Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, 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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 70 of 105
Found at i:12475980 original size:26 final size:26
Alignment explanation
Indices: 12475934--12475985 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
12475924 ATAGAATGTT
* *
12475934 ATCAAATTTTATCAAAGATTATCAAA
1 ATCAAATTATATCAAAAATTATCAAA
12475960 ATCAGAATTATAT-AAAAATTATCAAA
1 ATCA-AATTATATCAAAAATTATCAAA
12475986 TTTTACTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (26 bp):
ATCAAATTATATCAAAAATTATCAAA
Found at i:12479524 original size:7 final size:7
Alignment explanation
Indices: 12479512--12479552 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
12479502 AGATTCCTTT
12479512 TTTATAC
1 TTTATAC
12479519 TTTATAC
1 TTTATAC
12479526 TTTATAC
1 TTTATAC
*
12479533 TTTATGC
1 TTTATAC
*
12479540 TTTATGC
1 TTTATAC
12479547 TTTATA
1 TTTATA
12479553 TAGGGTATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.24, C:0.12, G:0.05, T:0.59
Consensus pattern (7 bp):
TTTATAC
Found at i:12484211 original size:27 final size:28
Alignment explanation
Indices: 12484173--12484225 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
12484163 CATTTTTGTC
*
12484173 AAATCATTTTAAATTTAAATTATTTTTA
1 AAATCATTTTAAATTTAAATAATTTTTA
12484201 AAAT-ATTTTAAATTTAAATAATTTT
1 AAATCATTTTAAATTTAAATAATTTT
12484226 GTGTTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
AAATCATTTTAAATTTAAATAATTTTTA
Found at i:12485241 original size:31 final size:30
Alignment explanation
Indices: 12485196--12485312 Score: 130
Period size: 30 Copynumber: 3.8 Consensus size: 30
12485186 TAATAAATCT
*
12485196 ATTTTTTAAATGATATAGAAATTTTACTTA
1 ATTTTTAAAATGATATAGAAATTTTACTTA
* * *
12485226 ATATTTTAAAATGATAT-GGAGTTTTATTTA
1 AT-TTTTAAAATGATATAGAAATTTTACTTA
* *
12485256 ATTCTTTAAATTGATATAGAAATTTTTACATA
1 ATT-TTTAAAATGATATAGAAA-TTTTACTTA
12485288 ACTTTTTAAAATGATATA-AAATTTT
1 A-TTTTTAAAATGATATAGAAATTTT
12485313 TTAAAAAAAG
Statistics
Matches: 72, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
29 1 0.01
30 30 0.42
31 18 0.25
32 21 0.29
33 2 0.03
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.49
Consensus pattern (30 bp):
ATTTTTAAAATGATATAGAAATTTTACTTA
Found at i:12487800 original size:22 final size:22
Alignment explanation
Indices: 12487775--12487837 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 22
12487765 CATTTTTATT
12487775 TTAAATAAAATATAAATTAAAA
1 TTAAATAAAATATAAATTAAAA
*
12487797 TTAAAAATAAAATATATTATTTAAAA
1 TT--AAATAAAATATA--AATTAAAA
12487823 TT--ATAAAATTATAAA
1 TTAAATAAAA-TATAAA
12487838 AATATATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
21 1 0.03
22 8 0.24
23 4 0.12
24 12 0.35
26 9 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TTAAATAAAATATAAATTAAAA
Found at i:12487820 original size:26 final size:25
Alignment explanation
Indices: 12487777--12487831 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
12487767 TTTTTATTTT
12487777 AAATAAAATATAAATTAAAATTA-A
1 AAATAAAATATAAATTAAAATTATA
*
12487801 AAATAAAATATATTATTTAAAATTATA
1 AAATAAAATATA--AATTAAAATTATA
12487828 AAAT
1 AAAT
12487832 TATAAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 12 0.44
26 10 0.37
27 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
AAATAAAATATAAATTAAAATTATA
Found at i:12488057 original size:19 final size:20
Alignment explanation
Indices: 12488025--12488066 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
12488015 ATATTTAATA
12488025 TTTTTAATAAAAAATA-TAT
1 TTTTTAATAAAAAATACTAT
* *
12488044 TTTTTGATAGAAAATACTAT
1 TTTTTAATAAAAAATACTAT
12488064 TTT
1 TTT
12488067 CTATTATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTTTAATAAAAAATACTAT
Found at i:12491388 original size:18 final size:18
Alignment explanation
Indices: 12491367--12491423 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
12491357 TTATGTAAAA
*
12491367 ATAAAATAAAATGTAATC
1 ATAAAATAAAATATAATC
* * *
12491385 ATAATATAATCATATTAT-
1 ATAAAATAA-AATATAATC
12491403 ATAAAATAAAATATAATC
1 ATAAAATAAAATATAATC
12491421 ATA
1 ATA
12491424 TTATATATAT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
17 6 0.20
18 19 0.63
19 5 0.17
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (18 bp):
ATAAAATAAAATATAATC
Found at i:12496222 original size:30 final size:30
Alignment explanation
Indices: 12496171--12496228 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
12496161 TTTAATTTAT
* *
12496171 AATTAAATATTTTTAATTTATATAAATAAA
1 AATTAAATATTTCTAACTTATATAAATAAA
*
12496201 AATTAAATATTATCT-ACTTATATCAATA
1 AATTAAATATT-TCTAACTTATATAAATA
12496229 TATAATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (30 bp):
AATTAAATATTTCTAACTTATATAAATAAA
Found at i:12496396 original size:32 final size:31
Alignment explanation
Indices: 12496345--12496406 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
12496335 ATTTAACGTT
12496345 AGCAATCAGCTCTTCCTTTCTTTCTCTAAAAG
1 AGCAATCAGCTCTTCCTTTCTTTCT-TAAAAG
* * *
12496377 AGCAATCGGTTCTTTCTTTCTTTCTTAAAA
1 AGCAATCAGCTCTTCCTTTCTTTCTTAAAA
12496407 AATTCTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.42
Consensus pattern (31 bp):
AGCAATCAGCTCTTCCTTTCTTTCTTAAAAG
Found at i:12509088 original size:17 final size:17
Alignment explanation
Indices: 12509051--12509098 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
12509041 TAATAAAGAA
**
12509051 GAAAAGATGTGAAAAAT
1 GAAAAGATGAAAAAAAT
12509068 -AAAAGATGAAAAAAAT
1 GAAAAGATGAAAAAAAT
12509084 GAAAAGA--AAAAAAAT
1 GAAAAGATGAAAAAAAT
12509099 ATGAAGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 8 0.29
16 14 0.50
17 6 0.21
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (17 bp):
GAAAAGATGAAAAAAAT
Found at i:12509411 original size:38 final size:36
Alignment explanation
Indices: 12509368--12509467 Score: 103
Period size: 38 Copynumber: 2.7 Consensus size: 36
12509358 TAGGGATGTC
*
12509368 AATAATGAATAAAGTGA-AAAAGAAATGAAAAGAAAAAT
1 AATAATGAA-AAAATGAGAAAA-AAATGAAAA-AAAAAT
*
12509406 AATAATGAAAAAATGAGAAAAAAATGAAAAAAAAAG
1 AATAATGAAAAAATGAGAAAAAAATGAAAAAAAAAT
* * *
12509442 AAAAATGTGAAAAAAAGAGGAAAAAA
1 AATAA--TGAAAAAATGAGAAAAAAA
12509468 GAAGACTCAA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
36 9 0.17
37 15 0.28
38 30 0.56
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (36 bp):
AATAATGAAAAAATGAGAAAAAAATGAAAAAAAAAT
Found at i:12509429 original size:11 final size:11
Alignment explanation
Indices: 12509413--12509467 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
12509403 AATAATAATG
12509413 AAAAAATGAGA
1 AAAAAATGAGA
12509424 AAAAAATGA-A
1 AAAAAATGAGA
12509434 AAAAAA--AG-
1 AAAAAATGAGA
*
12509442 -AAAAATGTGA
1 AAAAAATGAGA
12509452 AAAAAA-GAGGA
1 AAAAAATGA-GA
12509463 AAAAA
1 AAAAA
12509468 GAAGACTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
7 5 0.14
8 1 0.03
9 1 0.03
10 8 0.22
11 21 0.58
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.07
Consensus pattern (11 bp):
AAAAAATGAGA
Found at i:12509431 original size:19 final size:19
Alignment explanation
Indices: 12509395--12509467 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
12509385 AAAAGAAATG
*
12509395 AAAAGAAAAATAATAATGAAA
1 AAAAGAGAAA-AA-AATGAAA
*
12509416 AAATGAGAAAAAAATGAAA
1 AAAAGAGAAAAAAATGAAA
* **
12509435 AAAAAAGAAAAATGTGAAA
1 AAAAGAGAAAAAAATGAAA
12509454 AAAAGAGGAAAAAA
1 AAAAGA-GAAAAAA
12509468 GAAGACTCAA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
19 27 0.63
20 8 0.19
21 8 0.19
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (19 bp):
AAAAGAGAAAAAAATGAAA
Found at i:12510308 original size:15 final size:15
Alignment explanation
Indices: 12510261--12510308 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
12510251 ACAATTAGAG
*
12510261 TTGCATTCATAAACA
1 TTGCATTCATAAGCA
*
12510276 TTGCTTTCAT--GCA
1 TTGCATTCATAAGCA
*
12510289 TTGCATTCATAAGTA
1 TTGCATTCATAAGCA
12510304 TTGCA
1 TTGCA
12510309 CTAATGTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 11 0.41
15 16 0.59
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (15 bp):
TTGCATTCATAAGCA
Found at i:12511287 original size:19 final size:19
Alignment explanation
Indices: 12511263--12511344 Score: 62
Period size: 18 Copynumber: 4.4 Consensus size: 19
12511253 AGAGTTTCAA
*
12511263 TTGTGAATCTTTGAAT-TC
1 TTGTGAATCTTTAAATCTC
12511281 TTTGTGAAT-TTTAAATCTC
1 -TTGTGAATCTTTAAATCTC
* * * *
12511300 TTGCGAATCTTAAAATTTT
1 TTGTGAATCTTTAAATCTC
** *
12511319 TTACGAATC-TTAAATCTT
1 TTGTGAATCTTTAAATCTC
12511337 TTGTGAAT
1 TTGTGAAT
12511345 TTTGAATTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
18 26 0.51
19 25 0.49
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.49
Consensus pattern (19 bp):
TTGTGAATCTTTAAATCTC
Found at i:12511309 original size:37 final size:36
Alignment explanation
Indices: 12511267--12511370 Score: 111
Period size: 37 Copynumber: 2.9 Consensus size: 36
12511257 TTTCAATTGT
** *
12511267 GAATCTTTGAATTCTTTGTGAATTTTAAATCTCTTGC
1 GAATCTTTGAATT-TTTAAGAATCTTAAATCTCTTGC
** * * *
12511304 GAATCTTAAAATTTTTTACGAATCTTAAATCTTTTGT
1 GAATCTTTGAA-TTTTTAAGAATCTTAAATCTCTTGC
12511341 GAAT-TTTGAATTTTTAAGAATCTTAAATCT
1 GAATCTTTGAATTTTTAAGAATCTTAAATCT
12511371 TTTGAAAACT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
35 19 0.34
36 4 0.07
37 31 0.55
38 2 0.04
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.48
Consensus pattern (36 bp):
GAATCTTTGAATTTTTAAGAATCTTAAATCTCTTGC
Found at i:12511312 original size:18 final size:18
Alignment explanation
Indices: 12511286--12511335 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
12511276 AATTCTTTGT
* *
12511286 GAATTTTAAATCTCTTGC
1 GAATCTTAAATCTCTTAC
* *
12511304 GAATCTTAAAATTTTTTAC
1 GAATCTT-AAATCTCTTAC
12511323 GAATCTTAAATCT
1 GAATCTTAAATCT
12511336 TTTGTGAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (18 bp):
GAATCTTAAATCTCTTAC
Found at i:12511338 original size:18 final size:18
Alignment explanation
Indices: 12511286--12511373 Score: 79
Period size: 18 Copynumber: 4.9 Consensus size: 18
12511276 AATTCTTTGT
* * *
12511286 GAATTTTAAATCTCTTGC
1 GAATCTTAAATCTTTTAC
*
12511304 GAATCTTAAAATTTTTTAC
1 GAATCTT-AAATCTTTTAC
**
12511323 GAATCTTAAATCTTTTGT
1 GAATCTTAAATCTTTTAC
* * *
12511341 GAATTTTGAAT-TTTTAA
1 GAATCTTAAATCTTTTAC
12511358 GAATCTTAAATCTTTT
1 GAATCTTAAATCTTTT
12511374 GAAAACTTTG
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
17 13 0.24
18 27 0.49
19 15 0.27
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.49
Consensus pattern (18 bp):
GAATCTTAAATCTTTTAC
Found at i:12511384 original size:35 final size:35
Alignment explanation
Indices: 12511316--12511384 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
12511306 ATCTTAAAAT
* ** *
12511316 TTTTTACGAATCTTAAATCTTTTGTGAATTTTGAA
1 TTTTTAAGAATCTTAAATCTTTTGAAAACTTTGAA
12511351 TTTTTAAGAATCTTAAATCTTTTGAAAACTTTGA
1 TTTTTAAGAATCTTAAATCTTTTGAAAACTTTGA
12511385 TTCTCTAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.32, C:0.09, G:0.10, T:0.49
Consensus pattern (35 bp):
TTTTTAAGAATCTTAAATCTTTTGAAAACTTTGAA
Found at i:12511394 original size:35 final size:35
Alignment explanation
Indices: 12511323--12511396 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
12511313 AATTTTTTAC
** * *
12511323 GAATCTTAAATCTTTTGTGAATTTTGAATTTTTAA
1 GAATCTTAAATCTTTTGAAAACTTTGAATTTCTAA
12511358 GAATCTTAAATCTTTTGAAAACTTTG-ATTCTCTAA
1 GAATCTTAAATCTTTTGAAAACTTTGAATT-TCTAA
12511393 GAAT
1 GAAT
12511397 TTTTGAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 3 0.09
35 31 0.91
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (35 bp):
GAATCTTAAATCTTTTGAAAACTTTGAATTTCTAA
Found at i:12511527 original size:22 final size:22
Alignment explanation
Indices: 12511495--12511547 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
12511485 ATTGTGAGCT
* *
12511495 TTTAAACTTCAAGTTGAAAAT-
1 TTTAAATTTCAAATTGAAAATA
*
12511516 TCTTAAATTTCAAATTGCAAATA
1 T-TTAAATTTCAAATTGAAAATA
12511539 TTTAAATTT
1 TTTAAATTT
12511548 TCAGTTGCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 25 0.93
23 1 0.04
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (22 bp):
TTTAAATTTCAAATTGAAAATA
Found at i:12511555 original size:22 final size:21
Alignment explanation
Indices: 12511530--12511581 Score: 50
Period size: 23 Copynumber: 2.4 Consensus size: 21
12511520 AAATTTCAAA
*
12511530 TTGCAAATATTTAAATTTTCAG
1 TTGCAAATATTTAAATTAT-AG
* * *
12511552 TTGCGAACTTTTTGAATTATAG
1 TTGC-AAATATTTAAATTATAG
12511574 TTGCAAAT
1 TTGCAAAT
12511582 TGCGAATCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 3 0.12
22 10 0.42
23 11 0.46
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (21 bp):
TTGCAAATATTTAAATTATAG
Found at i:12512063 original size:21 final size:21
Alignment explanation
Indices: 12512031--12512078 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
12512021 AAAACTCCCC
* *
12512031 ATTAAG-ATCAATTAGAAACA
1 ATTAAGAATCAATCAGAAAAA
12512051 ATTAAGAATCAATCAGAAAAA
1 ATTAAGAATCAATCAGAAAAA
*
12512072 ATCAAGA
1 ATTAAGA
12512079 GAGAAAGAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.58, C:0.10, G:0.10, T:0.21
Consensus pattern (21 bp):
ATTAAGAATCAATCAGAAAAA
Found at i:12515611 original size:4 final size:4
Alignment explanation
Indices: 12515602--12515640 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
12515592 ATGATGATGA
* * *
12515602 TGAT TGAT TGAT TGAT TGAT TGAA TAAT TAAT TGAT TGA
1 TGAT TGAT TGAT TGAT TGAT TGAT TGAT TGAT TGAT TGA
12515641 CTTTGTTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (4 bp):
TGAT
Found at i:12515970 original size:33 final size:33
Alignment explanation
Indices: 12515933--12516003 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
12515923 TTTTATGAGA
*
12515933 AAAATGTCATTACTTT-GATGGCGTTTGTAACTG
1 AAAATGTCACTACTTTAGA-GGCGTTTGTAACTG
** *
12515966 AAAATGTTGCTACTTTAGAGGCGTTTGTATCTG
1 AAAATGTCACTACTTTAGAGGCGTTTGTAACTG
12515999 AAAAT
1 AAAAT
12516004 ACCTCTATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 31 0.94
34 2 0.06
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (33 bp):
AAAATGTCACTACTTTAGAGGCGTTTGTAACTG
Found at i:12516248 original size:134 final size:134
Alignment explanation
Indices: 12515884--12516340 Score: 501
Period size: 134 Copynumber: 3.4 Consensus size: 134
12515874 CCATTTTAGT
* * * * * *
12515884 GACGTTTCTATCTTTGAAACGCCACTAAATTAGTTG-TATTTTTATGAGAAAAATGTCATTACTT
1 GACGTTTGTATCTTTGAGACGCCACTAATTTAG-TGACATTTTTATGAGAAAAATATCGTTACTT
* * * * *
12515948 TGATGGCGTTTGTAACTGAAAATGTTGCTACTTTAGAGGCGTTTGTATCTGAAAATACCTCTATA
65 TGGTGGTGTTTGTAACTGAAAATGATGCTACTTTAGAGGCGTTTGTATCTGAAAATGCTTCTATA
12516013 TTAAC
130 TTAAC
* * * * * * *
12516018 GGCGTTTGTAT-TTTAGAGATGCCCGCTAATTTAGTGACGTTTTTATGAGAAAAACACCGTTGCT
1 GACGTTTGTATCTTT-GAGACG-CCACTAATTTAGTGACATTTTTATGAGAAAAATATCGTTACT
** * * *
12516082 TTGGAAGTATTTGTAACTAAAAAT-ATCGCTACTTTAGAGACGTTTGTATCTGAAAATGCTTCTA
64 TTGGTGGTGTTTGTAACTGAAAATGAT-GCTACTTTAGAGGCGTTTGTATCTGAAAATGCTTCTA
12516146 TATTAAC
128 TATTAAC
* *
12516153 GACGTTTGTATCTTTGAGACGCCACTAATTTAGTGGCATTTTTATGAGAAAAATTTCGTTACTTT
1 GACGTTTGTATCTTTGAGACGCCACTAATTTAGTGACATTTTTATGAGAAAAATATCGTTACTTT
* * * * *
12516218 GGTGGTGTTTGTAAATGAAAATGCTGCTACTTTAGAGGCATTTGCATCTGAAAATG-TGTCCATA
66 GGTGGTGTTTGTAACTGAAAATGATGCTACTTTAGAGGCGTTTGTATCTGAAAATGCT-TCTATA
*
12516282 TTAGC
130 TTAAC
* * * * *
12516287 -AGGTTTTTTCTCTTTGAGACGTCACTAATTTAGTGACGTTTTTATGAGAAAAAT
1 GACG-TTTGTATCTTTGAGACGCCACTAATTTAGTGACATTTTTATGAGAAAAAT
12516341 GCTGTTGCTT
Statistics
Matches: 266, Mismatches: 49, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
133 6 0.02
134 152 0.57
135 105 0.39
136 3 0.01
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.39
Consensus pattern (134 bp):
GACGTTTGTATCTTTGAGACGCCACTAATTTAGTGACATTTTTATGAGAAAAATATCGTTACTTT
GGTGGTGTTTGTAACTGAAAATGATGCTACTTTAGAGGCGTTTGTATCTGAAAATGCTTCTATAT
TAAC
Found at i:12516992 original size:21 final size:20
Alignment explanation
Indices: 12516940--12516988 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
12516930 GCAATTGCTA
*
12516940 AAATTTTGCACGTTCTTGCT
1 AAATTTTGCACGTTCTTCCT
** *
12516960 CTATTCTAGCACGTTCTTCCT
1 AAATT-TTGCACGTTCTTCCT
12516981 AAATTTTG
1 AAATTTTG
12516989 GCACACTTTT
Statistics
Matches: 21, Mismatches: 7, Indels: 2
0.70 0.23 0.07
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.45
Consensus pattern (20 bp):
AAATTTTGCACGTTCTTCCT
Found at i:12521877 original size:64 final size:64
Alignment explanation
Indices: 12521781--12521908 Score: 229
Period size: 64 Copynumber: 2.0 Consensus size: 64
12521771 CGACCTTTTA
* *
12521781 TACTCTAACCAGATAAATTCACATAAGTAAAAAAATTATTGATAGTCCATAATAAAGTAGCACG
1 TACTCTAACCAGATAAATTCACATAAGCAAAAAAATCATTGATAGTCCATAATAAAGTAGCACG
*
12521845 TACTCTAACCAGATAAATTCACATAAGCAAAAAAATCGTTGATAGTCCATAATAAAGTAGCACG
1 TACTCTAACCAGATAAATTCACATAAGCAAAAAAATCATTGATAGTCCATAATAAAGTAGCACG
12521909 CATATTAAAG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.25
Consensus pattern (64 bp):
TACTCTAACCAGATAAATTCACATAAGCAAAAAAATCATTGATAGTCCATAATAAAGTAGCACG
Found at i:12526341 original size:79 final size:79
Alignment explanation
Indices: 12526181--12526433 Score: 328
Period size: 80 Copynumber: 3.2 Consensus size: 79
12526171 CTTAAATATT
*
12526181 ATGGTTTGCTGAACCTTGTTGTCTGATATTTTTTGGCTGAATGGTATTGTATGATATTGGGGGGC
1 ATGGTTTGCTGAACCTTGTTGTCTGATATTTTTTGG-TCAATGGTATTGTATGATATTGGGGGGC
12526246 TGAATCGTATGCTGA
65 TGAATCGTATGCTGA
* * * * * *
12526261 ATGGTTTGCTGAACCTTGTTGTATGATATTGTATT-GTCAAAGGTATTGCATGATATTAGGAGGC
1 ATGGTTTGCTGAACCTTGTTGTCTGATATT-TTTTGGTCAATGGTATTGTATGATATTGGGGGGC
* *
12526325 TGAATCATATGTTGA
65 TGAATCGTATGCTGA
* * * *
12526340 ATGGTTTGTTGAACCTTGTTATCTGATATTATTTTGGTCAATGGTTTTGTATGATATTGGGGGGT
1 ATGGTTTGCTGAACCTTGTTGTCTGATATT-TTTTGGTCAATGGTATTGTATGATATTGGGGGGC
*
12526405 TGAATCGTATGCTAA
65 TGAATCGTATGCTGA
*
12526420 ATGGTGTTTCTGAA
1 ATGGT-TTGCTGAA
12526434 TGATTTACTG
Statistics
Matches: 145, Mismatches: 25, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
79 66 0.46
80 70 0.48
81 9 0.06
ACGTcount: A:0.22, C:0.09, G:0.27, T:0.42
Consensus pattern (79 bp):
ATGGTTTGCTGAACCTTGTTGTCTGATATTTTTTGGTCAATGGTATTGTATGATATTGGGGGGCT
GAATCGTATGCTGA
Found at i:12530558 original size:305 final size:304
Alignment explanation
Indices: 12529884--12530762 Score: 1054
Period size: 305 Copynumber: 2.9 Consensus size: 304
12529874 TTTGGAAAAA
** * * ** *
12529884 AAAAAACACCTTTAAGAATCCATTGTGCCTTTTTTGTATGGATTGTTGAAGGCATTTAAAAAAAA
1 AAAAAACACCTTTAAGAATCTGTTGAGTCTTTTTTGTATAAATTATTGAAGGCATTTAAAAAAAA
* * * *
12529949 TATCTTCAATAATACCAATTAAAAATTAATCGAATGGATTATGAAGGGCGTTTTCCTATGAGTAA
66 -ACCTTCAATAATACCAACTAAAAATTAATCAAATGGATTATGAAGGACGTTTTCCTATGAGTAA
* * *
12530014 CGCCTTTAATAATCCATAACAAAATGTTATTGAAGGCGTTTCTAGATATAACCGCCTTCAATAAT
130 CGCCTTGAATAATCC-TAACAAAATGTTATTGAAGGCGTTTCTGGATATAACCGCATTCAATAAT
** * *
12530079 CTGACCATAAAAAATTTATCGTCTGGAATATTAATGGTATTTTTTTACCAAAATTGCCTTTAATA
194 CTGACCATAAAAAATTTATCGTCTGGAATATTAATGGTACGTTTTTACCAAAATCGCCTTCAATA
* * * *
12530144 ATCCAACCAAAATTTTATTGTGTGGAATATTAAAGGCATTTTGTGC
259 ATCCAACCAAAAATTTATTGTGTGAAAAAATAAAGGCATTTTGTGC
* * **
12530190 -AAAAACGCCTTCAAGAATCTGTCAAGTCTTTTTTGTATAAATTATTGAAGGCATTTTAAAAAAA
1 AAAAAACACCTTTAAGAATCTGTTGAGTCTTTTTTGTATAAATTATTGAAGGCA-TTTAAAAAAA
** * * * *
12530254 CGCCTTTAATAATACAAACTAAAAATTAATCAAATGGATTATGAAGGACGTTTTTCTATGGGTAA
65 AACCTTCAATAATACCAACTAAAAATTAATCAAATGGATTATGAAGGACGTTTTCCTATGAGTAA
* * * ** * *
12530319 TGGCTTGAATAATCTCTAATAAAATGTTATTGAAGGTATTTCTGGATATAACTGCATTTAATAAT
130 CGCCTTGAATAATC-CTAACAAAATGTTATTGAAGGCGTTTCTGGATATAACCGCATTCAATAAT
*
12530384 CTGACCATAAAAAATTTATCGTCTGGAATATTAAT-G-ACGTTTTTATCAAAATCGCCTTCAATA
194 CTGACCATAAAAAATTTATCGTCTGGAATATTAATGGTACGTTTTTACCAAAATCGCCTTCAATA
* * *
12530447 ATCCCACTAAAAATTTATTGTGTGAAAAAATAAAGGCGTTTTAG-GC
259 ATCCAACCAAAAATTTATTGTGTGAAAAAATAAAGGCATTTT-GTGC
* **
12530493 AAAAAATACCTTTAAGAATCTGTTGAGTCTTTTTTGTATAAATTATTGAAGGTGTTTAAAAAAAA
1 AAAAAACACCTTTAAGAATCTGTTGAGTCTTTTTTGTATAAATTATTGAAGGCATTT-AAAAAAA
*
12530558 ATACCTTCAATAATACCAACTAAAAATTAATCAAATGGATTATGAAGGACGTTTTCCTACGAGTA
65 A-ACCTTCAATAATACCAACTAAAAATTAATCAAATGGATTATGAAGGACGTTTTCCTATGAGTA
* * * * *
12530623 ACGCCTTGAATAATCCCTAACAAAATTTTATTGAAGGCGTTTATGGATATAGCCACCTTCAATAA
129 ACGCCTTGAATAAT-CCTAACAAAATGTTATTGAAGGCGTTTCTGGATATAACCGCATTCAATAA
* * * * * * * *
12530688 TCCGATCAT-TAAAAGTTATCGTTTGAAATATTAAAGG--CGTTTTGAGCC-AAATACGCCTTCA
193 TCTGACCATAAAAAATTTATCGTCTGGAATATTAATGGTACGTTTTTA-CCAAAAT-CGCCTTCA
* *
12530749 ATCATCCATCCAAA
256 ATAATCCAACCAAA
12530763 CTTTTGTCTA
Statistics
Matches: 481, Mismatches: 82, Indels: 21
0.82 0.14 0.04
Matches are distributed among these distances:
303 62 0.13
304 87 0.18
305 320 0.67
306 12 0.02
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (304 bp):
AAAAAACACCTTTAAGAATCTGTTGAGTCTTTTTTGTATAAATTATTGAAGGCATTTAAAAAAAA
ACCTTCAATAATACCAACTAAAAATTAATCAAATGGATTATGAAGGACGTTTTCCTATGAGTAAC
GCCTTGAATAATCCTAACAAAATGTTATTGAAGGCGTTTCTGGATATAACCGCATTCAATAATCT
GACCATAAAAAATTTATCGTCTGGAATATTAATGGTACGTTTTTACCAAAATCGCCTTCAATAAT
CCAACCAAAAATTTATTGTGTGAAAAAATAAAGGCATTTTGTGC
Found at i:12532255 original size:2 final size:2
Alignment explanation
Indices: 12532250--12532278 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12532240 TGTGTGTGTC
12532250 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12532279 TTGGATCAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12542736 original size:20 final size:20
Alignment explanation
Indices: 12542711--12542806 Score: 131
Period size: 20 Copynumber: 4.8 Consensus size: 20
12542701 AAATAAAAAA
12542711 AATAAATCATGCAAATAAAT
1 AATAAATCATGCAAATAAAT
* *
12542731 AATAAATCATACAAATATATT
1 AATAAATCATGCAAATA-AAT
*
12542752 AAT-AATAATGCAAATAAAT
1 AATAAATCATGCAAATAAAT
12542771 AATATAATCATGCAAATAAAT
1 AATA-AATCATGCAAATAAAT
*
12542792 AAAAAATCATGCAAA
1 AATAAATCATGCAAA
12542807 GTTTTTTTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
19 5 0.08
20 38 0.58
21 23 0.35
ACGTcount: A:0.60, C:0.09, G:0.04, T:0.26
Consensus pattern (20 bp):
AATAAATCATGCAAATAAAT
Found at i:12542780 original size:41 final size:40
Alignment explanation
Indices: 12542714--12542806 Score: 123
Period size: 41 Copynumber: 2.3 Consensus size: 40
12542704 TAAAAAAAAT
* * *
12542714 AAATCATGCAAATAAATAATAAATCATACAAATATATTAA
1 AAATAATGCAAATAAATAATAAATCATACAAATAAATAAA
* *
12542754 TAATAATGCAAATAAATAATATAATCATGCAAATAAATAAA
1 AAATAATGCAAATAAATAATA-AATCATACAAATAAATAAA
*
12542795 AAATCATGCAAA
1 AAATAATGCAAA
12542807 GTTTTTTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 19 0.42
41 26 0.58
ACGTcount: A:0.60, C:0.10, G:0.04, T:0.26
Consensus pattern (40 bp):
AAATAATGCAAATAAATAATAAATCATACAAATAAATAAA
Found at i:12544133 original size:7 final size:7
Alignment explanation
Indices: 12544121--12544147 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
12544111 TTTCCCACTT
12544121 TTTTTTA
1 TTTTTTA
12544128 TTTTTTA
1 TTTTTTA
12544135 TTTTTTA
1 TTTTTTA
12544142 TTTTTT
1 TTTTTT
12544148 TTTACTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:12544186 original size:6 final size:6
Alignment explanation
Indices: 12544165--12544225 Score: 68
Period size: 6 Copynumber: 10.2 Consensus size: 6
12544155 TGACTGGTAC
* * * *
12544165 TAAAAA TAACAT TAAAAT TAAAAT CAAAAT GAAAAT TAAAAT TAAAAT
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT
* *
12544213 CAAAAT CAAAAT T
1 TAAAAT TAAAAT T
12544226 TTTGGGATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.26
Consensus pattern (6 bp):
TAAAAT
Found at i:12544202 original size:24 final size:23
Alignment explanation
Indices: 12544167--12544225 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 23
12544157 ACTGGTACTA
*
12544167 AAAATAACATTAAAATTAAAATC
1 AAAATAAAATTAAAATTAAAATC
12544190 AAAATGAAAATTAAAATTAAAATC
1 AAAAT-AAAATTAAAATTAAAATC
12544214 AAAATCAAAATT
1 AAAAT-AAAATT
12544226 TTTGGGATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
23 5 0.15
24 28 0.85
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.25
Consensus pattern (23 bp):
AAAATAAAATTAAAATTAAAATC
Found at i:12544510 original size:42 final size:42
Alignment explanation
Indices: 12544446--12544688 Score: 190
Period size: 43 Copynumber: 5.7 Consensus size: 42
12544436 CTTTTCAGCA
* * * *
12544446 AAGGCTTTGAAAATTTTAAAAAATAAAATGCTCTCCACAACC
1 AAGGCATTGAAACTTTTGAAAAATAAAATGCTCTCCACAACT
* * * *
12544488 AAGGCATT-AAGACTTTTGAAAAATAAATTGCTCCCCCATAATT
1 AAGGCATTGAA-ACTTTTGAAAAATAAAATGCT-CTCCACAACT
* * * * *
12544531 GAGGAATTGAAACATTTGAAAAATAAAATGTTCCCCCACAA-T
1 AAGGCATTGAAACTTTTGAAAAATAAAATGCT-CTCCACAACT
*
12544573 AGAGGCATTGAAACTTTTTGAAAAAT-AAATGCTCTCCCATAACT
1 A-AGGCATTGAAAC-TTTTGAAAAATAAAATGCTCT-CCACAACT
* * * *
12544617 GAGGTATTGAAATTTTTGAAAAATAAAATGCTTCTTCACAACCT
1 AAGGCATTGAAACTTTTGAAAAATAAAATGC-TCTCCACAA-CT
* *
12544661 -AGGTATTGAAACTTCT-AAAAAGTAAAAT
1 AAGGCATTGAAACTTTTGAAAAA-TAAAAT
12544689 AGATATCTAA
Statistics
Matches: 163, Mismatches: 27, Indels: 21
0.77 0.13 0.10
Matches are distributed among these distances:
41 2 0.01
42 43 0.26
43 100 0.61
44 18 0.11
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (42 bp):
AAGGCATTGAAACTTTTGAAAAATAAAATGCTCTCCACAACT
Found at i:12544550 original size:43 final size:43
Alignment explanation
Indices: 12544499--12544648 Score: 194
Period size: 43 Copynumber: 3.5 Consensus size: 43
12544489 AGGCATTAAG
*
12544499 ACTTTTGAAAAATAAATTGCTCCCCCATAATTGAGGAATTGAA
1 ACTTTTGAAAAATAAAATGCTCCCCCATAATTGAGGAATTGAA
* * * * *
12544542 ACATTTGAAAAATAAAATGTTCCCCCACAATAGAGGCATTGAA
1 ACTTTTGAAAAATAAAATGCTCCCCCATAATTGAGGAATTGAA
* * *
12544585 ACTTTTTGAAAAAT-AAATGCTCTCCCATAACTGAGGTATTGAA
1 AC-TTTTGAAAAATAAAATGCTCCCCCATAATTGAGGAATTGAA
*
12544628 ATTTTTGAAAAATAAAATGCT
1 ACTTTTGAAAAATAAAATGCT
12544649 TCTTCACAAC
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
42 11 0.12
43 70 0.77
44 10 0.11
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (43 bp):
ACTTTTGAAAAATAAAATGCTCCCCCATAATTGAGGAATTGAA
Found at i:12544581 original size:86 final size:85
Alignment explanation
Indices: 12544464--12544674 Score: 248
Period size: 86 Copynumber: 2.5 Consensus size: 85
12544454 GAAAATTTTA
*
12544464 AAAAATAAAATGCTCTCCACAACCAAGGCATT-AAGAC-TTTTGAAAAATAAATTGCTCCCCCAT
1 AAAAATAAAATGCTCCCCACAACCAAGGCATTGAA-ACTTTTTGAAAAATAAA-TGCTCCCCCAT
*
12544527 AATTGAGGAATTGAAACATTTG
64 AACTGAGGAATTGAAACATTTG
* * *
12544549 AAAAATAAAATGTTCCCCCACAA-TAGAGGCATTGAAACTTTTTGAAAAATAAATGCTCTCCCAT
1 AAAAATAAAATGCT-CCCCACAACCA-AGGCATTGAAACTTTTTGAAAAATAAATGCTCCCCCAT
* **
12544613 AACTGAGGTATTGAAATTTTTG
64 AACTGAGGAATTGAAACATTTG
** * *
12544635 AAAAATAAAATGCTTCTTCACAACCTAGGTATTGAAACTT
1 AAAAATAAAATGC-TCCCCACAACCAAGGCATTGAAACTT
12544675 CTAAAAAGTA
Statistics
Matches: 106, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
85 14 0.13
86 75 0.71
87 17 0.16
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (85 bp):
AAAAATAAAATGCTCCCCACAACCAAGGCATTGAAACTTTTTGAAAAATAAATGCTCCCCCATAA
CTGAGGAATTGAAACATTTG
Found at i:12544945 original size:13 final size:13
Alignment explanation
Indices: 12544927--12544951 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12544917 AGATTTTCCA
12544927 AAATTCTAAATTG
1 AAATTCTAAATTG
12544940 AAATTCTAAATT
1 AAATTCTAAATT
12544952 CGAACTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (13 bp):
AAATTCTAAATTG
Found at i:12545833 original size:32 final size:32
Alignment explanation
Indices: 12545773--12545834 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
12545763 TAACTATTTA
*
12545773 TTTTTATTTTTCTTTTATTTTTCAATTTTTTG
1 TTTTTATTTTTCATTTATTTTTCAATTTTTTG
12545805 TTTTTATTTTGT-ATTT-TTTTTCACATTTTT
1 TTTTTATTTT-TCATTTATTTTTCA-ATTTTT
12545835 CTTTATCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 7 0.26
32 19 0.70
33 1 0.04
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (32 bp):
TTTTTATTTTTCATTTATTTTTCAATTTTTTG
Found at i:12550837 original size:14 final size:15
Alignment explanation
Indices: 12550818--12550847 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12550808 AAATCATGCC
12550818 AAAAATATT-ATACA
1 AAAAATATTCATACA
12550832 AAAAATATTCATACA
1 AAAAATATTCATACA
12550847 A
1 A
12550848 TCATGCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAATATTCATACA
Found at i:12551012 original size:40 final size:40
Alignment explanation
Indices: 12550943--12551143 Score: 214
Period size: 40 Copynumber: 5.0 Consensus size: 40
12550933 AAATCAAAAA
12550943 AATAAA-CATGCAAA-AATATATAATAAATCATGCAAATAAAT
1 AATAAATCATGCAAATAA-ATA-AAT-AATCATGCAAATAAAT
* * *
12550984 AATAAATCATGCAAATATATTAATAATCATGTAAATAAAT
1 AATAAATCATGCAAATAAATAAATAATCATGCAAATAAAT
*
12551024 AAT-AATCATG-AAAGTAAATAATATAATCATGCAAATAAAC
1 AATAAATCATGCAAA-TAAATAA-ATAATCATGCAAATAAAT
*
12551064 AATATAATCATGCAAAT-AATAAATAATCAAGCAAATAAAT
1 AATA-AATCATGCAAATAAATAAATAATCATGCAAATAAAT
* * * *
12551104 AATATAAACATACAAGTAAATAATATAATTATGCAAATAA
1 AATA-AATCATGCAAATAAATAA-ATAATCATGCAAATAA
12551144 TAAATAATCA
Statistics
Matches: 137, Mismatches: 14, Indels: 17
0.82 0.08 0.10
Matches are distributed among these distances:
38 3 0.02
39 12 0.09
40 67 0.49
41 19 0.14
42 32 0.23
43 4 0.03
ACGTcount: A:0.59, C:0.09, G:0.05, T:0.27
Consensus pattern (40 bp):
AATAAATCATGCAAATAAATAAATAATCATGCAAATAAAT
Found at i:12551051 original size:21 final size:21
Alignment explanation
Indices: 12550956--12551154 Score: 229
Period size: 21 Copynumber: 9.9 Consensus size: 21
12550946 AAACATGCAA
*
12550956 AAATATATAATA-AATCATGC
1 AAATAAATAATATAATCATGC
12550976 AAATAAATAATA-AATCATGC
1 AAATAAATAATATAATCATGC
* * *
12550996 AAATATATTA-ATAATCATGT
1 AAATAAATAATATAATCATGC
12551016 AAATAAAT-A-ATAATCATG-
1 AAATAAATAATATAATCATGC
12551034 AAAGTAAATAATATAATCATGC
1 AAA-TAAATAATATAATCATGC
*
12551056 AAATAAACAATATAATCATGC
1 AAATAAATAATATAATCATGC
*
12551077 AAAT-AATAA-ATAATCAAGC
1 AAATAAATAATATAATCATGC
* *
12551096 AAATAAATAATATAAACATAC
1 AAATAAATAATATAATCATGC
* *
12551117 AAGTAAATAATATAATTATGC
1 AAATAAATAATATAATCATGC
12551138 AAAT-AATAA-ATAATCAT
1 AAATAAATAATATAATCAT
12551155 CACTACAAGA
Statistics
Matches: 155, Mismatches: 17, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
18 3 0.02
19 36 0.23
20 56 0.36
21 57 0.37
22 3 0.02
ACGTcount: A:0.58, C:0.09, G:0.05, T:0.28
Consensus pattern (21 bp):
AAATAAATAATATAATCATGC
Found at i:12551089 original size:61 final size:62
Alignment explanation
Indices: 12550944--12551154 Score: 254
Period size: 61 Copynumber: 3.5 Consensus size: 62
12550934 AATCAAAAAA
* * * *
12550944 ATAAACATGCAAAAATATATAATAAATCATGCAAATAAATAATA-AATCATGCAAATATATTA-
1 ATAATCATGCAAATA-ATATAAT-AATCATGCAAATAAATAATATAATCATGCAAATAAATAAT
* *
12551006 ATAATCATGTAAATAA-ATAATAATCATG-AAAGTAAATAATATAATCATGCAAATAAACAAT
1 ATAATCATGCAAATAATATAATAATCATGCAAA-TAAATAATATAATCATGCAAATAAATAAT
* * * *
12551067 ATAATCATGCAAATAATA-AATAATCAAGCAAATAAATAATATAAACATACAAGTAAATAAT
1 ATAATCATGCAAATAATATAATAATCATGCAAATAAATAATATAATCATGCAAATAAATAAT
*
12551128 ATAATTATGCAAATAATA-AATAATCAT
1 ATAATCATGCAAATAATATAATAATCAT
12551155 CACTACAAGA
Statistics
Matches: 130, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
58 3 0.02
59 16 0.12
60 20 0.15
61 75 0.58
62 16 0.12
ACGTcount: A:0.58, C:0.09, G:0.05, T:0.27
Consensus pattern (62 bp):
ATAATCATGCAAATAATATAATAATCATGCAAATAAATAATATAATCATGCAAATAAATAAT
Found at i:12551781 original size:42 final size:42
Alignment explanation
Indices: 12551735--12551908 Score: 135
Period size: 42 Copynumber: 4.1 Consensus size: 42
12551725 TAAATAGCAA
* *
12551735 AAAACCCTTACTATAAATTCGAATAATTAAGAACAATAATAG
1 AAAACCCTTACTATAAATTTGAATAATTAAGAACAATAACAG
* *
12551777 AAAACCC-TAGCTATAATTTTG-ATCAATTAA-AACCAACAACAG
1 AAAACCCTTA-CTATAAATTTGAAT-AATTAAGAA-CAATAACAG
* * * ** * *
12551819 AAAATCCTAACTAT-TATTTAGACCAATTAAGAACAATAGCAT
1 AAAACCCTTACTATAAATTT-GAATAATTAAGAACAATAACAG
* *
12551861 AAAA-CTTTAACTATAAATTTGAGA-AATTAAGAACAATAAAAG
1 AAAACCCTT-ACTATAAATTTGA-ATAATTAAGAACAATAACAG
12551903 AAAACC
1 AAAACC
12551909 ATAAATCAAA
Statistics
Matches: 101, Mismatches: 20, Indels: 21
0.71 0.14 0.15
Matches are distributed among these distances:
41 11 0.11
42 82 0.81
43 8 0.08
ACGTcount: A:0.52, C:0.16, G:0.07, T:0.25
Consensus pattern (42 bp):
AAAACCCTTACTATAAATTTGAATAATTAAGAACAATAACAG
Found at i:12553301 original size:12 final size:12
Alignment explanation
Indices: 12553275--12553312 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
12553265 TGGTTTTAGC
12553275 TTAGGGTTT-GT
1 TTAGGGTTTGGT
*
12553286 TTAGGCTTTGGT
1 TTAGGGTTTGGT
12553298 TTAGGGTTTAGGT
1 TTAGGGTTT-GGT
12553311 TT
1 TT
12553313 TAGGAGTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 8 0.35
12 10 0.43
13 5 0.22
ACGTcount: A:0.11, C:0.03, G:0.34, T:0.53
Consensus pattern (12 bp):
TTAGGGTTTGGT
Found at i:12553369 original size:13 final size:13
Alignment explanation
Indices: 12553295--12553372 Score: 75
Period size: 13 Copynumber: 5.8 Consensus size: 13
12553285 TTTAGGCTTT
12553295 GGTTTAGGGTTTAG
1 GGTTTA-GGTTTAG
* *
12553309 GTTTTAGGAGTTAG
1 GGTTTAGG-TTTAG
* *
12553323 TGTTTCGGTTTAG
1 GGTTTAGGTTTAG
* * *
12553336 GATTTAGATTTAA
1 GGTTTAGGTTTAG
12553349 GGTTTAGGTTTAG
1 GGTTTAGGTTTAG
12553362 GGTTTAGGTTT
1 GGTTTAGGTTT
12553373 TAAGCTTAGG
Statistics
Matches: 49, Mismatches: 14, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
13 35 0.71
14 14 0.29
ACGTcount: A:0.18, C:0.01, G:0.33, T:0.47
Consensus pattern (13 bp):
GGTTTAGGTTTAG
Found at i:12553412 original size:7 final size:6
Alignment explanation
Indices: 12553284--12553372 Score: 72
Period size: 7 Copynumber: 13.7 Consensus size: 6
12553274 CTTAGGGTTT
* *
12553284 GTTTAG GCTTT-G GTTTAGG GTTTAG GTTTTAG GAGTTAG TGTTTCG GTTTAG
1 GTTTAG G-TTTAG GTTTA-G GTTTAG G-TTTAG G-TTTAG -GTTTAG GTTTAG
*
12553336 GATTTAG ATTTAAG GTTTAG GTTTAGG GTTTAG GTTT
1 G-TTTAG GTTT-AG GTTTAG GTTTA-G GTTTAG GTTT
12553373 TAAGCTTAGG
Statistics
Matches: 68, Mismatches: 7, Indels: 16
0.75 0.08 0.18
Matches are distributed among these distances:
5 3 0.04
6 26 0.38
7 38 0.56
8 1 0.01
ACGTcount: A:0.17, C:0.02, G:0.33, T:0.48
Consensus pattern (6 bp):
GTTTAG
Found at i:12555203 original size:145 final size:143
Alignment explanation
Indices: 12554919--12555319 Score: 361
Period size: 145 Copynumber: 2.8 Consensus size: 143
12554909 AGTTTTCGTG
* * * * *
12554919 AAAAATTGATCTTGAAAAGGTCAAATTATGAAAATACCCCTGAA-GGTATTTTAGTAATTTCATA
1 AAAAATTGACCTTGAAAAGGTCAAATTA-CAAAATATCCCTTAAGGGTATTTTAATAATTTCATA
* * * * *
12554983 CATTCCAAGGTGCAATCAATGTTTTTAATGCAATAAAAATCATAAAATAATTTTAAAATATGATT
65 CATTCCAAGGTGCAATCAAGGTTTTTAATACAATAAAAATCATAAAATAATTATAAAACATGATC
**
12555048 TGGATCGTTTCAAAA
130 TAAATCGTTTC-AAA
12555063 AAAAATTGACCTTGAAAAGGTCAAATTACAAAAATATCCCTTAAGGGTATTTTAATAATTTCATA
1 AAAAATTGACCTTGAAAAGGTCAAATTAC-AAAATATCCCTTAAGGGTATTTTAATAATTTCATA
** * * * * * *
12555128 TTTTTCGAGGTGTAATCAAGGTTTTTACTACACTAAAAATCATGAAATAA-TATAAAACCATGAT
65 CATTCCAAGGTGCAATCAAGGTTTTTAATACAATAAAAATCATAAAATAATTATAAAA-CATGAT
***
12555192 CTAAAGT-GTTTCTTG
129 CTAAA-TCGTTTCAAA
* * * * * *
12555207 AAAAACTGACATTGGAAAGGTTAAATTACAAAGTAT-CCTTAAGGGTA-TTTGATAATTT--TAC
1 AAAAATTGACCTTGAAAAGGTCAAATTACAAAATATCCCTTAAGGGTATTTTAATAATTTCATAC
* ** *
12555268 ACCTCTCAAGGTGCAATC-AGGATTTTCGATGC-ATCAAAAATCATAAAATAAT
66 A-TTC-CAAGGTGCAATCAAGG-TTTTTAATACAAT-AAAAATCATAAAATAAT
12555320 ATTTAATGTA
Statistics
Matches: 207, Mismatches: 41, Indels: 20
0.77 0.15 0.07
Matches are distributed among these distances:
139 2 0.01
140 5 0.02
141 41 0.20
142 11 0.05
143 6 0.03
144 70 0.34
145 71 0.34
146 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (143 bp):
AAAAATTGACCTTGAAAAGGTCAAATTACAAAATATCCCTTAAGGGTATTTTAATAATTTCATAC
ATTCCAAGGTGCAATCAAGGTTTTTAATACAATAAAAATCATAAAATAATTATAAAACATGATCT
AAATCGTTTCAAA
Found at i:12556018 original size:20 final size:20
Alignment explanation
Indices: 12555993--12556032 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
12555983 CCACCATCTT
12555993 CTGGGTTTGGTTCAAACCTA
1 CTGGGTTTGGTTCAAACCTA
12556013 CTGGGTTTGGTTCAAACCTA
1 CTGGGTTTGGTTCAAACCTA
12556033 TCAAACTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CTGGGTTTGGTTCAAACCTA
Found at i:12557168 original size:41 final size:41
Alignment explanation
Indices: 12557123--12557258 Score: 128
Period size: 41 Copynumber: 3.3 Consensus size: 41
12557113 TTTATAACAA
* * * * *
12557123 AGTAAATGATTCATAGTTGAAAAACTTTACATTCATAATGG
1 AGTAAACGATTCACAATTGAAAAACTTTAGATTCATAATAG
* * *
12557164 AGTAAACGATTCACAATTGAAAGACTTTGGATTCATGATAG
1 AGTAAACGATTCACAATTGAAAAACTTTAGATTCATAATAG
* * * * * * *
12557205 AGAAAACAATTCACAATAGAATAACTCTAGATTCACAATAA
1 AGTAAACGATTCACAATTGAAAAACTTTAGATTCATAATAG
*
12557246 AGTAAATGATTCA
1 AGTAAACGATTCA
12557259 TAGTTGGAAG
Statistics
Matches: 74, Mismatches: 21, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
41 74 1.00
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (41 bp):
AGTAAACGATTCACAATTGAAAAACTTTAGATTCATAATAG
Found at i:12557273 original size:41 final size:40
Alignment explanation
Indices: 12557227--12557345 Score: 96
Period size: 41 Copynumber: 2.9 Consensus size: 40
12557217 ACAATAGAAT
12557227 AACTCTAGATTCACAATAAAGTAAATGATTCATAGTTGGA
1 AACTCTAGATTCACAATAAAGTAAATGATTCATAGTTGGA
* * ** * * *
12557267 AGACTCT-GAATTTACAACAAAGTAAAAAACTCACAATTGGA
1 A-ACTCTAG-ATTCACAATAAAGTAAATGATTCATAGTTGGA
* * * * *
12557308 AAGCTCTAGATTCTCAGTAGAGGAAATGATTTATAGTT
1 AA-CTCTAGATTCACAATAAAGTAAATGATTCATAGTT
12557346 TAGAAGATTT
Statistics
Matches: 56, Mismatches: 19, Indels: 7
0.68 0.23 0.09
Matches are distributed among these distances:
40 3 0.05
41 52 0.93
42 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (40 bp):
AACTCTAGATTCACAATAAAGTAAATGATTCATAGTTGGA
Found at i:12557430 original size:42 final size:42
Alignment explanation
Indices: 12557326--12557435 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 42
12557316 GATTCTCAGT
* * *
12557326 AGAGGAAATGATTTATAGTTTAGAAGATTTCAAATTCACAAT
1 AGAGTAAATGATTTATAGTTTAAAAGATTTCAAATTCACAAC
** * * * * *
12557368 AGAGTAAACAATTTACAGTTTAAAAGATTTTAGATTCATAGC
1 AGAGTAAATGATTTATAGTTTAAAAGATTTCAAATTCACAAC
*
12557410 AGAGTAAATGATTCATAGTTTGAAAA
1 AGAGTAAATGATTTATAGTTT-AAAA
12557436 CTCACAACAG
Statistics
Matches: 53, Mismatches: 14, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
42 49 0.92
43 4 0.08
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (42 bp):
AGAGTAAATGATTTATAGTTTAAAAGATTTCAAATTCACAAC
Found at i:12557520 original size:41 final size:41
Alignment explanation
Indices: 12557475--12557627 Score: 139
Period size: 41 Copynumber: 3.7 Consensus size: 41
12557465 GAGGATGATA
*
12557475 GATTCACAATTGTAAGACTCTAGGTTCACAACAAAGTAAAT
1 GATTCACAATTGTAAGACTCTAGATTCACAACAAAGTAAAT
* * * * *
12557516 GATTCACCATTATAAAACTCTAAATTCA-AAGCAAAGTAAAC
1 GATTCACAATTGTAAGACTCTAGATTCACAA-CAAAGTAAAT
* * ** * * *
12557557 AATTCACAGTTGGGAGACTCTAGGTTCACAATAGAGTAAAT
1 GATTCACAATTGTAAGACTCTAGATTCACAACAAAGTAAAT
* *
12557598 GATTCATAGTTG-AAGAACTCTAGATTCACA
1 GATTCACAATTGTAAG-ACTCTAGATTCACA
12557628 TATGCATAAA
Statistics
Matches: 87, Mismatches: 22, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
40 4 0.05
41 81 0.93
42 2 0.02
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (41 bp):
GATTCACAATTGTAAGACTCTAGATTCACAACAAAGTAAAT
Found at i:12557689 original size:23 final size:23
Alignment explanation
Indices: 12557663--12557767 Score: 129
Period size: 23 Copynumber: 4.6 Consensus size: 23
12557653 AAAGTTAACA
* *
12557663 ATTCATAATTGGAAGACTCAATG
1 ATTCATAATTGAAAAACTCAATG
* * *
12557686 ATTCATAGTTGGAAGACTCAATG
1 ATTCATAATTGAAAAACTCAATG
* *
12557709 ATTCACAAGTGAAAAACTCAATG
1 ATTCATAATTGAAAAACTCAATG
* *
12557732 ATCCACAATTGAAAAACTCAATG
1 ATTCATAATTGAAAAACTCAATG
12557755 ATTCATAATTGAA
1 ATTCATAATTGAA
12557768 GGATTTTTGA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 72 1.00
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (23 bp):
ATTCATAATTGAAAAACTCAATG
Found at i:12557831 original size:41 final size:41
Alignment explanation
Indices: 12557786--12557872 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 41
12557776 GATTCATAAT
12557786 AGAGTAAACAATTCACAGTCTGA-AGACTCTAGACTCACAAC
1 AGAGTAAACAATTCACAGT-TGATAGACTCTAGACTCACAAC
** * * * *
12557827 AGAGTAAATGATTCATAGTTGATGGATTCTAGATTCACAAC
1 AGAGTAAACAATTCACAGTTGATAGACTCTAGACTCACAAC
12557868 AGAGT
1 AGAGT
12557873 TTAAAGGCTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 3 0.08
41 36 0.92
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.25
Consensus pattern (41 bp):
AGAGTAAACAATTCACAGTTGATAGACTCTAGACTCACAAC
Found at i:12557980 original size:16 final size:18
Alignment explanation
Indices: 12557958--12558029 Score: 76
Period size: 18 Copynumber: 4.1 Consensus size: 18
12557948 ATTAAAAAGT
12557958 GTTTTAAGATTTA-AAAA
1 GTTTTAAGATTTACAAAA
*
12557975 -TTTTAAGATTCACAAAA
1 GTTTTAAGATTTACAAAA
* * *
12557992 GTTTTAGGATTTATAATA
1 GTTTTAAGATTTACAAAA
* *
12558010 GTTTAAAGATTTGCAAAA
1 GTTTTAAGATTTACAAAA
12558028 GT
1 GT
12558030 CAAATACTTA
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
16 11 0.26
17 4 0.09
18 28 0.65
ACGTcount: A:0.42, C:0.04, G:0.14, T:0.40
Consensus pattern (18 bp):
GTTTTAAGATTTACAAAA
Found at i:12558173 original size:17 final size:17
Alignment explanation
Indices: 12558151--12558245 Score: 57
Period size: 17 Copynumber: 5.4 Consensus size: 17
12558141 GCAAGAAAGG
*
12558151 TTAAAGATTTACAAATT
1 TTAAAGATTTAAAAATT
* *
12558168 TTAAAGATTCATAAAA-G
1 TTAAAGATTTA-AAAATT
*
12558185 TCAAAGATTTAAAAATT
1 TTAAAGATTTAAAAATT
* *
12558202 TTCAAACATTCATAAAAATGA
1 TT-AAAGATT--TAAAAAT-T
* *
12558223 TTAAAGATTCACAAATT
1 TTAAAGATTTAAAAATT
*
12558240 TCAAAG
1 TTAAAG
12558246 GTTCGCAAGA
Statistics
Matches: 58, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
16 4 0.07
17 25 0.43
18 14 0.24
20 13 0.22
21 2 0.03
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (17 bp):
TTAAAGATTTAAAAATT
Found at i:12558807 original size:7 final size:7
Alignment explanation
Indices: 12558792--12558841 Score: 55
Period size: 7 Copynumber: 7.1 Consensus size: 7
12558782 GTTTCAAACG
12558792 TACAACA
1 TACAACA
*
12558799 TATAACA
1 TACAACA
* *
12558806 TATAACC
1 TACAACA
12558813 TACAACA
1 TACAACA
*
12558820 TGCAACA
1 TACAACA
12558827 TACAACA
1 TACAACA
*
12558834 TGCAACA
1 TACAACA
12558841 T
1 T
12558842 GCATTTTGGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.50, C:0.26, G:0.04, T:0.20
Consensus pattern (7 bp):
TACAACA
Found at i:12558826 original size:21 final size:21
Alignment explanation
Indices: 12558792--12558844 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
12558782 GTTTCAAACG
** * *
12558792 TACAACATATAACATATAACC
1 TACAACATGCAACATACAACA
12558813 TACAACATGCAACATACAACA
1 TACAACATGCAACATACAACA
*
12558834 TGCAACATGCA
1 TACAACATGCA
12558845 TTTTGGACTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.49, C:0.26, G:0.06, T:0.19
Consensus pattern (21 bp):
TACAACATGCAACATACAACA
Found at i:12559960 original size:16 final size:17
Alignment explanation
Indices: 12559928--12559988 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 17
12559918 ATTCTTTCTT
* *
12559928 TCTTTTTT-TTTTGTTC
1 TCTTTTTTCATTTATTC
12559944 TCTTTTTTCATTT-TTC
1 TCTTTTTTCATTTATTC
*
12559960 TTCTTTCTTACATTTATT-
1 -TCTTT-TTTCATTTATTC
12559978 TCTTTTTTCAT
1 TCTTTTTTCAT
12559989 ATTTTCTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
16 16 0.42
17 13 0.34
18 7 0.18
19 2 0.05
ACGTcount: A:0.08, C:0.16, G:0.02, T:0.74
Consensus pattern (17 bp):
TCTTTTTTCATTTATTC
Found at i:12559961 original size:34 final size:33
Alignment explanation
Indices: 12559916--12560018 Score: 86
Period size: 35 Copynumber: 3.0 Consensus size: 33
12559906 TCCCACTTAA
12559916 TCATTCTTTCTTTCTTTTTTTTTTGTTCTCTTTTT
1 TCATT-TTTCTTTCTTTTTTTTTT-TTCTCTTTTT
* *
12559951 TCATTTTTC-TTCTTTCTTACATTTATT-TCTTTTT
1 TCATTTTTCTTTCTTT-TT--TTTTTTTCTCTTTTT
*
12559985 TCATATTTTCTTATTCTCTTTTTTTTTTCT-TTTT
1 TCAT-TTTTC-T-TTCTTTTTTTTTTTTCTCTTTT
12560019 CTTTGAATGG
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
33 6 0.11
34 17 0.31
35 21 0.38
36 4 0.07
37 2 0.04
38 5 0.09
ACGTcount: A:0.08, C:0.17, G:0.01, T:0.75
Consensus pattern (33 bp):
TCATTTTTCTTTCTTTTTTTTTTTTCTCTTTTT
Found at i:12559973 original size:18 final size:17
Alignment explanation
Indices: 12559944--12559996 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
12559934 TTTTTTGTTC
*
12559944 TCTTTTTTCATTTTTCT
1 TCTTTTTACATTTTTCT
*
12559961 TCTTTCTTACATTTAT-T
1 TCTTT-TTACATTTTTCT
*
12559978 TCTTTTTTCATATTTTCT
1 TCTTTTTACAT-TTTTCT
12559996 T
1 T
12559997 ATTCTCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
16 5 0.17
17 14 0.48
18 10 0.34
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (17 bp):
TCTTTTTACATTTTTCT
Found at i:12559999 original size:8 final size:7
Alignment explanation
Indices: 12559919--12560022 Score: 54
Period size: 7 Copynumber: 14.9 Consensus size: 7
12559909 CACTTAATCA
12559919 TTCTTTCT
1 TTCTTT-T
12559927 TTCTTTT
1 TTCTTTT
*
12559934 TTTTTTGT
1 TTCTTT-T
12559942 TCTCTTTT
1 T-TCTTTT
*
12559950 TTCATTT
1 TTCTTTT
*
12559957 TTCTTCT
1 TTCTTTT
**
12559964 TTCTTAC
1 TTCTTTT
* *
12559971 AT-TTAT
1 TTCTTTT
12559977 TTCTTTT
1 TTCTTTT
*
12559984 TTCATATT
1 TTC-TTTT
*
12559992 TTC-TTA
1 TTCTTTT
*
12559998 TTCTCTT
1 TTCTTTT
12560005 TT-TTTT
1 TTCTTTT
12560011 TTC-TTT
1 TTCTTTT
12560017 TTCTTT
1 TTCTTT
12560023 GAATGGATTT
Statistics
Matches: 72, Mismatches: 17, Indels: 15
0.69 0.16 0.14
Matches are distributed among these distances:
6 19 0.26
7 33 0.46
8 16 0.22
9 4 0.06
ACGTcount: A:0.07, C:0.16, G:0.01, T:0.76
Consensus pattern (7 bp):
TTCTTTT
Found at i:12567289 original size:18 final size:18
Alignment explanation
Indices: 12567262--12567309 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
12567252 TGAGGATTAT
*
12567262 ATTTGTGGTGGGGGATAC
1 ATTTGTGGTGGAGGATAC
*
12567280 ATTTGAGGTGGAGGATAC
1 ATTTGTGGTGGAGGATAC
12567298 ATTTGTGGTGGA
1 ATTTGTGGTGGA
12567310 TAATAACTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.21, C:0.04, G:0.42, T:0.33
Consensus pattern (18 bp):
ATTTGTGGTGGAGGATAC
Found at i:12571271 original size:50 final size:50
Alignment explanation
Indices: 12571196--12571340 Score: 218
Period size: 50 Copynumber: 2.9 Consensus size: 50
12571186 CACACCTCAT
*
12571196 CCTACCTTCCAATGCACCCAACCTCACCCAATCTCACCCCACCCCTCCAC
1 CCTACCCTCCAATGCACCCAACCTCACCCAATCTCACCCCACCCCTCCAC
* *
12571246 CCTACCCTCCAATGCACCCTACCTCACCCAATCTTACCCCACCCCTCCAC
1 CCTACCCTCCAATGCACCCAACCTCACCCAATCTCACCCCACCCCTCCAC
* * * * *
12571296 CTTATCCTCCAATGCACCCCACCCCACCGAATCTCACCCCACCCC
1 CCTACCCTCCAATGCACCCAACCTCACCCAATCTCACCCCACCCC
12571341 ACCCTAAACC
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 86 1.00
ACGTcount: A:0.23, C:0.58, G:0.03, T:0.17
Consensus pattern (50 bp):
CCTACCCTCCAATGCACCCAACCTCACCCAATCTCACCCCACCCCTCCAC
Found at i:12571366 original size:31 final size:31
Alignment explanation
Indices: 12571330--12571401 Score: 135
Period size: 31 Copynumber: 2.3 Consensus size: 31
12571320 CACCGAATCT
12571330 CACCCCACCCCACCCTAAACCCCAAACAGCC
1 CACCCCACCCCACCCTAAACCCCAAACAGCC
*
12571361 CACCCCGCCCCACCCTAAACCCCAAACAGCC
1 CACCCCACCCCACCCTAAACCCCAAACAGCC
12571392 CACCCCACCC
1 CACCCCACCC
12571402 AATCTCACGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.29, C:0.64, G:0.04, T:0.03
Consensus pattern (31 bp):
CACCCCACCCCACCCTAAACCCCAAACAGCC
Found at i:12579393 original size:114 final size:114
Alignment explanation
Indices: 12579268--12579491 Score: 396
Period size: 114 Copynumber: 2.0 Consensus size: 114
12579258 TTAAAAAACG
*
12579268 AAATTGATTATATTTATATTTTTATTATTAACATTAAATCACTCTCAATTCAATTCATATTAAAA
1 AAATTGATTATATTTATATTTTTATTAGTAACATTAAATCACTCTCAATTCAATTCATATTAAAA
12579333 ATATTAAAA-TTTAAAATTTTTCTTAATTTGACAAATTAAATCAATTACT
66 ATATTAAAATTTTAAAA-TTTTCTTAATTTGACAAATTAAATCAATTACT
* *
12579382 AAATTGATTATATTTATATTTTTATTAGTAACCTTAAATTACTCTCAATTCAATTCATATTAAAA
1 AAATTGATTATATTTATATTTTTATTAGTAACATTAAATCACTCTCAATTCAATTCATATTAAAA
*
12579447 GTATTAAAATTTTAAAATTTTCTTAATTTGACAAATTAAATCAAT
66 ATATTAAAATTTTAAAATTTTCTTAATTTGACAAATTAAATCAAT
12579492 CAATATATAA
Statistics
Matches: 105, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
114 98 0.93
115 7 0.07
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (114 bp):
AAATTGATTATATTTATATTTTTATTAGTAACATTAAATCACTCTCAATTCAATTCATATTAAAA
ATATTAAAATTTTAAAATTTTCTTAATTTGACAAATTAAATCAATTACT
Found at i:12579712 original size:19 final size:19
Alignment explanation
Indices: 12579688--12579778 Score: 69
Period size: 19 Copynumber: 4.5 Consensus size: 19
12579678 TATTTTATTA
12579688 ATTTATATTTGATTGATAG
1 ATTTATATTTGATTGATAG
* *
12579707 ATTTATATTTCATTAAATATG
1 ATTTATATTTGATT-GATA-G
* *
12579728 ATTTCAT-TTGGTTATTTCATTA-
1 ATTT-ATATT--TGA-TTGA-TAG
12579750 ATTTATATTTGATTGATAG
1 ATTTATATTTGATTGATAG
12579769 ATTTATATTT
1 ATTTATATTT
12579779 CATTAAATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
18 2 0.04
19 26 0.46
20 5 0.09
21 9 0.16
22 8 0.14
23 3 0.05
24 4 0.07
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.56
Consensus pattern (19 bp):
ATTTATATTTGATTGATAG
Found at i:12579716 original size:34 final size:34
Alignment explanation
Indices: 12579678--12579784 Score: 120
Period size: 34 Copynumber: 3.3 Consensus size: 34
12579668 TGAAATAAAG
*
12579678 TATTTTATTAATTTATATTTGATTGATAGATTTA
1 TATTTCATTAATTTATATTTGATTGATAGATTTA
* * *
12579712 TATTTCATTAA-ATATGATTTCATT--T-G--GT-
1 TATTTCATTAATTTAT-ATTTGATTGATAGATTTA
12579740 TATTTCATTAATTTATATTTGATTGATAGATTTA
1 TATTTCATTAATTTATATTTGATTGATAGATTTA
12579774 TATTTCATTAA
1 TATTTCATTAA
12579785 ATATGATTTC
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
28 18 0.31
29 4 0.07
30 1 0.02
31 2 0.03
32 1 0.02
33 4 0.07
34 28 0.48
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (34 bp):
TATTTCATTAATTTATATTTGATTGATAGATTTA
Found at i:12579753 original size:62 final size:62
Alignment explanation
Indices: 12579678--12579801 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
12579668 TGAAATAAAG
*
12579678 TATTTTATTAATTTATATTTGATTGATAGATTTATATTTCATTAAATATGATTTCATTTGGT
1 TATTTCATTAATTTATATTTGATTGATAGATTTATATTTCATTAAATATGATTTCATTTGGT
12579740 TATTTCATTAATTTATATTTGATTGATAGATTTATATTTCATTAAATATGATTTCATTTGGT
1 TATTTCATTAATTTATATTTGATTGATAGATTTATATTTCATTAAATATGATTTCATTTGGT
12579802 AAAATATTAA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.56
Consensus pattern (62 bp):
TATTTCATTAATTTATATTTGATTGATAGATTTATATTTCATTAAATATGATTTCATTTGGT
Found at i:12579862 original size:31 final size:31
Alignment explanation
Indices: 12579788--12579864 Score: 111
Period size: 32 Copynumber: 2.5 Consensus size: 31
12579778 TCATTAAATA
*
12579788 TGATTTCATTTGGTAAAATATTAATGCACGTT
1 TGATTTCATTTGATAAAATATTAATGCAC-TT
12579820 TGATTTCATTTGATAAAATATTAATGCA-TT
1 TGATTTCATTTGATAAAATATTAATGCACTT
*
12579850 TGGATTTTATTTGAT
1 T-GATTTCATTTGAT
12579865 TTTATTTGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
30 3 0.07
31 12 0.29
32 27 0.64
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.48
Consensus pattern (31 bp):
TGATTTCATTTGATAAAATATTAATGCACTT
Found at i:12583863 original size:29 final size:29
Alignment explanation
Indices: 12583830--12583906 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
12583820 ATAATTCAAA
* *
12583830 AATTATTTAAATTTTTATTATTTTATTTCT
1 AATTAATTAAATTTTTATT-TTTAATTTCT
*
12583860 -ATTAATTAAATTTTTAATTTTTAATTTTT
1 AATTAATTAAATTTTT-ATTTTTAATTTCT
12583889 AATTTAATTAAATTTTTA
1 AA-TTAATTAAATTTTTA
12583907 AATGGATGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 22 0.54
30 5 0.12
31 14 0.34
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (29 bp):
AATTAATTAAATTTTTATTTTTAATTTCT
Found at i:12583880 original size:7 final size:7
Alignment explanation
Indices: 12583868--12583907 Score: 53
Period size: 7 Copynumber: 5.3 Consensus size: 7
12583858 CTATTAATTA
12583868 AATTTTT
1 AATTTTT
12583875 AATTTTT
1 AATTTTT
12583882 AATTTTT
1 AATTTTT
12583889 AATTTAATT
1 AATTT--TT
12583898 AAATTTTT
1 -AATTTTT
12583906 AA
1 AA
12583908 ATGGATGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 21 0.70
8 2 0.07
9 2 0.07
10 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
AATTTTT
Found at i:12583887 original size:14 final size:16
Alignment explanation
Indices: 12583864--12583907 Score: 65
Period size: 14 Copynumber: 2.8 Consensus size: 16
12583854 ATTTCTATTA
12583864 ATTAAATTTTTAATTT
1 ATTAAATTTTTAATTT
12583880 -TT-AATTTTTAATTT
1 ATTAAATTTTTAATTT
12583894 AATTAAATTTTTAA
1 -ATTAAATTTTTAA
12583908 ATGGATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 12 0.48
15 2 0.08
16 2 0.08
17 9 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTAAATTTTTAATTT
Found at i:12587257 original size:6 final size:6
Alignment explanation
Indices: 12587243--12587293 Score: 59
Period size: 6 Copynumber: 8.2 Consensus size: 6
12587233 TGTTAATATA
*
12587243 AAAAAT AATAAT AATAACA- AAATAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AA-AA-AT AAA-AAT AAAAAT AAAAAT AAAAAT AAAAAT
12587293 A
1 A
12587294 TTTACGATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 31 0.79
7 7 0.18
8 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (6 bp):
AAAAAT
Found at i:12592804 original size:2 final size:2
Alignment explanation
Indices: 12592797--12592828 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12592787 CCAAGCAAAA
12592797 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12592829 CCATGTACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12593690 original size:44 final size:44
Alignment explanation
Indices: 12593630--12593731 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 44
12593620 TTGTAATTCT
*
12593630 TTATAATTTTTCATGTGCACTAACCTT-TTTGTTTATTTTGCAGC
1 TTATAATTTTTCATGTGCACTAA-CTTATTTATTTATTTTGCAGC
* * * * * *
12593674 TTATGATTTTTTATGTGTACTAATTTATTTATTTATTTTGTAGA
1 TTATAATTTTTCATGTGCACTAACTTATTTATTTATTTTGCAGC
*
12593718 TTTTAATTTTTCAT
1 TTATAATTTTTCAT
12593732 ATGTATAAAC
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
43 2 0.04
44 45 0.96
ACGTcount: A:0.23, C:0.09, G:0.10, T:0.59
Consensus pattern (44 bp):
TTATAATTTTTCATGTGCACTAACTTATTTATTTATTTTGCAGC
Found at i:12594772 original size:25 final size:24
Alignment explanation
Indices: 12594726--12594774 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
12594716 AATTCTTATT
*
12594726 TTTACTATACATTACATACATGTA
1 TTTACTATACATCACATACATGTA
* *
12594750 TTTACATATACATCATATCCATGTA
1 TTTAC-TATACATCACATACATGTA
12594775 AATATCTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.41
Consensus pattern (24 bp):
TTTACTATACATCACATACATGTA
Found at i:12594955 original size:137 final size:139
Alignment explanation
Indices: 12594469--12594942 Score: 545
Period size: 137 Copynumber: 3.4 Consensus size: 139
12594459 ATTTGCATAT
*
12594469 ATGTATTTGCATAATACATTTTTAT-CAATGTAAATATTTTTGTATGTATATTATTTCATTTGTT
1 ATGTATTTGCAT-ATACATTTTTATCCAA-GTAAATATTTTTGTATGTACATTATTTCATTTGTT
* * *
12594533 TGGAAAAATTTTTGCC-TTTTCAGTTTTGTACATAGTTGTGAATAT-AAATTCTTGTTGTTACTA
64 TGGAAAAATCTTTACCTTTTTCAGTTTTGTACATAGTTTTGAATATGAAATTCTTGTT-TTACTA
12594596 TGCATTATATAC
128 TGCATTATATAC
* * *
12594608 ATGTATTTGCATATACATATTTAGCCATGTAAATATTTTTGTATGTACATTATTTCATTTGTTTG
1 ATGTATTTGCATATACATTTTTATCCAAGTAAATATTTTTGTATGTACATTATTTCATTTGTTTG
** * * *
12594673 GAAAAAT-TTTTGCTTTTTCAGTTTTATTC-TGAG-TTTGAATATG-AATTCTTATTTTTACTAT
66 GAAAAATCTTTACCTTTTTCAGTTTTGTACAT-AGTTTTGAATATGAAATTCTT-GTTTTACTAT
* *
12594734 ACATTACATAC
129 GCATTATATAC
* ** * * *
12594745 ATGTATTTACATATACA-TCATATCCATGTAAATATCTTTATATGTACATTATTTCATTTGTTTG
1 ATGTATTTGCATATACATTTTTATCCAAGTAAATATTTTTGTATGTACATTATTTCATTTGTTTG
** * * * *
12594809 G-AGTATCTTTACCTTTTTTAGTTTTGTACATAGTTTTCAATATGAAATT-TTGTTTCACTATGT
66 GAAAAATCTTTACCTTTTTCAGTTTTGTACATAGTTTTGAATATGAAATTCTTGTTTTACTATGC
* * *
12594872 GTTGTATTC
131 ATTATATAC
* * *
12594881 ATATATTTGCATATACATTTTTATCCAAGTAAACATTTTTGTATGTATATTATTTCATTTGT
1 ATGTATTTGCATATACATTTTTATCCAAGTAAATATTTTTGTATGTACATTATTTCATTTGT
12594943 ATGGGTAATC
Statistics
Matches: 281, Mismatches: 44, Indels: 22
0.81 0.13 0.06
Matches are distributed among these distances:
135 3 0.01
136 89 0.32
137 101 0.36
138 74 0.26
139 14 0.05
ACGTcount: A:0.28, C:0.10, G:0.11, T:0.51
Consensus pattern (139 bp):
ATGTATTTGCATATACATTTTTATCCAAGTAAATATTTTTGTATGTACATTATTTCATTTGTTTG
GAAAAATCTTTACCTTTTTCAGTTTTGTACATAGTTTTGAATATGAAATTCTTGTTTTACTATGC
ATTATATAC
Found at i:12596196 original size:20 final size:20
Alignment explanation
Indices: 12596171--12596208 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12596161 GAAACATGAA
12596171 AGAAAAAA-GAAAAGAAAAAG
1 AGAAAAAAGGAAAA-AAAAAG
12596191 AGAAAAAAGGAAAAAAAA
1 AGAAAAAAGGAAAAAAAA
12596209 TGAAATGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (20 bp):
AGAAAAAAGGAAAAAAAAAG
Found at i:12596234 original size:9 final size:10
Alignment explanation
Indices: 12596206--12596237 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
12596196 AAAGGAAAAA
12596206 AAATGAAATG
1 AAATGAAATG
12596216 AAATGAAATG
1 AAATGAAATG
12596226 AAA-GAAATG
1 AAATGAAATG
12596235 AAA
1 AAA
12596238 AAAGAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.16
Consensus pattern (10 bp):
AAATGAAATG
Found at i:12597437 original size:13 final size:13
Alignment explanation
Indices: 12597419--12597444 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12597409 AAAATATGTT
12597419 CATTCATTGCATA
1 CATTCATTGCATA
12597432 CATTCATTGCATA
1 CATTCATTGCATA
12597445 TGTTTAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
CATTCATTGCATA
Found at i:12597712 original size:41 final size:41
Alignment explanation
Indices: 12597656--12597745 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 41
12597646 CAACTTTGAT
* **
12597656 TTTTCAAAAACTTCAAACCCCTAATGGGGGAGCACTTCAAA
1 TTTTCAAAAACTTCAAAACCCTAATAAGGGAGCACTTCAAA
** * *
12597697 TTTTCAAAAGTTTCAAAACCCTAGTAAGGGAGCACTTTAAA
1 TTTTCAAAAACTTCAAAACCCTAATAAGGGAGCACTTCAAA
12597738 TTTTCAAA
1 TTTTCAAA
12597746 TTTTTTCAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (41 bp):
TTTTCAAAAACTTCAAAACCCTAATAAGGGAGCACTTCAAA
Found at i:12597818 original size:40 final size:38
Alignment explanation
Indices: 12597773--12597957 Score: 154
Period size: 40 Copynumber: 4.6 Consensus size: 38
12597763 ATAGGGGTAG
12597773 ATTTATTTTTCAAAAGTTTCGAAACCCTAGTGAATGAGC
1 ATTTATTTTTCAAAAGTTTC-AAACCCTAGTGAATGAGC
* * * *
12597812 ATTTTATTTTTCAAAAAGTTTCAAAGCCTCCGATGAGTTAGC
1 A-TTTATTTTTC-AAAAGTTTCAAACCCT-AG-TGAATGAGC
* * * ***
12597854 ATTTAATTTTCCAAAGTTTCAAAGCCCTGGTGGGGGAGC
1 ATTTATTTTTCAAAAGTTTCAAA-CCCTAGTGAATGAGC
* * * *
12597893 ATTTATTTTTCAAAAGTTTTAAAACCTTTAGTGGAAAGACC
1 ATTTATTTTTCAAAAG-TTTCAAACC-CTAGT-GAATGAGC
12597934 ATTTTATTTTTCAAAAGTTTCAAA
1 A-TTTATTTTTCAAAAGTTTCAAA
12597958 GGCTCTGGTG
Statistics
Matches: 116, Mismatches: 21, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
39 23 0.20
40 37 0.32
41 33 0.28
42 23 0.20
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (38 bp):
ATTTATTTTTCAAAAGTTTCAAACCCTAGTGAATGAGC
Found at i:12597858 original size:81 final size:80
Alignment explanation
Indices: 12597695--12597911 Score: 208
Period size: 81 Copynumber: 2.7 Consensus size: 80
12597685 GAGCACTTCA
* * ***
12597695 AATTTTCAAAAGTTTCAAAACCCTAGT-AAGGGAGCACTTTAAATTTTCAAATTTTTTCAAAGCC
1 AATTTTCAAAAGTTTC-AAACCCTAGTGAA-GGAGCA-TTTTATTTTTCAAAAAGTTTCAAAGCC
* *
12597759 TTAAATAGGGGTAGATTT
63 TCAAATAGAGGTAGATTT
* *
12597777 ATTTTTCAAAAGTTTCGAAACCCTAGTGAATGAGCATTTTATTTTTCAAAAAGTTTCAAAGCCTC
1 AATTTTCAAAAGTTTC-AAACCCTAGTGAAGGAGCATTTTATTTTTCAAAAAGTTTCAAAGCCTC
** *
12597842 CGAT-GAGTTAGCATTT
65 AAATAGAGGTAG-ATTT
* * **
12597858 AATTTTCCAAAGTTTCAAAGCCCTGGTGGGGGAGCA-TTTATTTTTC-AAAAGTTT
1 AATTTTCAAAAGTTTCAAA-CCCTAGTGAAGGAGCATTTTATTTTTCAAAAAGTTT
12597912 TAAAACCTTT
Statistics
Matches: 113, Mismatches: 19, Indels: 9
0.80 0.13 0.06
Matches are distributed among these distances:
79 8 0.07
80 18 0.16
81 55 0.49
82 30 0.27
83 2 0.02
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (80 bp):
AATTTTCAAAAGTTTCAAACCCTAGTGAAGGAGCATTTTATTTTTCAAAAAGTTTCAAAGCCTCA
AATAGAGGTAGATTT
Found at i:12597993 original size:42 final size:40
Alignment explanation
Indices: 12597808--12598050 Score: 149
Period size: 42 Copynumber: 5.9 Consensus size: 40
12597798 CCTAGTGAAT
* * * *
12597808 GAGCATTTTATTTTTCAAAAAGTTTCAAAGCCTCCGATGA-GT
1 GAGCATTTTA-TTTTC--AAAGTTTCAAAGACTCTGGTGAGGG
* * *
12597850 TAGCATTTAATTTTCCAAAGTTTCAAAG-CCCTGGTG-GGG
1 GAGCATTTTATTTT-CAAAGTTTCAAAGACTCTGGTGAGGG
* * * **
12597889 GAGCA-TTTATTTTTCAAAAGTTTTAAA-ACCTTTAGTG-GAAA
1 GAGCATTTTA-TTTTC-AAAGTTTCAAAGA-CTCTGGTGAG-GG
* * *
12597930 GACCATTTTATTTTTCAAAAGTTTCAAAGGCTCTGGTGGGGGG
1 GAGCATTTTA-TTTTC-AAAGTTTCAAAGACTCTGGT-GAGGG
*
12597973 AGAGCATTTTATTTTCAAAGTTTCAAAGACTCTAGTGAGGG
1 -GAGCATTTTATTTTCAAAGTTTCAAAGACTCTGGTGAGGG
*
12598014 GAGCATTTTACATTATCAAAGTTTCAAA-ACCTCTGGT
1 GAGCATTTT--ATTTTCAAAGTTTCAAAGA-CTCTGGT
12598051 AAAAAGAGCC
Statistics
Matches: 159, Mismatches: 27, Indels: 30
0.74 0.12 0.14
Matches are distributed among these distances:
38 4 0.03
39 24 0.15
40 27 0.17
41 13 0.08
42 75 0.47
43 6 0.04
44 10 0.06
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (40 bp):
GAGCATTTTATTTTCAAAGTTTCAAAGACTCTGGTGAGGG
Found at i:12598570 original size:35 final size:35
Alignment explanation
Indices: 12598519--12598588 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
12598509 TGATATTATT
*
12598519 GGGTTTTGAATTGTATTATTGGGTTTTAAAAACTA
1 GGGTCTTGAATTGTATTATTGGGTTTTAAAAACTA
12598554 GGGTCTTGAATTGTATTATTGGGTTTTAAAAACTA
1 GGGTCTTGAATTGTATTATTGGGTTTTAAAAACTA
12598589 TTTTTTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.29, C:0.04, G:0.23, T:0.44
Consensus pattern (35 bp):
GGGTCTTGAATTGTATTATTGGGTTTTAAAAACTA
Found at i:12599913 original size:59 final size:58
Alignment explanation
Indices: 12599850--12599970 Score: 143
Period size: 58 Copynumber: 2.1 Consensus size: 58
12599840 AGAAACACTA
* ** * * * *
12599850 TAATTGATATAGAAAAGTTTAAAACAATTCCTACATCATTTCTAAATAGAGAAATATTG
1 TAATTAATATA-AAAAAATTAAAACAAATACTACATCATTTCTAAATAGAGAAACATCG
* * *
12599909 TAATTAATATAAAAAAATTAAATCAAATACTACATCATTTCTGAATATAGAAACATCG
1 TAATTAATATAAAAAAATTAAAACAAATACTACATCATTTCTAAATAGAGAAACATCG
12599967 TAAT
1 TAAT
12599971 CTACATCAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
58 42 0.81
59 10 0.19
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (58 bp):
TAATTAATATAAAAAAATTAAAACAAATACTACATCATTTCTAAATAGAGAAACATCG
Found at i:12601706 original size:30 final size:30
Alignment explanation
Indices: 12601668--12601735 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
12601658 CCATTATGCA
*
12601668 CGCCACCTCCACTCACTGAATTATCTCCAC
1 CGCCACCTCCACCCACTGAATTATCTCCAC
* *
12601698 CGCTACCTCCGCCCACTGAATTATCTCCAC
1 CGCCACCTCCACCCACTGAATTATCTCCAC
12601728 CGCCACCT
1 CGCCACCT
12601736 ATTCCAGAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.21, C:0.49, G:0.09, T:0.22
Consensus pattern (30 bp):
CGCCACCTCCACCCACTGAATTATCTCCAC
Found at i:12604425 original size:3 final size:3
Alignment explanation
Indices: 12604412--12604443 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
12604402 TGTGTTCTAT
*
12604412 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12604444 TATATAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:12607843 original size:143 final size:147
Alignment explanation
Indices: 12607517--12607916 Score: 506
Period size: 143 Copynumber: 2.7 Consensus size: 147
12607507 TTAAAGTTAA
* * * *
12607517 CCAGCCAGGCTGTCTTTCTCAAAACTATAAGGCAAACTTTATTTTGTAACTC-CGCATAGATGAT
1 CCAGCCAGGTTGTCTTTCTCAAAACTAGAAAGCAAACTTTATTTGGTAACTCTC-CATAGATGAT
* * * * * * *
12607581 AAACAGTTAGC-TATACTTATTCCTTAACAAGATATTCCACTACGGGCCTATGGCTACACCTGGA
65 AAACAGATA-CTTATCCCTATTCCTAAACCAGATATTCCACTACGAGCCTA--GCTA-ACCTAGA
*
12607645 CTAGATATTGAAATTTATAATG
126 CTAGACATTGAAATTTATAATG
* * *
12607667 CCAGCCAGGTTTTCTTTCTCAAAACTAGAAAGCAAAATTTATTTGGCAACTCTCCATAGATGATA
1 CCAGCCAGGTTGTCTTTCTCAAAACTAGAAAGCAAACTTTATTTGGTAACTCTCCATAGATGATA
* * * * *
12607732 AACAGATACTTGTCCCTATTACTGAACCAGATATTTCACTAC-AGCC-A-CT-ATCTAGACTAGA
66 AACAGATACTTATCCCTATTCCTAAACCAGATATTCCACTACGAGCCTAGCTAACCTAGACTAGA
12607793 CATTGAAATTTATAATG
131 CATTGAAATTTATAATG
*
12607810 CCAGCCAGGTTGTCTTTCTCAAAACTAGAAAGCAAACTTTATTTGGTAACTCTCCCTAGATGATA
1 CCAGCCAGGTTGTCTTTCTCAAAACTAGAAAGCAAACTTTATTTGGTAACTCTCCATAGATGATA
* *
12607875 AACAGATACTTATCCCGATTCCTAAACCAGAGATTCCACTAC
66 AACAGATACTTATCCCTATTCCTAAACCAGATATTCCACTAC
12607917 CTAGACTCCT
Statistics
Matches: 219, Mismatches: 29, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
143 123 0.56
145 2 0.01
148 1 0.00
149 4 0.02
150 88 0.40
151 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (147 bp):
CCAGCCAGGTTGTCTTTCTCAAAACTAGAAAGCAAACTTTATTTGGTAACTCTCCATAGATGATA
AACAGATACTTATCCCTATTCCTAAACCAGATATTCCACTACGAGCCTAGCTAACCTAGACTAGA
CATTGAAATTTATAATG
Found at i:12616176 original size:13 final size:13
Alignment explanation
Indices: 12616158--12616182 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12616148 GTCAAACCAT
12616158 AAGATGTTTTTAG
1 AAGATGTTTTTAG
12616171 AAGATGTTTTTA
1 AAGATGTTTTTA
12616183 TGCAATTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (13 bp):
AAGATGTTTTTAG
Found at i:12621209 original size:14 final size:16
Alignment explanation
Indices: 12621185--12621218 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
12621175 TACTTATTAA
12621185 AAATCTATTTTTTT-T
1 AAATCTATTTTTTTAT
12621200 AAAT-TATTTTTTTAT
1 AAATCTATTTTTTTAT
12621215 AAAT
1 AAAT
12621219 GTTTTTATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
AAATCTATTTTTTTAT
Found at i:12621542 original size:15 final size:16
Alignment explanation
Indices: 12621510--12621543 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
12621500 TTAAATAAAA
*
12621510 AAATAAATTTTGATTT
1 AAATAAATTTTAATTT
12621526 AAATAAA-TTTAATTT
1 AAATAAATTTTAATTT
12621541 AAA
1 AAA
12621544 GATAATGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
AAATAAATTTTAATTT
Found at i:12623234 original size:61 final size:62
Alignment explanation
Indices: 12623132--12623253 Score: 149
Period size: 61 Copynumber: 2.0 Consensus size: 62
12623122 TATTTAAAAT
**
12623132 GTTTTCTAGTCAAAAATACCTTAAATAATCATGATGAATTTTTTTTTAGAATA-TTTAAGGC
1 GTTTTCTAACCAAAAATACCTTAAATAATCATGATGAATTTTTTTTTAGAATATTTTAAGGC
* * ** * *
12623193 GTTTTCTAACCAAAAATGCCTTTAAATAATCTTG-TTCATTTTTTTTTGGATTATTTTAAGG
1 GTTTTCTAACCAAAAATACC-TTAAATAATCATGATGAATTTTTTTTTAGAATATTTTAAGG
12623254 TATTTTTTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
61 32 0.63
62 19 0.37
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (62 bp):
GTTTTCTAACCAAAAATACCTTAAATAATCATGATGAATTTTTTTTTAGAATATTTTAAGGC
Found at i:12623375 original size:59 final size:60
Alignment explanation
Indices: 12623305--12623445 Score: 162
Period size: 61 Copynumber: 2.4 Consensus size: 60
12623295 TTTATTAAGG
* *
12623305 AGATTATTTAAGGCATTTTCTAGTCA-AATA-TGCCTGAAATAATC-CCAAAAAATTAAACA
1 AGATTATTTAAGGCATTTTCTA-TCAGAAAACT-CCTGAAATAATCTCAAAAAAATTAAACA
* * * *
12623364 AGATTATTTAAGTCATTTTTTTATCAGAAAACTCCTTAAATAATCTCAAAAAAATTGAACA
1 AGATTATTTAAGGCA-TTTTCTATCAGAAAACTCCTGAAATAATCTCAAAAAAATTAAACA
* *
12623425 AGATTATTTAAAGCATCTTCT
1 AGATTATTTAAGGCATTTTCT
12623446 CCTAAAAAAG
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
59 17 0.25
60 24 0.35
61 27 0.40
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.35
Consensus pattern (60 bp):
AGATTATTTAAGGCATTTTCTATCAGAAAACTCCTGAAATAATCTCAAAAAAATTAAACA
Found at i:12628810 original size:21 final size:20
Alignment explanation
Indices: 12628786--12628824 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
12628776 CTATGAGTCA
12628786 TTGCTATTGATCATTCAAGAG
1 TTGCTATTGATCA-TCAAGAG
* *
12628807 TTGCTCTTGCTCATCAAG
1 TTGCTATTGATCATCAAG
12628825 TCTTTGTTGT
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:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (20 bp):
TTGCTATTGATCATCAAGAG
Found at i:12630833 original size:27 final size:28
Alignment explanation
Indices: 12630795--12630851 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 28
12630785 TATTTAAGGT
12630795 ATTTTTTGGATAGAAACAAC-TAAAATA
1 ATTTTTTGGATAGAAACAACTTAAAATA
* *
12630822 ATTTTTTTGATAGAAACAACTTTAAATA
1 ATTTTTTGGATAGAAACAACTTAAAATA
12630850 AT
1 AT
12630852 ACTTGTCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.39
Consensus pattern (28 bp):
ATTTTTTGGATAGAAACAACTTAAAATA
Found at i:12631570 original size:123 final size:122
Alignment explanation
Indices: 12631185--12632050 Score: 445
Period size: 125 Copynumber: 6.9 Consensus size: 122
12631175 TTTTTTAGGA
* * * ** ** **
12631185 GATTATTTAAAGCGTTTTATAGCCA-AAAATGCTTTTAATAATCCTT-TAAAAAATTTTAAGAAA
1 GATTATTTAAAGC-TTTT-TAGTCAGAAAATGCATTAAATAAT-CTTATTCAATTTTTTAAGGGA
* * * ** * * * * *
12631248 TTATTCAAGATATTTTCTGGTAAAAAATGCATTAAATAATCTTATAAAAAAATTTGTACAGG
63 TTATTTAAGGTATTTTCTAGCCAAAAATGCTTTCAATAATCTTTTACAAAAA-TTGTA-TGG
* * * * * ** * *
12631310 GATTACTTAATGCATTTTT-GTCAGAAAATACCTTATATAATCACATTTAATTTTTTTAAGAGAT
1 GATTATTTAAAGC-TTTTTAGTCAGAAAATGCATTAAATAATCTTATTCAA-TTTTTTAAGGGAT
* ** * *
12631374 TATTTAAGGTATTTTCTATTCGATCTAAAAATGCCCTAAATAATCTTTTATAAAAATTTGGTATA
64 TATTTAAGGTATTTTCTA---G--CCAAAAATGCTTTCAATAATCTTTTACAAAAA-TT-GTAT-
12631439 AGG
121 -GG
* * *
12631442 GATTATTTAAAGCTTTTTTAGTCAAAAAATGTC-TTAAATAATCTTATTCAATTTTTTAATGAAT
1 GATTATTTAAAGC-TTTTTAGTCAGAAAATG-CATTAAATAATCTTATTCAATTTTTTAAGGGAT
*
12631506 TATTTAAGGTATTTT-TAGCCAAAAACGCTTTCAATAATCTTTTA-AAATAATTGTATGGG
64 TATTTAAGGTATTTTCTAGCCAAAAATGCTTTCAATAATCTTTTACAAA-AATTGTAT-GG
* *
12631565 GATTATTTAAGGAGC-TTTTAATCAGAAAATGCATTAAATAAT-TTCATTCAAATTTTTAAGGGA
1 GATTATTTAA--AGCTTTTTAGTCAGAAAATGCATTAAATAATCTT-ATTCAATTTTTTAAGGGA
** * * * * * * *
12631628 TTATTTAAGACATTTTCAAGTCAAAAATGCCTTAAATAATCATTTACAAAAAATTATATTG
63 TTATTTAAGGTATTTTCTAGCCAAAAATGCTTTCAATAATCTTTTAC-AAAAATTGTATGG
* * * * *
12631689 AATTATTT-AAGCCATTTTTAGTCAGAAAATACTTTAAATAATCTCATTTAATTTTTTTAAGGGA
1 GATTATTTAAAG-C-TTTTTAGTCAGAAAATGCATTAAATAATCTTATTCAA-TTTTTTAAGGGA
* * * * * *
12631753 TTATTTAAAGTGTTTTCTATCCAAATATGCTTTCAATAATCCTTTAACAAAAATT-TACAGG
63 TTATTTAAGGTATTTTCTAGCCAAAAATGCTTTCAATAAT-CTTTTACAAAAATTGTA-TGG
* * * * * * * * *
12631814 AATTA-TTAAGGTTTTTTTG-CAAGAAAATACCA-TGAATAATCCTATTTAATTTTTTTAGAGGA
1 GATTATTTAAAGCTTTTTAGTC-AGAAAAT-GCATTAAATAATCTTATTCAATTTTTTAAG-GGA
** * * * * * *
12631876 TTATTTAAGACATTTT-TGGCAAAAAATGCTTT-ACATAATCGTTTAAAAAAATTTTACAT-T
63 TTATTTAAGGTATTTTCTAGCCAAAAATGCTTTCA-ATAATCTTTTACAAAAATTGT--ATGG
* * * * * * *
12631936 AATTATTTAAGGCGTTTTTTGTCAGAAAATACATTGAATAAT-TCCATTTAAATTTTTT-AGTGG
1 GATTATTTAAAGC-TTTTTAGTCAGAAAATGCATTAAATAATCT-TA-TTCAATTTTTTAAG-GG
* * * * * *
12631999 ATTATTTAAGGCATTTTCAACCCAAAAATGCCTTAAATAATCATTGTACAAA
62 ATTATTTAAGGTATTTTCTAGCCAAAAATGCTTTCAATAATC-TTTTACAAA
12632051 TTGTACAAGG
Statistics
Matches: 580, Mismatches: 116, Indels: 89
0.74 0.15 0.11
Matches are distributed among these distances:
121 14 0.02
122 36 0.06
123 119 0.21
124 130 0.22
125 140 0.24
126 38 0.07
128 2 0.00
130 29 0.05
131 5 0.01
132 43 0.07
133 23 0.04
134 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (122 bp):
GATTATTTAAAGCTTTTTAGTCAGAAAATGCATTAAATAATCTTATTCAATTTTTTAAGGGATTA
TTTAAGGTATTTTCTAGCCAAAAATGCTTTCAATAATCTTTTACAAAAATTGTATGG
Found at i:12631655 original size:61 final size:60
Alignment explanation
Indices: 12631563--12631760 Score: 170
Period size: 63 Copynumber: 3.2 Consensus size: 60
12631553 TAATTGTATG
12631563 GGGATTATTTAAGGAGC-TTTTAA-TCAGAAAATGCATTAAATAATTTCATTCAAATTTTTAA
1 GGGATTATTTAA-GA-CATTTTAAGTCAGAAAATGCATTAAATAA-TTCATTCAAATTTTTAA
* * * *
12631624 GGGATTATTTAAGACATTTTCAAGTCA-AAAATGCCTTAAATAA-TCATTTACAAAAAATTATAT
1 GGGATTATTTAAGACATTTT-AAGTCAGAAAATGCATTAAATAATTCA-TT-C--AAATTTTTAA
* * * * * * * *
12631687 TGAATTATTTAAGCCATTTTTAGTCAGAAAATACTTTAAATAATCTCATTTAATTTTTTTAA
1 GGGATTATTTAAGACATTTTAAGTCAGAAAATGCATTAAATAAT-TCATTCAA-ATTTTTAA
12631749 GGGATTATTTAA
1 GGGATTATTTAA
12631761 AGTGTTTTCT
Statistics
Matches: 109, Mismatches: 17, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
59 4 0.04
60 8 0.07
61 32 0.29
62 22 0.20
63 38 0.35
64 2 0.02
65 3 0.03
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (60 bp):
GGGATTATTTAAGACATTTTAAGTCAGAAAATGCATTAAATAATTCATTCAAATTTTTAA
Found at i:12631717 original size:124 final size:123
Alignment explanation
Indices: 12631270--12632127 Score: 464
Period size: 124 Copynumber: 6.9 Consensus size: 123
12631260 TTTTCTGGTA
* * *
12631270 AAAAATGCATTAAATAATC-TTATA-AAAAAATTTGTACA-GGGATTACTTAATGCATTTTT-GT
1 AAAAATGCTTTAAATAATCATT-TACAAAAAA--T-TACATGGAATTATTTAA-GCATTTTTAGT
* * ** * **
12631331 CAGAAAATACCTTATATAATCACATTTAATTTTTTTAAGAGATTATTTAAGGTATTTTCTATTCG
61 CAGAAAATACATTAAATAATTTCATTTAA-TTTTTTAAGGGATTATTTAAGACATTTTC-A----
* *
12631396 ATCT
120 AGCC
** * * * * * * *
12631400 AAAAATGCCCTAAATAATCTTTTATAAAAATTTGGTATAAGGGATTATTTAAAGCTTTTTTAGTC
1 AAAAATGCTTTAAATAATCATTTACAAAAA-AT--TACATGGAATTATTT-AAGCATTTTTAGTC
* * * * * ** *
12631465 AAAAAATGTC-TTAAATAATCTT-ATTCAATTTTTTAATGAATTATTTAAGGTATTTT-TAGCC
62 AGAAAAT-ACATTAAATAAT-TTCATTTAATTTTTTAAGGGATTATTTAAGACATTTTCAAGCC
* * * * ** * * * *
12631526 AAAAACGCTTTCAATAATCTTTTA-AAATAATTGTATGGGGATTATTTAAGGAGCTTTTAATCAG
1 AAAAATGCTTTAAATAATCATTTACAAAAAATTACAT-GGAATTATTTAAGCA-TTTTTAGTCAG
* * * *
12631590 AAAATGCATTAAATAATTTCATTCAAATTTTTAAGGGATTATTTAAGACATTTTCAAGTC
64 AAAATACATTAAATAATTTCATTTAATTTTTTAAGGGATTATTTAAGACATTTTCAAGCC
* * *
12631650 AAAAATGCCTTAAATAATCATTTACAAAAAATTATATTGAATTATTTAAGCCATTTTTAGTCAGA
1 AAAAATGCTTTAAATAATCATTTACAAAAAATTACATGGAATTATTTAAG-CATTTTTAGTCAGA
* * ** * *
12631715 AAATACTTTAAATAATCTCATTTAATTTTTTTAAGGGATTATTTAA-AGTGTTTTCTATCC
65 AAATACATTAAATAATTTCATTTAA-TTTTTTAAGGGATTATTTAAGA-CATTTTCAAGCC
* * * * ** *
12631775 AAATATGCTTTCAATAATCCTTTAACAAAAATTTACA-GGAATTA-TTAAGGTTTTTTTG-CAAG
1 AAAAATGCTTTAAATAATCATTT-ACAAAAAATTACATGGAATTATTTAAGCATTTTTAGTC-AG
* * * ** *
12631837 AAAATACCA-TGAATAA-TCCTATTTAATTTTTTTAGAGGATTATTTAAGACATTTT-TGGCA
64 AAAATA-CATTAAATAATTTC-ATTTAATTTTTTAAG-GGATTATTTAAGACATTTTCAAGCC
* * * * *
12631897 AAAAATGCTTTACATAATCGTTTA-AAAAAATTTTACAT-TAATTATTTAAGGCGTTTTTTGTCA
1 AAAAATGCTTTAAATAATCATTTACAAAAAA--TTACATGGAATTATTTAA-GCATTTTTAGTCA
* * * *
12631960 GAAAATACATTGAATAATTCCATTTAAATTTTTT-AGTGGATTATTTAAGGCATTTTCAACCC
63 GAAAATACATTAAATAATTTCATTT-AATTTTTTAAG-GGATTATTTAAGACATTTTCAAGCC
* * * * *
12632022 AAAAATGCCTTAAATAATCATTGTAC--AAATTGTACAAGG-ATTATTTAATTCATTTTTTA-CC
1 AAAAATGCTTTAAATAATCATT-TACAAAAAAT-TACATGGAATTATTTAA-GCA-TTTTTAGTC
* * * ** * *
12632083 AAAAAATACCTTGAATAATCCCATTCAATTTTTGAAGGGATTATT
62 AGAAAATACATTAAATAATTTCATTTAATTTTTTAAGGGATTATT
12632128 CAATGGCATT
Statistics
Matches: 578, Mismatches: 110, Indels: 87
0.75 0.14 0.11
Matches are distributed among these distances:
120 5 0.01
121 1 0.00
122 50 0.09
123 124 0.21
124 160 0.28
125 106 0.18
126 35 0.06
130 20 0.03
131 11 0.02
132 41 0.07
133 24 0.04
134 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (123 bp):
AAAAATGCTTTAAATAATCATTTACAAAAAATTACATGGAATTATTTAAGCATTTTTAGTCAGAA
AATACATTAAATAATTTCATTTAATTTTTTAAGGGATTATTTAAGACATTTTCAAGCC
Found at i:12631841 original size:247 final size:245
Alignment explanation
Indices: 12631443--12632232 Score: 573
Period size: 247 Copynumber: 3.2 Consensus size: 245
12631433 GGTATAAGGG
* * * * * * *
12631443 ATTATTTAAAGCTTTTTTAGTCAAAAAAT-GTCTTAAATAATCTTATTCAATTTTTTAATGAATT
1 ATTATTT-AAGCATTTTTAGTCAGAAAATACT-TTAAATAATCTCATTTAATTTTTTAAGGGATT
* * * ** *
12631507 ATTTAAGGTATTTTTAGCCAAAAACGCTTTCAATAATCTTTTAAAATAATTGTATGGGGATTATT
64 ATTTAAAGTATTTTTAGCCAAAAACGCTTTCAATAATCCTTTAAAAAAATTGTACAGGAATTATT
* *
12631572 TAAGGAGCTTTTAATCAGAAAAT-GCATTAAATAAT-TTCATTCAAATTTTTAAG-GGATTATTT
129 TAAGGAGCTTTTAATCAGAAAATACCA-TAAATAATCCT-ATTCAAATTTTTAAGAGGATTATTT
* *
12631634 AAGACATTTTCAAGTC-AAAAATGCCTTAAATAATCATTTACAAAAAA-TTATATTGA
192 AAGACATTTT--AGGCAAAAAATGCCTTAAATAATCATTTA-AAAAAATTTACATT-A
12631690 ATTATTTAAGCCATTTTTAGTCAGAAAATACTTTAAATAATCTCATTTAATTTTTTTAAGGGATT
1 ATTATTTAAG-CATTTTTAGTCAGAAAATACTTTAAATAATCTCATTTAA-TTTTTTAAGGGATT
* * * *
12631755 ATTTAAAGTGTTTTCTATCCAAATATGCTTTCAATAATCCTTTAACAAAAATT-TACAGGAATTA
64 ATTTAAAGTATTTT-TAGCCAAAAACGCTTTCAATAATCCTTTAA-AAAAATTGTACAGGAATTA
** * * * *
12631819 -TTAA-G-G-TTTTTTTGCAAGAAAATACCATGAATAATCCTATTTAATTTTTTTAGAGGATTAT
127 TTTAAGGAGCTTTTAAT-C-AGAAAATACCATAAATAATCCTATTCAAATTTTTAAGAGGATTAT
* * * *
12631880 TTAAGACATTTTTGGCAAAAAATGCTTTACATAATCGTTTAAAAAAATTTTACATTA
190 TTAAGACATTTTAGGCAAAAAATGCCTTAAATAATCATTTAAAAAAA-TTTACATTA
* * * *
12631937 ATTATTTAAGGCGTTTTTTGTCAGAAAATACATTGAATAAT-TCCATTTAAATTTTTT-AGTGGA
1 ATTATTTAA-GCATTTTTAGTCAGAAAATACTTTAAATAATCT-CATTT-AATTTTTTAAG-GGA
* * * * * * * * *
12632000 TTATTTAAGGCATTTTCAACCCAAAAATGCCTTAAATAATCATTGT--ACAAATTGTACAAGG-A
62 TTATTTAAAGTATTTT-TAGCCAAAAACGCTTTCAATAATCCTT-TAAAAAAATTGTAC-AGGAA
** * * * * * * *
12632062 TTATTTAATTCA-TTTTTTACCAAAAAATACCTTGAATAATCCCATTC-AATTTTTGAAG-GGAT
124 TTATTTAA-GGAGCTTTTAATCAGAAAATACCATAAATAATCCTATTCAAATTTTT-AAGAGGAT
* * * * * *
12632124 TATTCAATGGCATTTTCTGGCAAAAAA-ACCTTAAATAATCCTTTAAAAAATTTTGTACGA--A
187 TATTTAA-GACATTTT-AGGCAAAAAATGCCTTAAATAATCATTTAAAAAA-ATT-TAC-ATTA
* * *
12632185 GATTATTTAAGTCATTTTT-GATTAAAAAATACCTTAAATAATCTCATT
1 -ATTATTTAAG-CATTTTTAG-TCAGAAAATACTTTAAATAATCTCATT
12632233 CGATATCCGA
Statistics
Matches: 442, Mismatches: 66, Indels: 68
0.77 0.11 0.12
Matches are distributed among these distances:
245 11 0.02
246 23 0.05
247 195 0.44
248 116 0.26
249 84 0.19
250 13 0.03
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (245 bp):
ATTATTTAAGCATTTTTAGTCAGAAAATACTTTAAATAATCTCATTTAATTTTTTAAGGGATTAT
TTAAAGTATTTTTAGCCAAAAACGCTTTCAATAATCCTTTAAAAAAATTGTACAGGAATTATTTA
AGGAGCTTTTAATCAGAAAATACCATAAATAATCCTATTCAAATTTTTAAGAGGATTATTTAAGA
CATTTTAGGCAAAAAATGCCTTAAATAATCATTTAAAAAAATTTACATTA
Found at i:12634731 original size:28 final size:28
Alignment explanation
Indices: 12634659--12634731 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 28
12634649 ATAAATAAAG
*
12634659 AGAAAACATTTCTAAATTAACCAAAATGA
1 AGAAAA-ATTTCTAAATCAACCAAAATGA
* **
12634688 TGAAAAATTTAGAAATCCAA-CAAAAT-A
1 AGAAAAATTTCTAAAT-CAACCAAAATGA
12634715 AGAAAGAATTTCTAAAT
1 AGAAA-AATTTCTAAAT
12634732 AGGCCTAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
27 5 0.14
28 23 0.66
29 7 0.20
ACGTcount: A:0.56, C:0.11, G:0.08, T:0.25
Consensus pattern (28 bp):
AGAAAAATTTCTAAATCAACCAAAATGA
Found at i:12634742 original size:56 final size:55
Alignment explanation
Indices: 12634682--12634866 Score: 155
Period size: 56 Copynumber: 3.4 Consensus size: 55
12634672 AAATTAACCA
* *
12634682 AAATGATGAAAAATTTAGAAATCCAACAAAATAAGAAAGAATTTCTAAATAGGCCT
1 AAATGATGAAAAATTTAAAAATCCAACAAAA-AAGAAAGAATTTATAAATAGGCCT
* * ** * * * * *
12634738 AAATGGTGAAAATTTTAAAAAT--TTCGAAAAA-AAA-TATTTATAAATTGACCC
1 AAATGATGAAAAATTTAAAAATCCAACAAAAAAGAAAGAATTTATAAATAGGCCT
* * * * *
12634789 AAATTATGGAAAACTTAAAAATCCAACAAAAAAAGAGAGAATTTATAAATAAG-CT
1 AAATGATGAAAAATTTAAAAATCCAAC-AAAAAAGAAAGAATTTATAAATAGGCCT
*
12634844 CAAATGGTGAAAAATTTAAAAAT
1 -AAATGATGAAAAATTTAAAAAT
12634867 TAAAAAAAAA
Statistics
Matches: 94, Mismatches: 29, Indels: 12
0.70 0.21 0.09
Matches are distributed among these distances:
51 29 0.31
52 3 0.03
53 3 0.03
54 9 0.10
55 3 0.03
56 47 0.50
ACGTcount: A:0.55, C:0.09, G:0.11, T:0.25
Consensus pattern (55 bp):
AAATGATGAAAAATTTAAAAATCCAACAAAAAAGAAAGAATTTATAAATAGGCCT
Found at i:12634782 original size:107 final size:105
Alignment explanation
Indices: 12634661--12634881 Score: 282
Period size: 107 Copynumber: 2.1 Consensus size: 105
12634651 AAATAAAGAG
* * * * *
12634661 AAAACATTTCTAAATTAACCAAAATGATGAAAAATTTAGAAATCCAACAAAATAAGAAAGAATTT
1 AAAATATTTATAAATTAACCAAAATGATGAAAAACTTAAAAATCCAACAAAAAAAGAAAGAATTT
* * * *
12634726 CTAAATAGGC-CTAAATGGTGAAAATTTTAAAAATTTCGAAAA
66 ATAAATAAGCTC-AAATGGTGAAAAATTTAAAAA-TT-AAAAA
* * * * *
12634768 AAAATATTTATAAATTGACCCAAATTATGGAAAACTTAAAAATCCAACAAAAAAAGAGAGAATTT
1 AAAATATTTATAAATTAACCAAAATGATGAAAAACTTAAAAATCCAACAAAAAAAGAAAGAATTT
12634833 ATAAATAAGCTCAAATGGTGAAAAATTTAAAAATTAAAAA
66 ATAAATAAGCTCAAATGGTGAAAAATTTAAAAATTAAAAA
12634873 AAAATATTT
1 AAAATATTT
12634882 TTAATTTGGC
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
105 13 0.13
106 2 0.02
107 83 0.84
108 1 0.01
ACGTcount: A:0.55, C:0.09, G:0.10, T:0.26
Consensus pattern (105 bp):
AAAATATTTATAAATTAACCAAAATGATGAAAAACTTAAAAATCCAACAAAAAAAGAAAGAATTT
ATAAATAAGCTCAAATGGTGAAAAATTTAAAAATTAAAAA
Found at i:12639937 original size:8 final size:8
Alignment explanation
Indices: 12639926--12639980 Score: 58
Period size: 8 Copynumber: 6.8 Consensus size: 8
12639916 AAAAATGAGA
12639926 AAAAAATG
1 AAAAAATG
**
12639934 AAAAGGTG
1 AAAAAATG
12639942 AAAAAATG
1 AAAAAATG
12639950 AAAAAAAATG
1 --AAAAAATG
*
12639960 AACAAATG
1 AAAAAATG
12639968 AAAAAA-G
1 AAAAAATG
12639975 AAAAAA
1 AAAAAA
12639981 AAAAACTCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
7 7 0.18
8 24 0.62
10 8 0.21
ACGTcount: A:0.75, C:0.02, G:0.15, T:0.09
Consensus pattern (8 bp):
AAAAAATG
Found at i:12639955 original size:18 final size:18
Alignment explanation
Indices: 12639926--12639975 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
12639916 AAAAATGAGA
*
12639926 AAAAAATG--AAAAGGTG
1 AAAAAATGAAAAAAGATG
*
12639942 AAAAAATGAAAAAAAATG
1 AAAAAATGAAAAAAGATG
*
12639960 AACAAATGAAAAAAGA
1 AAAAAATGAAAAAAGA
12639976 AAAAAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 8 0.29
18 20 0.71
ACGTcount: A:0.72, C:0.02, G:0.16, T:0.10
Consensus pattern (18 bp):
AAAAAATGAAAAAAGATG
Found at i:12639971 original size:25 final size:26
Alignment explanation
Indices: 12639915--12639982 Score: 95
Period size: 26 Copynumber: 2.6 Consensus size: 26
12639905 AATGGATAGA
*
12639915 AAAAAATGAGAAAAAAATGAAAAGGTG
1 AAAAAATGA-AAAAAAATGAAAAGATG
12639942 AAAAAATGAAAAAAAATGAACAA-ATG
1 AAAAAATGAAAAAAAATGAA-AAGATG
12639968 AAAAAA-GAAAAAAAA
1 AAAAAATGAAAAAAAA
12639983 AAACTCAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
25 9 0.23
26 19 0.49
27 11 0.28
ACGTcount: A:0.75, C:0.01, G:0.15, T:0.09
Consensus pattern (26 bp):
AAAAAATGAAAAAAAATGAAAAGATG
Found at i:12640684 original size:79 final size:79
Alignment explanation
Indices: 12640593--12640742 Score: 246
Period size: 79 Copynumber: 1.9 Consensus size: 79
12640583 TCGATATGGC
** *
12640593 TAGTGCTGAGAAACCTGTCAATGGTGATCAAGTGATGAACATAATGTGGACCAAATGATAGAATT
1 TAGTGCTGAGAAACCTGTCAATGGTGATCAAGTGATGAACATAATGTAAACCAAATGACAGAATT
12640658 TATTCTGGAATGAT
66 TATTCTGGAATGAT
* * *
12640672 TAGTGCTGAGAAACCTGTGAATGGTGATCAAGTGATGAACATAATGTAAATCAATTGACAGAATT
1 TAGTGCTGAGAAACCTGTCAATGGTGATCAAGTGATGAACATAATGTAAACCAAATGACAGAATT
12640737 TATTCT
66 TATTCT
12640743 AAGATTGATA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 65 1.00
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (79 bp):
TAGTGCTGAGAAACCTGTCAATGGTGATCAAGTGATGAACATAATGTAAACCAAATGACAGAATT
TATTCTGGAATGAT
Found at i:12640763 original size:79 final size:79
Alignment explanation
Indices: 12640596--12640766 Score: 236
Period size: 79 Copynumber: 2.2 Consensus size: 79
12640586 ATATGGCTAG
** *
12640596 TGCTGAGAAACCTGTCAATGGTGATCAAGTGATGAACATAATGTGGACCAAATGATAGAATTTAT
1 TGCTGAGAAACCTGTCAATGGTGATCAAGTGATGAACATAATGTAAACCAAATGACAGAATTTAT
* *
12640661 TCTGGAATGATTAG
66 TCTAGAATGATTAA
* * *
12640675 TGCTGAGAAACCTGTGAATGGTGATCAAGTGATGAACATAATGTAAATCAATTGACAGAATTTAT
1 TGCTGAGAAACCTGTCAATGGTGATCAAGTGATGAACATAATGTAAACCAAATGACAGAATTTAT
*
12640740 TCTAAGATTGA-TAA
66 TCT-AGAATGATTAA
*
12640754 TGCTAAGAAACCT
1 TGCTGAGAAACCT
12640767 ATGAGTTATG
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
79 76 0.94
80 5 0.06
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (79 bp):
TGCTGAGAAACCTGTCAATGGTGATCAAGTGATGAACATAATGTAAACCAAATGACAGAATTTAT
TCTAGAATGATTAA
Found at i:12641265 original size:21 final size:21
Alignment explanation
Indices: 12641239--12641365 Score: 139
Period size: 21 Copynumber: 5.8 Consensus size: 21
12641229 AAGAATCCTC
*
12641239 AAATGAGAATCTTTGACTCTT
1 AAATGAGAATCTTTGAGTCTT
*
12641260 AAATGAGAATCTTTGAGTTTT
1 AAATGAGAATCTTTGAGTCTT
* *
12641281 AAATGAGAATATTTAAAAAGTCCTT
1 AAATGAGAATCTTT---GAGT-CTT
*
12641306 AAATGAGAATCTTTGAGTATT
1 AAATGAGAATCTTTGAGTCTT
*
12641327 CAAATGAAAATCTTTGAGT-TT
1 -AAATGAGAATCTTTGAGTCTT
12641348 CAAATGAGAATCTTTGAG
1 -AAATGAGAATCTTTGAG
12641366 AAGTGAAACC
Statistics
Matches: 91, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
21 53 0.58
22 20 0.22
24 3 0.03
25 15 0.16
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.36
Consensus pattern (21 bp):
AAATGAGAATCTTTGAGTCTT
Found at i:12641310 original size:67 final size:68
Alignment explanation
Indices: 12641225--12641358 Score: 200
Period size: 67 Copynumber: 2.0 Consensus size: 68
12641215 TAAAGATATC
* * *
12641225 TTTAAAGAATCCTCAAATGAGAATCTTTGACTCTT-AAATGAGAATCTTTGAGTTTTAAATGAGA
1 TTTAAAGAATCCTCAAATGAGAATCTTTGACTATTCAAATGAAAATCTTTGAGTTTCAAATGAGA
12641289 ATA
66 ATA
* *
12641292 TTTAAA-AAGTCCTTAAATGAGAATCTTTGAGTATTCAAATGAAAATCTTTGAGTTTCAAATGAG
1 TTTAAAGAA-TCCTCAAATGAGAATCTTTGACTATTCAAATGAAAATCTTTGAGTTTCAAATGAG
12641356 AAT
65 AAT
12641359 CTTTGAGAAG
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
66 2 0.03
67 29 0.48
68 29 0.48
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36
Consensus pattern (68 bp):
TTTAAAGAATCCTCAAATGAGAATCTTTGACTATTCAAATGAAAATCTTTGAGTTTCAAATGAGA
ATA
Found at i:12641435 original size:42 final size:45
Alignment explanation
Indices: 12641388--12641484 Score: 123
Period size: 43 Copynumber: 2.2 Consensus size: 45
12641378 AAAGTTCATC
* *
12641388 GGATGTGAACCTT-C-AAATT-AGAATGAAAAGTTTTAAAC-TTTT
1 GGATGTGAACCTTCCAAAATTCA-AACGAAAAGCTTTAAACTTTTT
*
12641430 GGATGTGAA-TTTCCAAAATTCAAACGAAAAGCTTTAAACTTTTT
1 GGATGTGAACCTTCCAAAATTCAAACGAAAAGCTTTAAACTTTTT
12641474 GGATGTGAACC
1 GGATGTGAACC
12641485 CCAAATTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
41 2 0.04
42 10 0.22
43 20 0.43
44 14 0.30
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (45 bp):
GGATGTGAACCTTCCAAAATTCAAACGAAAAGCTTTAAACTTTTT
Found at i:12641845 original size:41 final size:41
Alignment explanation
Indices: 12641799--12642066 Score: 294
Period size: 41 Copynumber: 6.5 Consensus size: 41
12641789 TATGATTATC
* * *
12641799 GAGGAGC-TTTTATTTTTCTAAAGCTGTGGTGCATCTGTTTCA
1 GAGGAGCATTTTATTTTTC-AAAGTTGTGGTGCCTCTATTT-A
** *
12641841 -AGGAGCATTTTATTTTTTTCAAAGTTACGATGCCTCTATTTA
1 GAGGAGCATTTTA--TTTTTCAAAGTTGTGGTGCCTCTATTTA
* * * *
12641883 GAGGAACATATTATTTTTCAAATTTGTGGTGCATCTATTTA
1 GAGGAGCATTTTATTTTTCAAAGTTGTGGTGCCTCTATTTA
* * *
12641924 -AAGAGCATATTATTTTTCAAAGTTGTGGTGCCTTTATTTA
1 GAGGAGCATTTTATTTTTCAAAGTTGTGGTGCCTCTATTTA
12641964 GAGGAGCATTTTATTTTTCAAAGTTGTGGTGCCTCTATTTA
1 GAGGAGCATTTTATTTTTCAAAGTTGTGGTGCCTCTATTTA
* * * * *
12642005 GATGAGCCTTCTATTTTTCAAAGTTGTGATGCCTCTGTTTA
1 GAGGAGCATTTTATTTTTCAAAGTTGTGGTGCCTCTATTTA
12642046 GAGGAGTC-TTTTA-TTTTCAAA
1 GAGGAG-CATTTTATTTTTCAAA
12642067 AGTCATTGAA
Statistics
Matches: 192, Mismatches: 28, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
40 43 0.22
41 111 0.58
42 7 0.04
43 25 0.13
44 6 0.03
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (41 bp):
GAGGAGCATTTTATTTTTCAAAGTTGTGGTGCCTCTATTTA
Found at i:12642063 original size:81 final size:81
Alignment explanation
Indices: 12641799--12642066 Score: 310
Period size: 81 Copynumber: 3.3 Consensus size: 81
12641789 TATGATTATC
* * * *
12641799 GAGGAGC-TTTTATTTTTCTAAAGCTGTGGTGCATCTGTTTCAAGGAGCATTTTATTTTTTTCAA
1 GAGGAGCATTTTATTTTTC-AAAGTTGTGGTGCATCTATTT-AAAGAGCATATTA--TTTTTCAA
**
12641863 AGTTACGATGCCTCTATTTA
62 AGTTGTGATGCCTCTATTTA
* * *
12641883 GAGGAACATATTATTTTTCAAATTTGTGGTGCATCTATTTAAAGAGCATATTATTTTTCAAAGTT
1 GAGGAGCATTTTATTTTTCAAAGTTGTGGTGCATCTATTTAAAGAGCATATTATTTTTCAAAGTT
* *
12641948 GTGGTGCCTTTATTTA
66 GTGATGCCTCTATTTA
* * *
12641964 GAGGAGCATTTTATTTTTCAAAGTTGTGGTGCCTCTATTTAGATGAGCCT-TCTATTTTTCAAAG
1 GAGGAGCATTTTATTTTTCAAAGTTGTGGTGCATCTATTTA-AAGAGCATAT-TATTTTTCAAAG
*
12642028 TTGTGATGCCTCTGTTTA
64 TTGTGATGCCTCTATTTA
12642046 GAGGAGTC-TTTTA-TTTTCAAA
1 GAGGAG-CATTTTATTTTTCAAA
12642067 AGTCATTGAA
Statistics
Matches: 160, Mismatches: 20, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
81 70 0.44
82 44 0.28
83 12 0.08
84 24 0.15
85 10 0.06
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (81 bp):
GAGGAGCATTTTATTTTTCAAAGTTGTGGTGCATCTATTTAAAGAGCATATTATTTTTCAAAGTT
GTGATGCCTCTATTTA
Found at i:12642063 original size:122 final size:123
Alignment explanation
Indices: 12641799--12642066 Score: 303
Period size: 122 Copynumber: 2.2 Consensus size: 123
12641789 TATGATTATC
*
12641799 GAGGAGCTTTTATTTTTCTAAAGCTGTGGTGCATCTGTTTCAAGGAGCATTTTATTTTTTTCAAA
1 GAGGAGCTTTTATTTTTC-AAAGCTGTGGTGCATCTATTTCAAGGAGCATTTTA-TTTTTTCAAA
* *
12641864 GTTACGATGCCTCTATTTAGAGGAACATATTATTTTTCAAATTTGTGGTGCATCTATTTA
64 GTTACGATGCCTCTATTTAGAGGAACATATTATTTTTCAAAGTTGTGATGCATCTATTTA
* * * * *
12641924 -AAGAGCATATTATTTTTCAAAGTTGTGGTGCCTTTATTT-AGAGGAGCATTTTA-TTTTTCAAA
1 GAGGAGC-TTTTATTTTTCAAAGCTGTGGTGCATCTATTTCA-AGGAGCATTTTATTTTTTCAAA
** * * * * * *
12641986 GTTGTGGTGCCTCTATTTAGATGAGCCT-TCTATTTTTCAAAGTTGTGATGCCTCTGTTTA
64 GTTACGATGCCTCTATTTAGAGGAACATAT-TATTTTTCAAAGTTGTGATGCATCTATTTA
12642046 GAGGAGTCTTTTA-TTTTCAAA
1 GAGGAG-CTTTTATTTTTCAAA
12642067 AGTCATTGAA
Statistics
Matches: 120, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
121 1 0.01
122 65 0.54
123 9 0.08
124 35 0.29
125 10 0.08
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (123 bp):
GAGGAGCTTTTATTTTTCAAAGCTGTGGTGCATCTATTTCAAGGAGCATTTTATTTTTTCAAAGT
TACGATGCCTCTATTTAGAGGAACATATTATTTTTCAAAGTTGTGATGCATCTATTTA
Found at i:12642962 original size:15 final size:17
Alignment explanation
Indices: 12642933--12642965 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
12642923 TTTCAAAACA
12642933 AAAAAAAGTAGAAAAAT
1 AAAAAAAGTAGAAAAAT
12642950 AAAAAAA-TA-AAAAAT
1 AAAAAAAGTAGAAAAAT
12642965 A
1 A
12642966 TTGATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAAAAAGTAGAAAAAT
Done.