAAAA
* * *
20979493 TTCTAAATTGACCCAAATGGTGAAGAATTTATAAATAAAAA
1 TTCTAAATTAACCCAAATGGTGAAAAATTTAGAAATAAAAA
20979534 TAAAAGAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 35 0.95
45 2 0.05
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.27
Consensus pattern (44 bp):
TTCTAAATTAACCCAAATGGTGAAAAATTTAGAAATAAAAAAAA
Found at i:20984903 original size:16 final size:16
Alignment explanation
Indices: 20984882--20984912 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20984872 AATGATAATG
20984882 ATGATTTATAATGATA
1 ATGATTTATAATGATA
*
20984898 ATGATTTATGATGAT
1 ATGATTTATAATGAT
20984913 TTTAAAGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (16 bp):
ATGATTTATAATGATA
Found at i:20986008 original size:27 final size:27
Alignment explanation
Indices: 20985977--20986046 Score: 79
Period size: 26 Copynumber: 2.6 Consensus size: 27
20985967 TGATTTGATA
*
20985977 AATTTTGGAGTAATTAAAGTTTCAATG
1 AATTTTGGAGTAATTAAAGATTCAATG
* *
20986004 AATTTTGAAG-AATTAATGATTCAATG
1 AATTTTGGAGTAATTAAAGATTCAATG
* *
20986030 GATTCTTGGTGTAATTA
1 AATT-TTGGAGTAATTA
20986047 TTTTGGTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
26 17 0.49
27 13 0.37
28 5 0.14
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.41
Consensus pattern (27 bp):
AATTTTGGAGTAATTAAAGATTCAATG
Found at i:20986582 original size:20 final size:21
Alignment explanation
Indices: 20986546--20986587 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
20986536 ATCATACGAG
*
20986546 TTGAATGTTTGTATAGTTAAT
1 TTGAATGTTTGTATAGTAAAT
20986567 TTGAA-GTTTG-ATTAGTAAAT
1 TTGAATGTTTGTA-TAGTAAAT
20986587 T
1 T
20986588 CCTATTTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 1 0.05
20 13 0.68
21 5 0.26
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (21 bp):
TTGAATGTTTGTATAGTAAAT
Found at i:20986891 original size:28 final size:28
Alignment explanation
Indices: 20986852--20986923 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
20986842 GGCTAAGAAT
20986852 GATTG-TTGAAATCTTACAAGTGCAAAA
1 GATTGTTTGAAATCTTACAAGTGCAAAA
*
20986879 GATTGTTTGAAATCTTACAAGTGCACAA
1 GATTGTTTGAAATCTTACAAGTGCAAAA
20986907 GATTGTTTGAAATCTTA
1 GATTGTTTGAAATCTTA
20986924 TAAATGATGA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
27 5 0.12
28 38 0.88
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (28 bp):
GATTGTTTGAAATCTTACAAGTGCAAAA
Found at i:20990100 original size:16 final size:16
Alignment explanation
Indices: 20990081--20990111 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20990071 AATGATAATG
*
20990081 ATGATTTATGATGATA
1 ATGATTCATGATGATA
20990097 ATGATTCATGATGAT
1 ATGATTCATGATGAT
20990112 TTTAAAGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.19, T:0.42
Consensus pattern (16 bp):
ATGATTCATGATGATA
Found at i:20992275 original size:16 final size:16
Alignment explanation
Indices: 20992256--20992366 Score: 75
Period size: 16 Copynumber: 6.9 Consensus size: 16
20992246 TTTACTTCCT
*
20992256 AAGTTTTTTATTTTTC
1 AAGTTATTTATTTTTC
*
20992272 AAGTTCTTTA-TTTTC
1 AAGTTATTTATTTTTC
* **
20992287 AAGTCATTTATTTGACC
1 AAGTTATTTATTT-TTC
* *
20992304 AACTT-TTTCATTTTTT
1 AAGTTATTT-ATTTTTC
* *
20992320 AAGATCTTTAATTTTTC
1 AAGTTATTT-ATTTTTC
*
20992337 AA-TTATTTACTTTTTA
1 AAGTTATTTA-TTTTTC
20992353 AAGTTATTTATTTT
1 AAGTTATTTATTTT
20992367 AGTTTTTTGT
Statistics
Matches: 72, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
15 14 0.19
16 32 0.44
17 26 0.36
ACGTcount: A:0.25, C:0.10, G:0.05, T:0.59
Consensus pattern (16 bp):
AAGTTATTTATTTTTC
Found at i:20992287 original size:15 final size:15
Alignment explanation
Indices: 20992256--20992299 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
20992246 TTTACTTCCT
*
20992256 AAGTTTTTTATTTTTC
1 AAGTTCTTTA-TTTTC
20992272 AAGTTCTTTATTTTC
1 AAGTTCTTTATTTTC
20992287 AAG-TCATTTATTT
1 AAGTTC-TTTATTT
20992300 GACCAACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 2 0.08
15 15 0.58
16 9 0.35
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.61
Consensus pattern (15 bp):
AAGTTCTTTATTTTC
Found at i:20994847 original size:18 final size:18
Alignment explanation
Indices: 20994824--20994858 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20994814 TGGATAGCTG
20994824 AAAAAAAAAAAGAAGAAA
1 AAAAAAAAAAAGAAGAAA
* *
20994842 AAAAAAACAACGAAGAA
1 AAAAAAAAAAAGAAGAA
20994859 TTTCTTCAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAGAAGAAA
Found at i:21000183 original size:41 final size:41
Alignment explanation
Indices: 21000133--21000244 Score: 106
Period size: 41 Copynumber: 2.7 Consensus size: 41
21000123 TCTAAACTAA
*
21000133 TAAAGGCAATTAAACTTTAAATTTTGAAAAG-T-TTCTCTAAC
1 TAAAAGCAATTAAACTTTAAATTTTGAAAAGCTCTT-T-TAAC
* * *
21000174 -AAGAAGCAA-TATAACCTTAAAATTTAAAAAGCTCTTTTAAC
1 TAA-AAGCAATTA-AACTTTAAATTTTGAAAAGCTCTTTTAAC
* *
21000215 TTAAAGCAATGAAACTTTAAATTTTGAAAA
1 TAAAAGCAATTAAACTTTAAATTTTGAAAA
21000245 AAAAAAAACC
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
40 4 0.07
41 46 0.82
42 4 0.07
43 2 0.04
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (41 bp):
TAAAAGCAATTAAACTTTAAATTTTGAAAAGCTCTTTTAAC
Found at i:21000787 original size:13 final size:13
Alignment explanation
Indices: 21000769--21000827 Score: 82
Period size: 13 Copynumber: 4.5 Consensus size: 13
21000759 AATATATGGA
*
21000769 ATGAATGTAGTGC
1 ATGAATGTAATGC
21000782 ATGAATGTAATGC
1 ATGAATGTAATGC
*
21000795 ACGAATGTAATGC
1 ATGAATGTAATGC
*
21000808 ACGAATGTAATGCC
1 ATGAATGTAATG-C
21000822 ATGAAT
1 ATGAAT
21000828 ACAATACATG
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
13 36 0.86
14 6 0.14
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (13 bp):
ATGAATGTAATGC
Found at i:21000949 original size:18 final size:18
Alignment explanation
Indices: 21000926--21000970 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
21000916 AATTTCTTAT
21000926 ATGCAATGTATGGAATG-A
1 ATGCAATGTAT-GAATGCA
*
21000944 ATGCAATGCATGAATGCA
1 ATGCAATGTATGAATGCA
21000962 ATGC-ATGTA
1 ATGCAATGTA
21000971 ATGTCAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (18 bp):
ATGCAATGTATGAATGCA
Found at i:21000956 original size:13 final size:13
Alignment explanation
Indices: 21000940--21000973 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
21000930 AATGTATGGA
21000940 ATGAATGCAATGC
1 ATGAATGCAATGC
21000953 ATGAATGCAATGC
1 ATGAATGCAATGC
21000966 ATGTAATG
1 ATG-AATG
21000974 TCAACATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (13 bp):
ATGAATGCAATGC
Found at i:21001973 original size:181 final size:181
Alignment explanation
Indices: 21001630--21003215 Score: 1436
Period size: 181 Copynumber: 8.7 Consensus size: 181
21001620 TCATCTTAAA
* * * * * * * *
21001630 TTTTATCATAAAACAATTATTTCTATTCGA-AGAAGTTTATTCGAAATAAAGTAATA-AAATTTT
1 TTTTGTCATAAAATAATTGTTTCTGTTC-ATATAAGCTTATTCGAAATAAAATAATATTAA-TTT
* * * * * * *
21001693 TTTAATATTTTAAAAATTAATAAGTAAAAGATTTAAAATATAAGTTTTTTTACCGAACAAGTACA
64 ATTAATATTTTAAAAATTAATAAGTAAAAGATTTAAAAGATAAATCTATTTAACGAACAAGTTCA
** * * *
21001758 AATAGTCACAACTA-TTTAACCAATTATGTATTTCAAATAATTATGACCTTCTG
129 AATAGTCATGATTATTTTAA-CAATTATCTATTTCAAATAATTATGACCTTTTG
* * * * * *
21001811 TTTTATAATAGAATAATTGTTTCTGTTCATATAAGTTTATTTGAAATAAAATAATATTTATTTAT
1 TTTTGTCATAAAATAATTGTTTCTGTTCATATAAGCTTATTCGAAATAAAATAATATTAATTTAT
* *
21001876 TAATATTTTAAAAATTAATAAGTAAAAAATTTAAAAGATAAATCTATTTAACGAATAAGTTCAAA
66 TAATATTTTAAAAATTAATAAGTAAAAGATTTAAAAGATAAATCTATTTAACGAACAAGTTCAAA
* *
21001941 TAGTCATGATTATTTTAACAATTATCTATTTCAAATAATTATGACTTTTTA
131 TAGTCATGATTATTTTAACAATTATCTATTTCAAATAATTATGACCTTTTG
* * * * * * *
21001992 TTTTGTCATAAAATAATTATTTTTATTCAAACAAGCTTATACAAAATAAAATAATATTAATTTAT
1 TTTTGTCATAAAATAATTGTTTCTGTTCATATAAGCTTATTCGAAATAAAATAATATTAATTTAT
*** * * * * * *
21002057 TAATATTCCCAAAGTTAACAAGTAAAATATTTAAAAGATAAATCTATTTACCAAACAAATTCAAA
66 TAATATTTTAAAAATTAATAAGTAAAAGATTTAAAAGATAAATCTATTTAACGAACAAGTTCAAA
* * * * * ** *
21002122 TAATCA-CACTTATTTGT-CCAATTATTTATTTCAAATAATTATTATATTTTA
131 TAGTCATGA-TTATTT-TAACAATTATCTATTTCAAATAATTATGACCTTTTG
* * * *
21002173 TTTTGTCATAACATAATTGTTTTTGTTCGA-AAAAACTTATTCGAAATAAAATAATATTAATTTA
1 TTTTGTCATAAAATAATTGTTTCTGTTC-ATATAAGCTTATTCGAAATAAAATAATATTAATTTA
* * * *
21002237 TTAATATATTGAAAATTAATAAGTAAAA-ATTTTCAAAA-ATAAATATATTTAACTAACAAGTTC
65 TTAATATTTTAAAAATTAATAAGTAAAAGA-TTT-AAAAGATAAATCTATTTAACGAACAAGTTC
* * * * * * *
21002300 AAATACTCATGACTATCTAAACATTTAGCTATTTCAAATAATTAAGACCTTTTTG
128 AAATAGTCATGATTATTTTAACAATTATCTATTTCAAATAATTATGACC-TTTTG
* * * * * *
21002355 TTTTGTCGTAGAACATTTGTGTCTGTTCAAATAAGCTTATTCGAAATAAAATAATATTAATTTAT
1 TTTTGTCATAAAATAATTGTTTCTGTTCATATAAGCTTATTCGAAATAAAATAATATTAATTTAT
* **
21002420 TAACA-TTCCAAAATTAATAAGTAAAAGATTTAAAAGATAAATCTATTT-ACTGAACAAGTTCAA
66 TAATATTTTAAAAATTAATAAGTAAAAGATTTAAAAGATAAATCTATTTAAC-GAACAAGTTCAA
* * * * * * * *
21002483 ATAGTTACGATCATTTTGATAATTATTTATTTCAAATAATTATGACATTTTA
130 ATAGTCATGATTATTTTAACAATTATCTATTTCAAATAATTATGACCTTTTG
* * ** * * * *
21002535 TTTTGTCATAAAACAATTGTTCCAATTCAAACAAGATTATTCGAAATAATATAAT-TTAATTTAT
1 TTTTGTCATAAAATAATTGTTTCTGTTCATATAAGCTTATTCGAAATAAAATAATATTAATTTAT
* * * * * ** * *
21002599 TAATATTTCAAAAACTAATAAGTAAAAGATTTCAAAGATAAATTTGTTTATTGAACAAATTTAAA
66 TAATATTTTAAAAATTAATAAGTAAAAGATTTAAAAGATAAATCTATTTAACGAACAAGTTCAAA
* *
21002664 TAGTCACGATTATTTAAACAATTATCTATTTCAAATAATTATGA-C-TTT-
131 TAGTCATGATTATTTTAACAATTATCTATTTCAAATAATTATGACCTTTTG
** * * * *
21002712 TTTTGTCATAGGATAGTTATTTCTGTTTATATAAGTTTATTC-ATAATAAAATAATATTAATTTA
1 TTTTGTCATAAAATAATTGTTTCTGTTCATATAAGCTTATTCGA-AATAAAATAATATTAATTTA
** ** * * * *
21002776 TTAATATTCCAAAAGCTAATAACTAAAAGATTTTAAAGATAAACCTATTT-ACGAAATAAGTTCA
65 TTAATATTTTAAAAATTAATAAGTAAAAGATTTAAAAGATAAATCTATTTAACG-AACAAGTTCA
* * * **
21002840 AACAGT--TGACTATTTGAACAATTATCTATTTCAAATAATTATGATATTTTG
129 AATAGTCATGATTATTTTAACAATTATCTATTTCAAATAATTATGACCTTTTG
* * * * ***
21002891 TTTTATCATAAAATAATTGTTT-TGATTGTACAAGTTTAATCATAATAAAAAATAAAATAAAATA
1 TTTTGTCATAAAATAATTGTTTCTG--T-T-C-A-TATAAGC-TTATTCGAAATAAAAT--AAT-
* * * *
21002955 ATATCAATTTATTAATATTCTAAACATTAACAAGTAAAAGATTTAAAAGATAAATCCATTTAACG
56 AT-T-AATTTATTAATATTTTAAAAATTAATAAGTAAAAGATTTAAAAGATAAATCTATTTAACG
* * * * * *
21003020 AACACGTTTAAATAGTTATAATTGTTTGAACAATTATCTATTTCAAATAATTATGACCTTTTG
119 AACAAGTTCAAATAGTCATGATTATTTTAACAATTATCTATTTCAAATAATTATGACCTTTTG
* * * *
21003083 TTTTGTCATAAAATAAATATTTCTATTCATATAAGCTTATT--AAGAAAAAATAATATTAATTTA
1 TTTTGTCATAAAATAATTGTTTCTGTTCATATAAGCTTATTCGAA-ATAAAATAATATTAATTTA
* * *
21003146 TTAATATTTTAAAAATTAATAAGTAAAAGATTTAAAGGATAAAT-TCATTT-ACTGAACAAATTA
65 TTAATATTTTAAAAATTAATAAGTAAAAGATTTAAAAGATAAATCT-ATTTAAC-GAACAAGTTC
21003209 AAATAGT
128 AAATAGT
21003216 TATTGTTAAG
Statistics
Matches: 1141, Mismatches: 221, Indels: 87
0.79 0.15 0.06
Matches are distributed among these distances:
176 36 0.03
177 41 0.04
178 71 0.06
179 32 0.03
180 210 0.18
181 505 0.44
182 78 0.07
183 4 0.00
184 6 0.01
185 17 0.01
186 4 0.00
187 8 0.01
188 3 0.00
189 2 0.00
190 60 0.05
191 4 0.00
192 59 0.05
193 1 0.00
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (181 bp):
TTTTGTCATAAAATAATTGTTTCTGTTCATATAAGCTTATTCGAAATAAAATAATATTAATTTAT
TAATATTTTAAAAATTAATAAGTAAAAGATTTAAAAGATAAATCTATTTAACGAACAAGTTCAAA
TAGTCATGATTATTTTAACAATTATCTATTTCAAATAATTATGACCTTTTG
Found at i:21002062 original size:362 final size:361
Alignment explanation
Indices: 21001629--21003215 Score: 1590
Period size: 362 Copynumber: 4.4 Consensus size: 361
21001619 TTCATCTTAA
* * * * * * * *
21001629 ATTTTATCATAAAACAATTATTTCTATTCGAAGAAGTTTATTCGAAATAAAGTAATA-AAATTTT
1 ATTTTGTCATAAAATAATTATTTCTATTCAAATAAGCTTATTCAAAATAAAATAATATTAA-TTT
* * * * * * *
21001693 TTTAATATTTTAAAAATTAATAAGTAAAAGATTTAAAATATAAGTTTTTTTACCGAACAAGTACA
65 ATTAATATTTCAAAAATTAATAAGTAAAAGATTTAAAAGATAAATCTATTTACCGAACAAGTTCA
* * * * * * *
21001758 AATAGTCACAACTATTTAACCAATTATGTATTTCAAATAATTATGACCTTCTGTTTTATAATAGA
130 AATAGTCACGACTATTTAA-CAATTATTTATTTCAAATAATTATGACATTTTATTTTATCATAAA
* * *
21001823 ATAATTGTTTCTGTTCATATAAGTTTATTTGAAATAAAATAATATTTATTTATTAATATTTTAAA
194 ATAATTGTTTCTGTTCATACAAGTTTATTCGAAATAAAATAATATTAATTTATTAATATTTTAAA
*
21001888 AATTAATAAGTAAAAAATTTAAAAGATAAATCTATTTAACGAATAAGTTCAAATAGTCATGATTA
259 AATTAATAAGTAAAAAATTTAAAAGATAAATCTATTTAACGAACAAGTTCAAATAGTCATGATTA
*
21001953 TTTTAACAATTATCTATTTCAAATAATTATGACTTTTT
324 TTTAAACAATTATCTATTTCAAATAATTATGACTTTTT
* * *
21001991 ATTTTGTCATAAAATAATTATTTTTATTCAAACAAGCTTATACAAAATAAAATAATATTAATTTA
1 ATTTTGTCATAAAATAATTATTTCTATTCAAATAAGCTTATTCAAAATAAAATAATATTAATTTA
* * * * * * *
21002056 TTAATATTCCCAAAGTTAACAAGTAAAATATTTAAAAGATAAATCTATTTACCAAACAAATTCAA
66 TTAATATTTCAAAAATTAATAAGTAAAAGATTTAAAAGATAAATCTATTTACCGAACAAGTTCAA
* ** * * * *
21002121 ATAATCAC-ACTTATTTGTCCAATTATTTATTTCAAATAATTATTATATTTTATTTTGTCATAAC
131 ATAGTCACGAC-TATTT-AACAATTATTTATTTCAAATAATTATGACATTTTATTTTATCATAAA
* * ** * *
21002185 ATAATTGTTTTTGTTCGA-AAAAACTTATTCGAAATAAAATAATATTAATTTATTAATATATTGA
194 ATAATTGTTTCTGTTC-ATACAAGTTTATTCGAAATAAAATAATATTAATTTATTAATATTTTAA
* * * * *
21002249 AAATTAATAAGTAAAAATTTTCAAAA-ATAAATATATTTAACTAACAAGTTCAAATACTCATGAC
258 AAATTAATAAGTAAAAAATTT-AAAAGATAAATCTATTTAACGAACAAGTTCAAATAGTCATGAT
* * * *
21002313 TATCTAAACATTTAGCTATTTCAAATAATTAAGACCTTTTT
322 TATTTAAACAATTATCTATTTCAAATAATTATGA-CTTTTT
* * * * * * * * *
21002354 GTTTTGTCGTAGAACATTTGTGTCTGTTCAAATAAGCTTATTCGAAATAAAATAATATTAATTTA
1 ATTTTGTCATAAAATAATTATTTCTATTCAAATAAGCTTATTCAAAATAAAATAATATTAATTTA
* * *
21002419 TTAACA-TTCCAAAATTAATAAGTAAAAGATTTAAAAGATAAATCTATTTACTGAACAAGTTCAA
66 TTAATATTTCAAAAATTAATAAGTAAAAGATTTAAAAGATAAATCTATTTACCGAACAAGTTCAA
* * * *
21002483 ATAGTTACGA-TCATTTTGATAATTATTTATTTCAAATAATTATGACATTTTATTTTGTCATAAA
131 ATAGTCACGACT-A-TTTAACAATTATTTATTTCAAATAATTATGACATTTTATTTTATCATAAA
* * ** * * * *
21002547 ACAATTGTTCCAATTCAAACAAGATTATTCGAAATAATATAAT-TTAATTTATTAATATTTCAAA
194 ATAATTGTTTCTGTTCATACAAGTTTATTCGAAATAAAATAATATTAATTTATTAATATTTTAAA
* * * * * ** * * *
21002611 AACTAATAAGTAAAAGATTTCAAAGATAAATTTGTTTATTGAACAAATTTAAATAGTCACGATTA
259 AATTAATAAGTAAAAAATTTAAAAGATAAATCTATTTAACGAACAAGTTCAAATAGTCATGATTA
21002676 TTTAAACAATTATCTATTTCAAATAATTATGAC--TTT
324 TTTAAACAATTATCTATTTCAAATAATTATGACTTTTT
** * * * * * *
21002712 -TTTTGTCATAGGATAGTTATTTCTGTTTATATAAGTTTATTCATAATAAAATAATATTAATTTA
1 ATTTTGTCATAAAATAATTATTTCTATTCAAATAAGCTTATTCAAAATAAAATAATATTAATTTA
* ** * * * *
21002776 TTAATATTCCAAAAGCTAATAACTAAAAGATTTTAAAGATAAACCTATTTA-CGAAATAAGTTCA
66 TTAATATTTCAAAAATTAATAAGTAAAAGATTTAAAAGATAAATCTATTTACCG-AACAAGTTCA
* * * * *
21002840 AACAGT--TGACTATTTGAACAATTATCTATTTCAAATAATTATGATATTTTGTTTTATCATAAA
130 AATAGTCACGACTATTT-AACAATTATTTATTTCAAATAATTATGACATTTTATTTTATCATAAA
* **
21002903 ATAATTGTTT-TGATT-GTACAAGTTTAATCATAATAAAAAATAAAATAAAATAATATCAATTTA
194 ATAATTGTTTCTG-TTCATACAAG-TT--T-AT--T-CGAAATAAAAT--AAT-AT-T-AATTTA
* * * * * * *
21002966 TTAATATTCTAAACATTAACAAGTAAAAGATTTAAAAGATAAATCCATTTAACGAACACGTTTAA
246 TTAATATTTTAAAAATTAATAAGTAAAAAATTTAAAAGATAAATCTATTTAACGAACAAGTTCAA
* * * * *
21003031 ATAGTTATAATTGTTTGAACAATTATCTATTTCAAATAATTATGACCTTTT
311 ATAGTCATGATTATTTAAACAATTATCTATTTCAAATAATTATGACTTTTT
* * *
21003082 GTTTTGTCATAAAATAAATATTTCTATTCATATAAGCTTATT-AAGAA-AAAATAATATTAATTT
1 ATTTTGTCATAAAATAATTATTTCTATTCAAATAAGCTTATTCAA-AATAAAATAATATTAATTT
* * * * *
21003145 ATTAATATTTTAAAAATTAATAAGTAAAAGATTTAAAGGATAAAT-TCATTTACTGAACAAATTA
65 ATTAATATTTCAAAAATTAATAAGTAAAAGATTTAAAAGATAAATCT-ATTTACCGAACAAGTTC
21003209 AAATAGT
129 AAATAGT
21003216 TATTGTTAAG
Statistics
Matches: 998, Mismatches: 192, Indels: 62
0.80 0.15 0.05
Matches are distributed among these distances:
355 8 0.01
356 55 0.06
357 60 0.06
358 55 0.06
359 2 0.00
360 4 0.00
361 98 0.10
362 425 0.43
363 75 0.08
364 3 0.00
366 1 0.00
367 1 0.00
368 99 0.10
369 1 0.00
370 74 0.07
371 37 0.04
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (361 bp):
ATTTTGTCATAAAATAATTATTTCTATTCAAATAAGCTTATTCAAAATAAAATAATATTAATTTA
TTAATATTTCAAAAATTAATAAGTAAAAGATTTAAAAGATAAATCTATTTACCGAACAAGTTCAA
ATAGTCACGACTATTTAACAATTATTTATTTCAAATAATTATGACATTTTATTTTATCATAAAAT
AATTGTTTCTGTTCATACAAGTTTATTCGAAATAAAATAATATTAATTTATTAATATTTTAAAAA
TTAATAAGTAAAAAATTTAAAAGATAAATCTATTTAACGAACAAGTTCAAATAGTCATGATTATT
TAAACAATTATCTATTTCAAATAATTATGACTTTTT
Found at i:21005540 original size:18 final size:18
Alignment explanation
Indices: 21005517--21005564 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
21005507 AAGTTAAAAT
21005517 AATTATGACTATTTAAAC
1 AATTATGACTATTTAAAC
* * *
21005535 AATTATCAAT-TTTAAAT
1 AATTATGACTATTTAAAC
21005552 AATTATGAC-ATTT
1 AATTATGACTATTT
21005565 TATTTTGTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (18 bp):
AATTATGACTATTTAAAC
Found at i:21005554 original size:181 final size:181
Alignment explanation
Indices: 21005235--21005621 Score: 490
Period size: 181 Copynumber: 2.1 Consensus size: 181
21005225 ACGTTATGAC
* * * *
21005235 ACAAGTTTATTCGAAATAAAATAATATTAATTTATTAAGATTCTAAAAATTAATAAGTAAAATAT
1 ACAAGCTTATTTGAAATAAAATAATATTAATTTATTAAGATTCTAAAAATTAACAAGTAAAAGAT
* * * *
21005300 TTAAAAGATAAATCCGTTTACTGAACAAATTAAAATAATTATAACAATTTGAATAATTATCTATT
66 TTAAAAGATAAATCCATTTACTGAACAAATTAAAATAATTATAACAATTTAAACAATTATCAATT
* * *
21005365 TCAAATAATGACAACTTTTTATTCTATAAAAGAACAATTGTTTCTATTCAT
131 TCAAATAATGACAACATTTTATTCTATAAAAGAACAATTATTTATATTCAT
* *
21005416 ACAAGCTTATTTGGAATAAAATAATATTAATTTATTAATATT-TCAAAAATTAACAAGTAAAAGA
1 ACAAGCTTATTTGAAATAAAATAATATTAATTTATTAAGATTCT-AAAAATTAACAAGTAAAAGA
* * * * *
21005480 TTTAAAAGATAAATCTATTTACTGAGCAAGTTAAAATAATTATGACTATTTAAACAATTATCAAT
65 TTTAAAAGATAAATCCATTTACTGAACAAATTAAAATAATTATAACAATTTAAACAATTATCAAT
* * ** * * * * *
21005545 TTTAAATAATTATGACATTTTATTTTGTCATAGAATAATTATTTATATTCAT
130 TTCAAATAATGACAACATTTTATTCTATAAAAGAACAATTATTTATATTCAT
* *
21005597 ACAAGCATATTTGAAA-AAAAAAATA
1 ACAAGCTTATTTGAAATAAAATAATA
21005622 CTAAATCTGT
Statistics
Matches: 175, Mismatches: 30, Indels: 3
0.84 0.14 0.01
Matches are distributed among these distances:
180 9 0.05
181 166 0.95
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (181 bp):
ACAAGCTTATTTGAAATAAAATAATATTAATTTATTAAGATTCTAAAAATTAACAAGTAAAAGAT
TTAAAAGATAAATCCATTTACTGAACAAATTAAAATAATTATAACAATTTAAACAATTATCAATT
TCAAATAATGACAACATTTTATTCTATAAAAGAACAATTATTTATATTCAT
Found at i:21005566 original size:18 final size:18
Alignment explanation
Indices: 21005513--21005566 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
21005503 GAGCAAGTTA
21005513 AAATAATTATGAC-TATTT
1 AAATAATTATGACAT-TTT
* *
21005531 AAACAATTATCA-ATTTT
1 AAATAATTATGACATTTT
21005548 AAATAATTATGACATTTT
1 AAATAATTATGACATTTT
21005566 A
1 A
21005567 TTTTGTCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 13 0.43
18 17 0.57
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (18 bp):
AAATAATTATGACATTTT
Found at i:21006206 original size:13 final size:13
Alignment explanation
Indices: 21006181--21006216 Score: 63
Period size: 13 Copynumber: 2.7 Consensus size: 13
21006171 AACTCATACC
21006181 AAAATATCTATGCA
1 AAAATATC-ATGCA
21006195 AAAATATCATGCA
1 AAAATATCATGCA
21006208 AAAATATCA
1 AAAATATCA
21006217 AAGATTATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.25
Consensus pattern (13 bp):
AAAATATCATGCA
Found at i:21006256 original size:54 final size:55
Alignment explanation
Indices: 21006180--21006309 Score: 158
Period size: 54 Copynumber: 2.4 Consensus size: 55
21006170 AAACTCATAC
* * *
21006180 CAAAATATCTATGCAA-AA-ATATCATGCAAAAATATCAAAGATTATGCAATAATA
1 CAAAATATC-ATGCAATAATATATCATGCAAAAATATAAAAGATCATGCAAAAATA
* * * *
21006234 TAAAATATCATG-AATAATATATCATGTAACAATATAAAATATCATGCAAAAATA
1 CAAAATATCATGCAATAATATATCATGCAAAAATATAAAAGATCATGCAAAAATA
*
21006288 CAAAATATCATGCAATTATATA
1 CAAAATATCATGCAATAATATA
21006310 ATAAGTCATG
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
52 2 0.03
53 5 0.08
54 49 0.77
55 8 0.12
ACGTcount: A:0.54, C:0.12, G:0.06, T:0.28
Consensus pattern (55 bp):
CAAAATATCATGCAATAATATATCATGCAAAAATATAAAAGATCATGCAAAAATA
Found at i:21006275 original size:20 final size:20
Alignment explanation
Indices: 21006247--21006302 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
21006237 AATATCATGA
* * *
21006247 ATAATATATCATGTAACAAT
1 ATAAAATATCATGCAAAAAT
21006267 ATAAAATATCATGCAAAAAT
1 ATAAAATATCATGCAAAAAT
*
21006287 ACAAAATATCATGCAA
1 ATAAAATATCATGCAA
21006303 TTATATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.27
Consensus pattern (20 bp):
ATAAAATATCATGCAAAAAT
Found at i:21006326 original size:18 final size:17
Alignment explanation
Indices: 21006294--21006347 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
21006284 AATACAAAAT
21006294 ATCATGCAATTATATAATA
1 ATCATGCAA--ATATAATA
21006313 AGTCATGCAAATATAATGA
1 A-TCATGCAAATATAAT-A
21006332 ATCATG-AAA-ATAATA
1 ATCATGCAAATATAATA
21006347 A
1 A
21006348 ATATCATGCG
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
15 2 0.06
16 5 0.15
17 3 0.09
18 12 0.36
19 3 0.09
20 8 0.24
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (17 bp):
ATCATGCAAATATAATA
Found at i:21006353 original size:18 final size:18
Alignment explanation
Indices: 21006236--21006355 Score: 51
Period size: 20 Copynumber: 6.6 Consensus size: 18
21006226 CAATAATATA
21006236 AAATATCATG--AATAAT
1 AAATATCATGAAAATAAT
21006252 --ATATCATGTAACAAT-AT
1 AAATATCATG-AA-AATAAT
21006269 AAAATATCATGCAAAAATACA-
1 -AAATATCATG--AAAATA-AT
* *
21006290 AAATATCATG-CAATTAT
1 AAATATCATGAAAATAAT
*
21006307 ATAATAAGTCATGCAAAT-AT
1 A-AAT-A-TCATGAAAATAAT
21006327 -AATGAATCATGAAAATAAT
1 AAAT--ATCATGAAAATAAT
21006346 AAATATCATG
1 AAATATCATG
21006356 CGAATTTATA
Statistics
Matches: 81, Mismatches: 5, Indels: 34
0.68 0.04 0.28
Matches are distributed among these distances:
14 8 0.10
16 1 0.01
17 6 0.07
18 24 0.30
19 5 0.06
20 31 0.38
21 5 0.06
22 1 0.01
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.29
Consensus pattern (18 bp):
AAATATCATGAAAATAAT
Found at i:21006406 original size:30 final size:30
Alignment explanation
Indices: 21006344--21006404 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
21006334 CATGAAAATA
21006344 ATAAATATCATGCGAATTTATAAATATCAT
1 ATAAATATCATGCGAATTTATAAATATCAT
* * *
21006374 ATAAATGTCATGC-AATATATATATAT-AT
1 ATAAATATCATGCGAATTTATAAATATCAT
21006402 ATA
1 ATA
21006405 TATTAAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 5 0.18
29 11 0.39
30 12 0.43
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.38
Consensus pattern (30 bp):
ATAAATATCATGCGAATTTATAAATATCAT
Found at i:21007246 original size:3 final size:3
Alignment explanation
Indices: 21007238--21007264 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
21007228 CCCACTTTTT
21007238 CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
21007265 TAATAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:21007581 original size:43 final size:43
Alignment explanation
Indices: 21007525--21007670 Score: 181
Period size: 43 Copynumber: 3.4 Consensus size: 43
21007515 TGAAGCTTGC
* *
21007525 AACTTTTAAAAAATAAAATGCTCCTCCACAACTGAAACTTTGA
1 AACTTTTGAAAAATAAAATGCTCCTCCACAACTGAGACTTTGA
* * * *
21007568 TA-TTTTTAGAAAATAAAATGCT-CTCCTACAACTTAGATTTTGA
1 AACTTTTGA-AAAATAAAATGCTCCTCC-ACAACTGAGACTTTGA
*
21007611 AACTTTTGAAAAATAAAATGCTCC-CACACAATTGAGACTTTGA
1 AACTTTTGAAAAATAAAATGCTCCTC-CACAACTGAGACTTTGA
21007654 AACTTTTGAAAAATAAA
1 AACTTTTGAAAAATAAA
21007671 GTACTCATCC
Statistics
Matches: 88, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
42 9 0.10
43 72 0.82
44 7 0.08
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (43 bp):
AACTTTTGAAAAATAAAATGCTCCTCCACAACTGAGACTTTGA
Found at i:21007696 original size:38 final size:38
Alignment explanation
Indices: 21007654--21007975 Score: 357
Period size: 38 Copynumber: 8.5 Consensus size: 38
21007644 GAGACTTTGA
* *
21007654 AACTTTTGAAAAATAAAGTACTCATCCATTGATGCTTC
1 AACTTTTGAAAAATAAAGTACTCATCCATTAAGGCTTC
* * *
21007692 AAC-TTTAAAAAATAAAGTACTCATTCATTGAGGCTTC
1 AACTTTTGAAAAATAAAGTACTCATCCATTAAGGCTTC
* *
21007729 AA-TTTTGAAAAATAAAATACTCATCCATTGAGGCTTC
1 AACTTTTGAAAAATAAAGTACTCATCCATTAAGGCTTC
* * * * *
21007766 AGC-TTTGAAAAATATAAAGTACTCCTCTACTAAGACTTC
1 AACTTTTG-AAAA-ATAAAGTACTCATCCATTAAGGCTTC
*
21007805 AACTTTTGAAAAATAAAGTACTCATCCACTAAGGCTTC
1 AACTTTTGAAAAATAAAGTACTCATCCATTAAGGCTTC
* **
21007843 AAC-TTTGAAAAAATAAAGTACTCCTCCACCAAGGCTTC
1 AACTTTTG-AAAAATAAAGTACTCATCCATTAAGGCTTC
* *
21007881 AACTTTTGAAAAATAAAGTACTCCTCCATTCAA-ACTTC
1 AACTTTTGAAAAATAAAGTACTCATCCATT-AAGGCTTC
* * * *
21007919 AACTTTGGAAAAATAAAATACTCTTCCATCAAGGCTTC
1 AACTTTTGAAAAATAAAGTACTCATCCATTAAGGCTTC
**
21007957 AAAATTTGAAAAATAAAGT
1 AACTTTTGAAAAATAAAGT
21007976 CATGTATAGG
Statistics
Matches: 244, Mismatches: 31, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
37 75 0.31
38 133 0.55
39 32 0.13
40 4 0.02
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (38 bp):
AACTTTTGAAAAATAAAGTACTCATCCATTAAGGCTTC
Found at i:21007864 original size:76 final size:76
Alignment explanation
Indices: 21007654--21007975 Score: 409
Period size: 76 Copynumber: 4.2 Consensus size: 76
21007644 GAGACTTTGA
* * * *
21007654 AACTTTTGAAAAATAAAGTACTCATCCATTGATGCTTCAACTTT-AAAAAATAAAGTACTCATTC
1 AACTTTTGAAAAATAAAGTACTCATCCATTAAGGCTTCAACTTTGAAAAAATAAAGTACTCCTCC
* *
21007718 ATTGAGGCTTC
66 ACTAAGGCTTC
* * *
21007729 AA-TTTTGAAAAATAAAATACTCATCCATTGAGGCTTCAGCTTTGAAAAATATAAAGTACTCCTC
1 AACTTTTGAAAAATAAAGTACTCATCCATTAAGGCTTCAACTTTGAAAAA-ATAAAGTACTCCTC
* *
21007793 TACTAAGACTTC
65 CACTAAGGCTTC
*
21007805 AACTTTTGAAAAATAAAGTACTCATCCACTAAGGCTTCAACTTTGAAAAAATAAAGTACTCCTCC
1 AACTTTTGAAAAATAAAGTACTCATCCATTAAGGCTTCAACTTTGAAAAAATAAAGTACTCCTCC
*
21007870 ACCAAGGCTTC
66 ACTAAGGCTTC
* * * * *
21007881 AACTTTTGAAAAATAAAGTACTCCTCCATTCAA-ACTTCAACTTTGGAAAAATAAAATACTCTTC
1 AACTTTTGAAAAATAAAGTACTCATCCATT-AAGGCTTCAACTTTGAAAAAATAAAGTACTCCTC
21007945 CA-TCAAGGCTTC
65 CACT-AAGGCTTC
**
21007957 AAAATTTGAAAAATAAAGT
1 AACTTTTGAAAAATAAAGT
21007976 CATGTATAGG
Statistics
Matches: 217, Mismatches: 25, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
74 38 0.18
75 7 0.03
76 127 0.59
77 45 0.21
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (76 bp):
AACTTTTGAAAAATAAAGTACTCATCCATTAAGGCTTCAACTTTGAAAAAATAAAGTACTCCTCC
ACTAAGGCTTC
Found at i:21008460 original size:22 final size:22
Alignment explanation
Indices: 21008419--21008460 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
21008409 ACAACATGTA
*
21008419 ATGAATGCAATGACTGCAAAGC
1 ATGAATGCAATGAATGCAAAGC
*
21008441 ATGAATGCAATGAATTCAAA
1 ATGAATGCAATGAATGCAAA
21008461 TTTCCAACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.14, G:0.19, T:0.21
Consensus pattern (22 bp):
ATGAATGCAATGAATGCAAAGC
Found at i:21009459 original size:19 final size:19
Alignment explanation
Indices: 21009437--21009483 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
21009427 TCATTTTAAG
*
21009437 TTTTTTTTTCCTTT-TT-T
1 TTTTTTTTTTCTTTCTTGT
21009454 TATTTTTTTTTCTTTCTTGT
1 T-TTTTTTTTTCTTTCTTGT
21009474 TTTTTTTTTT
1 TTTTTTTTTT
21009484 TTGCACACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 1 0.04
18 12 0.46
19 11 0.42
20 2 0.08
ACGTcount: A:0.02, C:0.09, G:0.02, T:0.87
Consensus pattern (19 bp):
TTTTTTTTTTCTTTCTTGT
Found at i:21009476 original size:22 final size:20
Alignment explanation
Indices: 21009437--21009485 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
21009427 TCATTTTAAG
*
21009437 TTTTTTTTTCCTTTTTTTATT
1 TTTTTTTTTCCTTGTTTT-TT
*
21009458 TTTTTTTCTTTCTTGTTTTTT
1 TTTTTTT-TTCCTTGTTTTTT
21009479 TTTTTTT
1 TTTTTTT
21009486 GCACACCTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.02, C:0.08, G:0.02, T:0.88
Consensus pattern (20 bp):
TTTTTTTTTCCTTGTTTTTT
Found at i:21010973 original size:19 final size:19
Alignment explanation
Indices: 21010949--21010990 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
21010939 ACATAGTAGC
21010949 TGAACTAGTAAAACTATAT
1 TGAACTAGTAAAACTATAT
* *
21010968 TGAACTAGTAAGACTATCT
1 TGAACTAGTAAAACTATAT
21010987 TGAA
1 TGAA
21010991 AAATATGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (19 bp):
TGAACTAGTAAAACTATAT
Found at i:21019393 original size:21 final size:22
Alignment explanation
Indices: 21019367--21019419 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
21019357 GATATTTTTA
*
21019367 AATATTTTATATTT-AAAAATT
1 AATATTTTATATTTAAAAAAAT
21019388 AATATTTTATATTTAAAAAAAT
1 AATATTTTATATTTAAAAAAAT
21019410 AATATTTTAT
1 AATATTTTAT
21019420 TAATTTTGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATATTTTATATTTAAAAAAAT
Found at i:21021491 original size:21 final size:22
Alignment explanation
Indices: 21021467--21021507 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
21021457 ACCAAAAAAT
* *
21021467 ATATATAATTAGA-CAAATTTA
1 ATATAAAATTAAATCAAATTTA
21021488 ATATAAAATTAAATCAAATT
1 ATATAAAATTAAATCAAATT
21021508 CACAAACAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (22 bp):
ATATAAAATTAAATCAAATTTA
Found at i:21028198 original size:11 final size:11
Alignment explanation
Indices: 21028182--21028206 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21028172 TTGAAAATCG
21028182 GGGGTCGGGTC
1 GGGGTCGGGTC
21028193 GGGGTCGGGTC
1 GGGGTCGGGTC
21028204 GGG
1 GGG
21028207 TAGGATGAAG
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:0.68, T:0.16
Consensus pattern (11 bp):
GGGGTCGGGTC
Found at i:21028373 original size:21 final size:22
Alignment explanation
Indices: 21028347--21028399 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
21028337 GATATTTTTA
*
21028347 AATATTTTATATTT-AAAAATT
1 AATATTTTATATTTAAAAAAAT
21028368 AATATTTTATATTTAAAAAAAT
1 AATATTTTATATTTAAAAAAAT
21028390 AATATTTTAT
1 AATATTTTAT
21028400 TAATTTTGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATATTTTATATTTAAAAAAAT
Found at i:21030470 original size:21 final size:22
Alignment explanation
Indices: 21030446--21030486 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
21030436 ACCAAAAAAT
* *
21030446 ATATATAATTAGA-CAAATTTA
1 ATATAAAATTAAATCAAATTTA
21030467 ATATAAAATTAAATCAAATT
1 ATATAAAATTAAATCAAATT
21030487 CACAAACAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (22 bp):
ATATAAAATTAAATCAAATTTA
Found at i:21034294 original size:15 final size:17
Alignment explanation
Indices: 21034265--21034301 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
21034255 TAAACACCTT
21034265 AAAATAAAAGACAAT-A
1 AAAATAAAAGACAATGA
*
21034281 AAAATAAAA-TCAATGA
1 AAAATAAAAGACAATGA
21034297 AAAAT
1 AAAAT
21034302 TTGATTGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.16
Consensus pattern (17 bp):
AAAATAAAAGACAATGA
Found at i:21036537 original size:20 final size:20
Alignment explanation
Indices: 21036507--21036585 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
21036497 CCAAAAGTTT
* *
21036507 TCCAGAAATTCACACCTAAA
1 TCCAAAAATTCAAACCTAAA
*
21036527 TTCAAAAATTCAAACTCTCAAA
1 TCCAAAAATTCAAAC-CT-AAA
* *
21036549 TCCAAAACTTCAAACCAAAA
1 TCCAAAAATTCAAACCTAAA
*
21036569 TCCAGAAATTCAAACCT
1 TCCAAAAATTCAAACCT
21036586 TAAGAAATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
20 29 0.60
21 3 0.06
22 16 0.33
ACGTcount: A:0.48, C:0.28, G:0.03, T:0.22
Consensus pattern (20 bp):
TCCAAAAATTCAAACCTAAA
Found at i:21036944 original size:3 final size:3
Alignment explanation
Indices: 21036938--21036981 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
21036928 AAAAGGAAAG
21036938 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA CATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA A
21036982 AAAATAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:21039992 original size:14 final size:14
Alignment explanation
Indices: 21039975--21040005 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
21039965 TTTATATTGT
*
21039975 TAAAAAAATATAAA
1 TAAAAAAATAGAAA
21039989 TAAAAAAATAGAAA
1 TAAAAAAATAGAAA
21040003 TAA
1 TAA
21040006 TATAAAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (14 bp):
TAAAAAAATAGAAA
Found at i:21042860 original size:19 final size:20
Alignment explanation
Indices: 21042815--21042866 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
21042805 TATTAGAAAA
*
21042815 TAAAAT-AATATTATTTTAT
1 TAAAATAAATATTAATTTAT
21042834 TAATAAATAAATATTAATTT-T
1 T-A-AAATAAATATTAATTTAT
21042855 TAAAATAAATAT
1 TAAAATAAATAT
21042867 ATAAAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 11 0.38
20 2 0.07
21 6 0.21
22 10 0.34
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAAATAAATATTAATTTAT
Found at i:21045429 original size:13 final size:13
Alignment explanation
Indices: 21045411--21045443 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
21045401 CAAACTGCAA
21045411 ATAAAAAAAAAGT
1 ATAAAAAAAAAGT
21045424 ATAAAAAAAAAGT
1 ATAAAAAAAAAGT
21045437 ATAAAAA
1 ATAAAAA
21045444 TTATATTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (13 bp):
ATAAAAAAAAAGT
Found at i:21049690 original size:21 final size:21
Alignment explanation
Indices: 21049648--21049690 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
21049638 GGCCTAATCT
*
21049648 TTATCATCTTCCTCATCTTTC
1 TTATCATCTTCCTCATCCTTC
* * *
21049669 TTATCATGTTCTTTATCCTTC
1 TTATCATCTTCCTCATCCTTC
21049690 T
1 T
21049691 AGGGTTGATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.28, G:0.02, T:0.56
Consensus pattern (21 bp):
TTATCATCTTCCTCATCCTTC
Found at i:21059161 original size:2 final size:2
Alignment explanation
Indices: 21059154--21059189 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
21059144 GGCTTAACAG
* *
21059154 TA TA TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21059190 AGAATAGTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:21063847 original size:8 final size:8
Alignment explanation
Indices: 21063811--21063840 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
21063801 CCCATTACTA
*
21063811 TTTTTTCT
1 TTTTTTGT
21063819 TTTTTTGT
1 TTTTTTGT
21063827 TTTTTTGT
1 TTTTTTGT
21063835 TTTTTT
1 TTTTTT
21063841 TTGTTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (8 bp):
TTTTTTGT
Found at i:21085874 original size:20 final size:20
Alignment explanation
Indices: 21085849--21085912 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
21085839 CTTTTGGAAT
21085849 TTAAAGTTTGTTGCCTTTGG
1 TTAAAGTTTGTTGCCTTTGG
* * *
21085869 TTAAAG---G-AGCTTTTGAAT
1 TTAAAGTTTGTTGCCTTTG--G
21085887 TTAAAGTTTGTTGCCTTTGG
1 TTAAAGTTTGTTGCCTTTGG
21085907 TTAAAG
1 TTAAAG
21085913 GAGCTTTCGG
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
16 6 0.19
17 1 0.03
18 6 0.19
20 12 0.38
21 1 0.03
22 6 0.19
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.45
Consensus pattern (20 bp):
TTAAAGTTTGTTGCCTTTGG
Found at i:21085896 original size:38 final size:38
Alignment explanation
Indices: 21085808--21086088 Score: 274
Period size: 39 Copynumber: 7.3 Consensus size: 38
21085798 GATCTTTAAT
** *
21085808 ATTTAAAGTTTGTTGTTTTTGGTTAAATGAGCTTTTGGA
1 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTT-GA
21085847 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTGA
1 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTGA
* *
21085885 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTCGG
1 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTGA
* * * * * * * *
21085923 ATTTAAAGTTGGTTACCTCTAGTGAGAGAAGCTTTTTTA
1 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGC-TTTTGA
* * * * * *
21085962 ATTTAAAGTTTGTTACCTCTGATGAGATGAGCCTTTTGA
1 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAG-CTTTTGA
** *
21086001 ATTTAAAGTCCGTTGCCTTTGGTTAAAGGAGCATTTGA
1 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTGA
** * * * *
21086039 ATTTAAAGTTCATTGTCTCTGGTTAGAGAAGCCTTTTGA
1 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAG-CTTTTGA
21086078 ATTTAAAGTTT
1 ATTTAAAGTTT
21086089 TATAGCCTCT
Statistics
Matches: 201, Mismatches: 38, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
38 94 0.47
39 106 0.53
40 1 0.00
ACGTcount: A:0.25, C:0.10, G:0.22, T:0.43
Consensus pattern (38 bp):
ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTGA
Found at i:21085965 original size:77 final size:77
Alignment explanation
Indices: 21085808--21085975 Score: 212
Period size: 77 Copynumber: 2.2 Consensus size: 77
21085798 GATCTTTAAT
** * * * * * * *
21085808 ATTTAAAGTTTGTTGTTTTTGGTTAAATGAGCTTTTGGAATTTAAAGTTTGTTGCCTTTGGTTAA
1 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTCGGAATTTAAAGTTGGTTACCTCTAGTGAA
*
21085873 AGGAGCTTTTGA
66 AGAAGCTTTTGA
*
21085885 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTCGG-ATTTAAAGTTGGTTACCTCTAGTGAG
1 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTCGGAATTTAAAGTTGGTTACCTCTAGTGAA
*
21085949 AGAAGCTTTTTTA
66 AGAAGC-TTTTGA
21085962 ATTTAAAGTTTGTT
1 ATTTAAAGTTTGTT
21085976 ACCTCTGATG
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
76 25 0.32
77 53 0.68
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (77 bp):
ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTCGGAATTTAAAGTTGGTTACCTCTAGTGAA
AGAAGCTTTTGA
Done.