Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, 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: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 58 of 106
Found at i:10321923 original size:12 final size:12
Alignment explanation
Indices: 10321906--10321931 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10321896 TCAATTTCCT
10321906 AAAACAAAATAA
1 AAAACAAAATAA
10321918 AAAACAAAATAA
1 AAAACAAAATAA
10321930 AA
1 AA
10321932 TTTATGTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.08, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAACAAAATAA
Found at i:10325028 original size:19 final size:19
Alignment explanation
Indices: 10325004--10325043 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
10324994 GTTTCATGTA
10325004 AAATTGCAAAATGTAAACT
1 AAATTGCAAAATGTAAACT
10325023 AAATTGCAAAATGTAAACT
1 AAATTGCAAAATGTAAACT
10325042 AA
1 AA
10325044 GTAAAGTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.25
Consensus pattern (19 bp):
AAATTGCAAAATGTAAACT
Found at i:10325224 original size:20 final size:21
Alignment explanation
Indices: 10325187--10325226 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
10325177 AAGTATAGCA
*
10325187 AAATCTAGAAACTAGAATTTC
1 AAATCTAGAAAATAGAATTTC
*
10325208 AAAT-TAGAAAATTGAATTT
1 AAATCTAGAAAATAGAATTT
10325227 AATTCATGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (21 bp):
AAATCTAGAAAATAGAATTTC
Found at i:10328193 original size:16 final size:18
Alignment explanation
Indices: 10328160--10328194 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
10328150 CTTTCTTTTA
10328160 TTTTTTAGACTTCTCTCT
1 TTTTTTAGACTTCTCTCT
10328178 TTTTTTAGA-TTC-CTCT
1 TTTTTTAGACTTCTCTCT
10328194 T
1 T
10328195 CTCATTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 3 0.18
18 9 0.53
ACGTcount: A:0.11, C:0.20, G:0.06, T:0.63
Consensus pattern (18 bp):
TTTTTTAGACTTCTCTCT
Found at i:10329236 original size:21 final size:22
Alignment explanation
Indices: 10329196--10329239 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
10329186 TATAAACTAT
* *
10329196 TTTTACTTGCAAACTTTATATA
1 TTTTACTTGAAAAATTTATATA
10329218 TTTTACTT-AAAAATTTATATA
1 TTTTACTTGAAAAATTTATATA
10329239 T
1 T
10329240 CTTGTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTTACTTGAAAAATTTATATA
Found at i:10330391 original size:14 final size:14
Alignment explanation
Indices: 10330372--10330399 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10330362 CTTTTTCTAA
10330372 TATATTTTATAAAG
1 TATATTTTATAAAG
10330386 TATATTTTATAAAG
1 TATATTTTATAAAG
10330400 AAGAAATAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TATATTTTATAAAG
Found at i:10330493 original size:17 final size:17
Alignment explanation
Indices: 10330449--10330493 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
10330439 TCTACATTTC
*
10330449 ATATATATTT-TATAAA
1 ATATATATTTATTTAAA
*
10330465 ATAT-TA-TAATTTAAA
1 ATATATATTTATTTAAA
10330480 ATATATATTTATTT
1 ATATATATTTATTT
10330494 TTATTATGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
14 1 0.04
15 11 0.48
16 6 0.26
17 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATATATTTATTTAAA
Found at i:10330523 original size:18 final size:17
Alignment explanation
Indices: 10330488--10330534 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
10330478 AAATATATAT
* *
10330488 TTATTTTTATTATGATA
1 TTATTTTTAGTATAATA
10330505 TTATTTATTAGTATAATA
1 TTATTT-TTAGTATAATA
*
10330523 TTATTTTAAGTA
1 TTATTTTTAGTA
10330535 AAAAAATACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (17 bp):
TTATTTTTAGTATAATA
Found at i:10330625 original size:33 final size:33
Alignment explanation
Indices: 10330587--10330676 Score: 112
Period size: 33 Copynumber: 2.8 Consensus size: 33
10330577 TATATTTTTT
*
10330587 AAAATTCTATATCATTTAAAAAAATTAAAG-AAA
1 AAAATTCTATATCATTTTAAAAAATT-AAGTAAA
* * *
10330620 AAAATTTTGTATCATTTTAAAATATTAAGTAAA
1 AAAATTCTATATCATTTTAAAAAATTAAGTAAA
*
10330653 AAAATTC-ATATAATTTTAAAAAAT
1 AAAATTCTATATCATTTTAAAAAAT
10330677 AAATTTATTA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
32 17 0.35
33 31 0.65
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (33 bp):
AAAATTCTATATCATTTTAAAAAATTAAGTAAA
Found at i:10331197 original size:16 final size:18
Alignment explanation
Indices: 10331164--10331199 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
10331154 TTGAATATTT
10331164 TATAAAATAAATTTGAAA
1 TATAAAATAAATTTGAAA
10331182 TATAAAA-AAA-TTGAAA
1 TATAAAATAAATTTGAAA
10331198 TA
1 TA
10331200 GTAGCATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 3 0.17
18 7 0.39
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
TATAAAATAAATTTGAAA
Found at i:10331551 original size:21 final size:20
Alignment explanation
Indices: 10331516--10331554 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
10331506 TCATTTTATT
10331516 TTTCTTTGTTTTCTTACTTC
1 TTTCTTTGTTTTCTTACTTC
*
10331536 TTTCTTTTTCTTTCTTACT
1 TTTCTTTGT-TTTCTTACT
10331555 CCTCCTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.05, C:0.21, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTCTTTGTTTTCTTACTTC
Found at i:10332951 original size:19 final size:17
Alignment explanation
Indices: 10332929--10332984 Score: 67
Period size: 19 Copynumber: 3.1 Consensus size: 17
10332919 TCTAAATTTT
10332929 AAAATTTTACAAACATTCA
1 AAAATTTTA-AAA-ATTCA
10332948 AAAATTTTAAAAATTCTTA
1 AAAATTTTAAAAATTC--A
*
10332967 AAAATATTAAAAATTCA
1 AAAATTTTAAAAATTCA
10332984 A
1 A
10332985 TAAAAAATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
17 6 0.18
18 3 0.09
19 25 0.74
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTTTAAAAATTCA
Found at i:10332989 original size:19 final size:19
Alignment explanation
Indices: 10332947--10332990 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
10332937 ACAAACATTC
* *
10332947 AAAAATTTTAAAAATTCTT
1 AAAAATATTAAAAATTCAT
10332966 AAAAATATTAAAAATTCAAT
1 AAAAATATTAAAAATTC-AT
10332986 AAAAA
1 AAAAA
10332991 ATTCTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAATATTAAAAATTCAT
Found at i:10333081 original size:15 final size:16
Alignment explanation
Indices: 10333055--10333087 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
10333045 AACATTTTAA
10333055 AATTTATAAAAATATT
1 AATTTATAAAAATATT
*
10333071 AATTT-TAAAAATTTT
1 AATTTATAAAAATATT
10333086 AA
1 AA
10333088 AAAATTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTATAAAAATATT
Found at i:10333110 original size:9 final size:9
Alignment explanation
Indices: 10332890--10333090 Score: 83
Period size: 9 Copynumber: 21.6 Consensus size: 9
10332880 AAAATTCAGA
*
10332890 AAAAATTAT
1 AAAAATTTT
*
10332899 AAGAAATTATA
1 AA-AAATT-TT
10332910 AAAAATTTTT
1 AAAAA-TTTT
**
10332920 CTAAATTTT
1 AAAAATTTT
10332929 -AAAATTTT
1 AAAAATTTT
*
10332937 ACAAACA-TTC
1 A-AAA-ATTTT
10332947 AAAAATTTT
1 AAAAATTTT
10332956 AAAAATTCTT
1 AAAAATT-TT
*
10332966 AAAAATATT
1 AAAAATTTT
*
10332975 AAAAATTCAATA
1 AAAAATT---TT
*
10332987 AAAAATTCT
1 AAAAATTTT
**
10332996 AAATTTTTT
1 AAAAATTTT
10333005 AAAAATTTT
1 AAAAATTTT
*
10333014 CAAAA-TTT
1 AAAAATTTT
* *
10333022 AAATTACTTTA
1 AAA--AATTTT
10333033 AAAATATTATT
1 AAAA-ATT-TT
* *
10333044 GAACATTTT
1 AAAAATTTT
10333053 -AAAATTTAT
1 AAAAATTT-T
*
10333062 AAAAATATT
1 AAAAATTTT
10333071 ---AATTTT
1 AAAAATTTT
10333077 AAAAATTTT
1 AAAAATTTT
10333086 AAAAA
1 AAAAA
10333091 ATTCAAAAAA
Statistics
Matches: 142, Mismatches: 29, Indels: 42
0.67 0.14 0.20
Matches are distributed among these distances:
6 5 0.04
8 19 0.13
9 59 0.42
10 38 0.27
11 13 0.09
12 8 0.06
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (9 bp):
AAAAATTTT
Found at i:10333135 original size:20 final size:20
Alignment explanation
Indices: 10333107--10333144 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10333097 AAAAAATTTT
*
10333107 AAAACATTTTTTTAATTTGC
1 AAAACATTTTTTAAATTTGC
*
10333127 AAAATATTTTTTAAATTT
1 AAAACATTTTTTAAATTT
10333145 CTCCAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (20 bp):
AAAACATTTTTTAAATTTGC
Found at i:10333249 original size:9 final size:9
Alignment explanation
Indices: 10333180--10333330 Score: 62
Period size: 9 Copynumber: 16.9 Consensus size: 9
10333170 AAATTTTTGA
10333180 AAAAATTAT
1 AAAAATTAT
10333189 AATAAATT-T
1 AA-AAATTAT
* *
10333198 TAAATTTAT
1 AAAAATTAT
10333207 -AAAA--AT
1 AAAAATTAT
*
10333213 AAAAATAAT
1 AAAAATTAT
* *
10333222 GAAATATTTTT
1 -AAA-AATTAT
*
10333233 ATAAATTAT
1 AAAAATTAT
10333242 AAAAATTAT
1 AAAAATTAT
* *
10333251 TATAATT-T
1 AAAAATTAT
* *
10333259 GGAAAATTTT
1 -AAAAATTAT
*
10333269 TAAAATTAT
1 AAAAATTAT
*
10333278 GAAAATTAT
1 AAAAATTAT
* *
10333287 GAAAATTTTT
1 -AAAAATTAT
* *
10333297 AAAAAATAA
1 AAAAATTAT
10333306 AAAAATT-T
1 AAAAATTAT
*
10333314 AAAATTTAT
1 AAAAATTAT
10333323 AAAAATTA
1 AAAAATTA
10333331 GATTTTCTTA
Statistics
Matches: 103, Mismatches: 28, Indels: 22
0.67 0.18 0.14
Matches are distributed among these distances:
6 2 0.02
7 4 0.04
8 14 0.14
9 63 0.61
10 17 0.17
11 3 0.03
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (9 bp):
AAAAATTAT
Found at i:10333264 original size:18 final size:18
Alignment explanation
Indices: 10333181--10333293 Score: 74
Period size: 18 Copynumber: 6.3 Consensus size: 18
10333171 AATTTTTGAA
*
10333181 AAAATTATAATAAATT-TT
1 AAAATTATGA-AAATTATT
* *
10333199 AAATTTAT-AAAA--ATA
1 AAAATTATGAAAATTATT
* *
10333214 AAAATAATGAAATATTTTT
1 AAAATTATGAAA-ATTATT
*
10333233 ATAAATTATAAAAATTATT
1 A-AAATTATGAAAATTATT
* *
10333252 ATAATT-TGGAAAATTTTT
1 AAAATTAT-GAAAATTATT
*
10333270 AAAATTATGAAAATTATG
1 AAAATTATGAAAATTATT
10333288 AAAATT
1 AAAATT
10333294 TTTAAAAAAT
Statistics
Matches: 72, Mismatches: 15, Indels: 16
0.70 0.15 0.16
Matches are distributed among these distances:
15 7 0.10
16 6 0.08
17 3 0.04
18 38 0.53
19 9 0.12
20 9 0.12
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (18 bp):
AAAATTATGAAAATTATT
Found at i:10333273 original size:27 final size:27
Alignment explanation
Indices: 10333243--10333300 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
10333233 ATAAATTATA
* *
10333243 AAAATTATTATAATT-TGGAAAATTTTT
1 AAAATTATGAAAATTAT-GAAAATTTTT
10333270 AAAATTATGAAAATTATGAAAATTTTT
1 AAAATTATGAAAATTATGAAAATTTTT
10333297 AAAA
1 AAAA
10333301 AATAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 27 0.96
28 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (27 bp):
AAAATTATGAAAATTATGAAAATTTTT
Found at i:10333317 original size:26 final size:28
Alignment explanation
Indices: 10333260--10333327 Score: 79
Period size: 26 Copynumber: 2.5 Consensus size: 28
10333250 TTATAATTTG
* **
10333260 GAAAATTTTT-AAAATTATGAAAATTAT
1 GAAAATTTTTAAAAAATAAAAAAATTAT
10333287 GAAAATTTTTAAAAAATAAAAAAATT-T
1 GAAAATTTTTAAAAAATAAAAAAATTAT
*
10333314 -AAAATTTATAAAAA
1 GAAAATTTTTAAAAA
10333328 TTAGATTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 13 0.36
27 11 0.31
28 12 0.33
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (28 bp):
GAAAATTTTTAAAAAATAAAAAAATTAT
Found at i:10333487 original size:9 final size:9
Alignment explanation
Indices: 10333449--10333532 Score: 57
Period size: 9 Copynumber: 9.2 Consensus size: 9
10333439 AACATTCTTT
10333449 AAAATTAAA
1 AAAATTAAA
10333458 AAAATATAAA
1 AAAAT-TAAA
*
10333468 AAAATAAAAA
1 AAAAT-TAAA
10333478 AAAATT--A
1 AAAATTAAA
* *
10333485 AAATTTAAT
1 AAAATTAAA
* *
10333494 AAAATCAAT
1 AAAATTAAA
10333503 AAAATGTCAAA
1 AAAAT-T-AAA
*
10333514 AAAATT-TA
1 AAAATTAAA
10333522 AAAATTAAA
1 AAAATTAAA
10333531 AA
1 AA
10333533 TTATATAAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
7 6 0.10
8 7 0.12
9 20 0.34
10 19 0.32
11 7 0.12
ACGTcount: A:0.73, C:0.02, G:0.01, T:0.24
Consensus pattern (9 bp):
AAAATTAAA
Found at i:10333750 original size:10 final size:10
Alignment explanation
Indices: 10333735--10333863 Score: 55
Period size: 10 Copynumber: 13.6 Consensus size: 10
10333725 AATTTGGAAG
10333735 TTTTTTAAAA
1 TTTTTTAAAA
10333745 TTTTTT--AA
1 TTTTTTAAAA
*
10333753 TTTTCCTT-AAT
1 TTTT--TTAAAA
* *
10333764 TCTTTTTGAAT
1 T-TTTTTAAAA
10333775 TTTTTTAAAA
1 TTTTTTAAAA
* *
10333785 TTTTCTAGAA
1 TTTTTTAAAA
* * *
10333795 TCTTCT-AGA
1 TTTTTTAAAA
*
10333804 TTTTTTTAAA
1 TTTTTTAAAA
10333814 TTTTTT---A
1 TTTTTTAAAA
10333821 -TTTTTAAAA
1 TTTTTTAAAA
10333830 --TTTTAAAA
1 TTTTTTAAAA
*
10333838 GTTTTTCAAAA
1 -TTTTTTAAAA
10333849 -TTTTTAAAA
1 TTTTTTAAAA
10333858 TTTTTT
1 TTTTTT
10333864 TGATTTTTTT
Statistics
Matches: 93, Mismatches: 13, Indels: 26
0.70 0.10 0.20
Matches are distributed among these distances:
6 5 0.05
7 1 0.01
8 14 0.15
9 14 0.15
10 43 0.46
11 13 0.14
12 3 0.03
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.61
Consensus pattern (10 bp):
TTTTTTAAAA
Found at i:10333788 original size:9 final size:9
Alignment explanation
Indices: 10333776--10333862 Score: 63
Period size: 9 Copynumber: 9.6 Consensus size: 9
10333766 TTTTTGAATT
10333776 TTTTTAAAA
1 TTTTTAAAA
*
10333785 TTTTCTAGAA
1 TTTT-TAAAA
* * *
10333795 TCTTCTAGAT
1 T-TTTTAAAA
*
10333805 TTTTTTAAA
1 TTTTTAAAA
*
10333814 TTTTT--TA
1 TTTTTAAAA
10333821 TTTTTAAAA
1 TTTTTAAAA
10333830 -TTTTAAAA
1 TTTTTAAAA
10333838 GTTTTTCAAAA
1 -TTTTT-AAAA
10333849 TTTTTAAAA
1 TTTTTAAAA
10333858 TTTTT
1 TTTTT
10333863 TTGATTTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
7 6 0.10
8 8 0.13
9 23 0.37
10 19 0.31
11 6 0.10
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:10333848 original size:19 final size:18
Alignment explanation
Indices: 10333776--10333862 Score: 63
Period size: 20 Copynumber: 4.8 Consensus size: 18
10333766 TTTTTGAATT
*
10333776 TTTTTAAAATTTTCTAGAA
1 TTTTTAAAATTTT-TAAAA
* * * *
10333795 TCTTCTAGATTTTTTTAAA
1 T-TTTTAAAATTTTTAAAA
*
10333814 TTTTT--TATTTTTAAAA
1 TTTTTAAAATTTTTAAAA
10333830 -TTTTAAAAGTTTTTCAAAA
1 TTTTTAAAA-TTTTT-AAAA
10333849 TTTTTAAAATTTTT
1 TTTTTAAAATTTTT
10333863 TTGATTTTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
15 4 0.08
16 8 0.15
17 1 0.02
18 8 0.15
19 14 0.27
20 17 0.33
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTTTAAAATTTTTAAAA
Found at i:10334167 original size:10 final size:9
Alignment explanation
Indices: 10334144--10334205 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
10334134 TTTAGGATTC
*
10334144 TTTTTAGAAC
1 TTTTTA-AAA
*
10334154 TTTTGAAAA
1 TTTTTAAAA
10334163 TTTTTAAAA
1 TTTTTAAAA
*
10334172 TTATTTATAA
1 TT-TTTAAAA
*
10334182 TTTGTAAAA
1 TTTTTAAAA
*
10334191 GTTTTTAGAA
1 -TTTTTAAAA
10334201 TTTTT
1 TTTTT
10334206 TTAAATTTCT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
9 22 0.52
10 20 0.48
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:10334183 original size:19 final size:19
Alignment explanation
Indices: 10334161--10334205 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
10334151 AACTTTTGAA
*
10334161 AATTTTTAAAA-TTATTTAT
1 AATTTTTAAAAGTT-TTTAG
*
10334180 AATTTGTAAAAGTTTTTAG
1 AATTTTTAAAAGTTTTTAG
10334199 AATTTTT
1 AATTTTT
10334206 TTAAATTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 20 0.91
20 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (19 bp):
AATTTTTAAAAGTTTTTAG
Found at i:10334208 original size:11 final size:11
Alignment explanation
Indices: 10334192--10334248 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
10334182 TTTGTAAAAG
10334192 TTTTTAGAATT
1 TTTTTAGAATT
10334203 TTTTTA-AA-T
1 TTTTTAGAATT
* *
10334212 TTCTT-GGATT
1 TTTTTAGAATT
10334222 TTTTTAGAATT
1 TTTTTAGAATT
10334233 TTTTATA-AATT
1 TTTT-TAGAATT
10334244 TTTTT
1 TTTTT
10334249 TAAAAAATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
9 6 0.16
10 8 0.21
11 22 0.58
12 2 0.05
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.67
Consensus pattern (11 bp):
TTTTTAGAATT
Found at i:10334855 original size:14 final size:14
Alignment explanation
Indices: 10334838--10334865 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10334828 TATAACTATA
10334838 TTAATATATTATTT
1 TTAATATATTATTT
10334852 TTAATATATTATTT
1 TTAATATATTATTT
10334866 ATAAGTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTAATATATTATTT
Found at i:10334900 original size:19 final size:20
Alignment explanation
Indices: 10334873--10334914 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
10334863 TTTATAAGTG
10334873 TTATATTAA-TAACATA-ATA
1 TTATATTAATTAA-ATATATA
*
10334892 TTATTTTAATTAAATATATA
1 TTATATTAATTAAATATATA
10334912 TTA
1 TTA
10334915 ATATCTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATATTAATTAAATATATA
Found at i:10335033 original size:11 final size:11
Alignment explanation
Indices: 10334992--10335121 Score: 58
Period size: 11 Copynumber: 11.7 Consensus size: 11
10334982 TATAATATAT
*
10334992 TATTAATAAAA
1 TATTAATAATA
*
10335003 TATAAAATTAATA
1 TAT-TAA-TAATA
*
10335016 -ATAAATAATA
1 TATTAATAATA
10335026 TATTAATAA-A
1 TATTAATAATA
10335036 TATT-ATAA-A
1 TATTAATAATA
* * *
10335045 GAAT-ATATTA
1 TATTAATAATA
10335055 TATTAAT-ATGA
1 TATTAATAAT-A
*
10335066 TATAAATAATA
1 TATTAATAATA
*
10335077 TATTAATAGCTATTTT
1 TATTAATA---A--TA
10335093 TATTAATAATA
1 TATTAATAATA
*
10335104 TATTATTAATA
1 TATTAATAATA
10335115 T-TTAATA
1 TATTAATA
10335122 TCTTTATATT
Statistics
Matches: 92, Mismatches: 15, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
9 10 0.11
10 19 0.21
11 42 0.46
12 6 0.07
13 5 0.05
14 1 0.01
16 9 0.10
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (11 bp):
TATTAATAATA
Found at i:10335034 original size:27 final size:25
Alignment explanation
Indices: 10335004--10335084 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 25
10334994 TTAATAAAAT
10335004 ATAAAATTAATAATAAATAATATATTA
1 ATAAAATT-AT-ATAAATAATATATTA
*
10335031 AT-AAA-TATTATAAAGAATATATTA
1 ATAAAATTA-TATAAATAATATATTA
* *
10335055 TATTAATATGATATAAATAATATATTA
1 -A-TAAAATTATATAAATAATATATTA
10335082 ATA
1 ATA
10335085 GCTATTTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
24 15 0.33
25 5 0.11
26 5 0.11
27 19 0.42
28 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
ATAAAATTATATAAATAATATATTA
Found at i:10335040 original size:47 final size:52
Alignment explanation
Indices: 10334983--10335084 Score: 124
Period size: 47 Copynumber: 2.1 Consensus size: 52
10334973 CTTATTCAAT
* *
10334983 ATAATATATTATTAATAAAATATAAAATT-A-AT-A-ATAAATAATATATTA
1 ATAATATATTATAAAGAAAATATAAAATTAATATGATATAAATAATATATTA
* * *
10335031 ATAA-ATATTATAAAGAATATATTATATTAATATGATATAAATAATATATTA
1 ATAATATATTATAAAGAAAATATAAAATTAATATGATATAAATAATATATTA
10335082 ATA
1 ATA
10335085 GCTATTTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
47 19 0.42
48 5 0.11
49 2 0.04
50 1 0.02
51 18 0.40
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (52 bp):
ATAATATATTATAAAGAAAATATAAAATTAATATGATATAAATAATATATTA
Found at i:10335139 original size:18 final size:17
Alignment explanation
Indices: 10334873--10335157 Score: 77
Period size: 18 Copynumber: 16.9 Consensus size: 17
10334863 TTTATAAGTG
10334873 TTATATTAATAACATAATA
1 TTATATTAATAA-AT-ATA
* *
10334892 TTATTTTAATTAA-ATA
1 TTATATTAATAAATATA
**
10334908 -TATATTAATATCTTATA
1 TTATATTAATA-AATATA
*
10334925 TTATGTTAAT-AATA-A
1 TTATATTAATAAATATA
* *
10334940 TTA-AGTAAATATAATGTAA
1 TTATA-TTAATA-AATAT-A
*
10334959 TTATA--AATAGATA-A
1 TTATATTAATAAATATA
*
10334973 CTTAT-TCAATATAATATA
1 -TTATATTAATA-AATATA
10334991 -T-TATTAATAAA-ATA
1 TTATATTAATAAATATA
* * *
10335005 TAAAATTAATAATAAATA
1 TTATATTAATAA-ATATA
*
10335023 ATATATTAAT-AA-ATA
1 TTATATTAATAAATATA
*
10335038 TTATA--AA-GAATATA
1 TTATATTAATAAATATA
10335052 TTATATTAATATGATATAAATA
1 TTATATTAATA--A-AT--ATA
* **
10335074 ATATATTAATAGCTAT-
1 TTATATTAATAAATATA
*
10335090 TTTTATTAAT-AATATA
1 TTATATTAATAAATATA
* * * *
10335106 TTATTAATATTTAATATCT
1 TTA-TATTAATAAATAT-A
*
10335125 TTATATTACTAAATAATA
1 TTATATTAATAAAT-ATA
10335143 TTATATTAATAAATA
1 TTATATTAATAAATA
10335158 AATATTATTG
Statistics
Matches: 193, Mismatches: 39, Indels: 70
0.64 0.13 0.23
Matches are distributed among these distances:
13 4 0.02
14 12 0.06
15 33 0.17
16 38 0.20
17 23 0.12
18 46 0.24
19 21 0.11
20 3 0.02
22 13 0.07
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TTATATTAATAAATATA
Found at i:10335158 original size:18 final size:19
Alignment explanation
Indices: 10335125--10335165 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
10335115 TTTAATATCT
*
10335125 TTATATTACTAAAT-AATA
1 TTATATTAATAAATAAATA
10335143 TTATATTAATAAATAAATA
1 TTATATTAATAAATAAATA
10335162 TTAT
1 TTAT
10335166 TGTATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TTATATTAATAAATAAATA
Found at i:10335161 original size:22 final size:22
Alignment explanation
Indices: 10335134--10335268 Score: 84
Period size: 22 Copynumber: 6.1 Consensus size: 22
10335124 TTTATATTAC
10335134 TAAATAATATTATATTAATAAA
1 TAAATAATATTATATTAATAAA
* * *
10335156 TAAATATTATTGTATT-ATTAA
1 TAAATAATATTATATTAATAAA
*
10335177 TATAAT-ATATTATTATTAGTAGAA
1 TA-AATAATATTA-TATTAATA-AA
* * * *
10335201 T-ATTATTTATT-TATTTATTAA
1 TAAATA-ATATTATATTAATAAA
*
10335222 TAGAATATTA-TATATGTAATAAA
1 TA-AATAATATTATAT-TAATAAA
10335245 TAAATAATATT-TATTAATATAA
1 TAAATAATATTATATTAATA-AA
10335267 TA
1 TA
10335269 TTTATATAAC
Statistics
Matches: 85, Mismatches: 16, Indels: 24
0.68 0.13 0.19
Matches are distributed among these distances:
21 19 0.22
22 47 0.55
23 12 0.14
24 7 0.08
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (22 bp):
TAAATAATATTATATTAATAAA
Found at i:10335256 original size:48 final size:44
Alignment explanation
Indices: 10335140--10335259 Score: 111
Period size: 45 Copynumber: 2.6 Consensus size: 44
10335130 TTACTAAATA
* *
10335140 ATATTA-TATTAATAAATAA-ATATTATTGTATTATTAATATAAT
1 ATATTATTATAAATAAATAATAT-TTATTGTATTATTAATAGAAT
* * *
10335183 ATATTATTATTAGTAGAATATTATTTATT-TATTTATTAATAGAAT
1 ATATTATTATAAATA-AATAATATTTATTGTA-TTATTAATAGAAT
10335228 ATTATATATGTAATAAATAAATAATATTTATT
1 A-TAT-TAT-T-ATAAATAAATAATATTTATT
10335260 AATATAATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
43 6 0.10
44 9 0.14
45 22 0.35
46 5 0.08
47 3 0.05
48 13 0.21
49 5 0.08
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (44 bp):
ATATTATTATAAATAAATAATATTTATTGTATTATTAATAGAAT
Found at i:10335264 original size:35 final size:37
Alignment explanation
Indices: 10335225--10335300 Score: 88
Period size: 35 Copynumber: 2.1 Consensus size: 37
10335215 TTATTAATAG
*
10335225 AATATTATATATGTA-ATAA-ATAAATAATA-TTTATT
1 AATATTA-ATATGTATATAACAAAAATAATATTTTATT
* *
10335260 AATA-TAATATTTATATAACAAAAATATTATTTTATT
1 AATATTAATATGTATATAACAAAAATAATATTTTATT
10335296 AATAT
1 AATAT
10335301 ATTATTTGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
33 6 0.18
34 6 0.18
35 12 0.35
36 10 0.29
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (37 bp):
AATATTAATATGTATATAACAAAAATAATATTTTATT
Found at i:10335268 original size:18 final size:18
Alignment explanation
Indices: 10335212--10335268 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 18
10335202 ATTATTTATT
* *
10335212 TATTTATTAATAGAATAT
1 TATTTATTAATATAATAA
*
10335230 TATATATGTAATAAATAAATAA
1 TATTTAT-TAAT--AT-AATAA
10335252 TATTTATTAATATAATA
1 TATTTATTAATATAATA
10335269 TTTATATAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
18 10 0.32
19 6 0.19
21 5 0.16
22 10 0.32
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (18 bp):
TATTTATTAATATAATAA
Found at i:10338987 original size:13 final size:14
Alignment explanation
Indices: 10338963--10338993 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
10338953 TTTCATATAC
10338963 AATTATAATAATAA
1 AATTATAATAATAA
10338977 AATTA-AATAATAA
1 AATTATAATAATAA
10338990 AATT
1 AATT
10338994 CAAAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AATTATAATAATAA
Found at i:10348622 original size:27 final size:26
Alignment explanation
Indices: 10348592--10348684 Score: 114
Period size: 27 Copynumber: 3.5 Consensus size: 26
10348582 TGGGTATGTA
10348592 GAGAATCTGGTTTTGAAGGGACTGGTT
1 GAGAATCTGGTTTTGAAGGG-CTGGTT
* *
10348619 GAGAATCTGATTTTGAATGGGCTGATT
1 GAGAATCTGGTTTTGAA-GGGCTGGTT
* *
10348646 GAGAATCTAGTTTTGAAGGGGTTGGTT
1 GAGAATCTGGTTTTGAA-GGGCTGGTT
*
10348673 GGGAATCTGGTT
1 GAGAATCTGGTT
10348685 GAGAAATTGG
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
27 53 0.95
28 3 0.05
ACGTcount: A:0.23, C:0.06, G:0.35, T:0.35
Consensus pattern (26 bp):
GAGAATCTGGTTTTGAAGGGCTGGTT
Found at i:10362812 original size:43 final size:43
Alignment explanation
Indices: 10362764--10362856 Score: 113
Period size: 42 Copynumber: 2.2 Consensus size: 43
10362754 ATGCATGCCA
*
10362764 AACATATTC-TATTC-TTCTTTTTCCTGAATAAATAGC-AAAATAG
1 AACATATTCATATTCGTTCTCTTT--T-AATAAATAGCAAAAATAG
*
10362807 AACATA-TCATATTCGTTCTCTTTTAATAAATTGCAAAAATAG
1 AACATATTCATATTCGTTCTCTTTTAATAAATAGCAAAAATAG
10362849 AACATATT
1 AACATATT
10362857 TTTGCGTTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
41 9 0.20
42 16 0.36
43 12 0.27
44 7 0.16
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.39
Consensus pattern (43 bp):
AACATATTCATATTCGTTCTCTTTTAATAAATAGCAAAAATAG
Found at i:10362865 original size:41 final size:40
Alignment explanation
Indices: 10362790--10362871 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 40
10362780 CTTTTTCCTG
*
10362790 AATAAATAGCAAAATAGAACATATCATATTCGTTCTCTTTT
1 AATAAATAGCAAAATAGAACATAT-ATATTCGTTCTATTTT
* *
10362831 AATAAATTGCAAAAATAGAACATAT-TTTTGCGTTCTATTTT
1 AATAAATAGC-AAAATAGAACATATATATT-CGTTCTATTTT
10362872 TGCAGTTCAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 3 0.08
41 19 0.53
42 14 0.39
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (40 bp):
AATAAATAGCAAAATAGAACATATATATTCGTTCTATTTT
Found at i:10366947 original size:14 final size:14
Alignment explanation
Indices: 10366930--10366957 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10366920 TCCTTTCTTC
10366930 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
10366944 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
10366958 CCCCTTTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (14 bp):
TTTTTCTTTTTTTT
Found at i:10369402 original size:18 final size:18
Alignment explanation
Indices: 10369379--10369414 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
10369369 TTTTTGATTT
*
10369379 AATATAAATATATTTATA
1 AATATAAATAAATTTATA
*
10369397 AATATACATAAATTTATA
1 AATATAAATAAATTTATA
10369415 CATAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
AATATAAATAAATTTATA
Found at i:10369538 original size:27 final size:28
Alignment explanation
Indices: 10369505--10369558 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
10369495 AATAATATCA
*
10369505 TTAATTT-ATCATGAT-ATTTTTAAATAC
1 TTAATTTAATCAT-ATGATATTTAAATAC
10369532 TTAATTTAATCATATGATATTTAAATA
1 TTAATTTAATCATATGATATTTAAATA
10369559 AGTATTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.50
Consensus pattern (28 bp):
TTAATTTAATCATATGATATTTAAATAC
Found at i:10371736 original size:19 final size:20
Alignment explanation
Indices: 10371701--10371741 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
10371691 GCCCAATGTA
*
10371701 TTATTTGTCCATTTTAACAT
1 TTATTTGTACATTTTAACAT
10371721 TTATTTGTAC-TTTTAACAT
1 TTATTTGTACATTTTAACAT
10371740 TT
1 TT
10371742 TTAGCATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.24, C:0.12, G:0.05, T:0.59
Consensus pattern (20 bp):
TTATTTGTACATTTTAACAT
Found at i:10374546 original size:34 final size:36
Alignment explanation
Indices: 10374478--10374553 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 36
10374468 AGTATCAAAG
* *
10374478 ATATCAAATATTTATTTACAAAGATATATATATTTGAT
1 ATATAAAATATTTATTTACAAAG--ACATATATTTGAT
10374516 ATATAAAATATTTATTTACAAAG-CAT-TATTTGAT
1 ATATAAAATATTTATTTACAAAGACATATATTTGAT
10374550 ATAT
1 ATAT
10374554 TGTGGTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
34 12 0.33
35 2 0.06
38 22 0.61
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (36 bp):
ATATAAAATATTTATTTACAAAGACATATATTTGAT
Found at i:10374665 original size:4 final size:4
Alignment explanation
Indices: 10374648--10374699 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
10374638 ATTAACATGT
* * *
10374648 TAAA TAAG TAAA TAAA TAATT TAACA T-AT TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAA-A TAA-A TAAA TAAA TAAA TAAA TAAA TAAA
10374697 TAA
1 TAA
10374700 TCATTTAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
3 1 0.03
4 34 0.87
5 4 0.10
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (4 bp):
TAAA
Found at i:10374679 original size:29 final size:28
Alignment explanation
Indices: 10374628--10374710 Score: 105
Period size: 29 Copynumber: 2.9 Consensus size: 28
10374618 TTATGAATAT
* * *
10374628 TAAATAAATCATTAACATGTTAAATAAG
1 TAAATAAATAATTAACATATTAAATAAA
10374656 TAAATAAATAATTTAACATATTAAATAAA
1 TAAATAAATAA-TTAACATATTAAATAAA
*
10374685 TAAATAAATAAATAATCAT-TTAAATA
1 TAAATAAATAATTAA-CATATTAAATA
10374711 TAATTATTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
28 20 0.41
29 29 0.59
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (28 bp):
TAAATAAATAATTAACATATTAAATAAA
Found at i:10375287 original size:19 final size:19
Alignment explanation
Indices: 10375265--10375326 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 19
10375255 TAGGAAACTT
*
10375265 AAAAATTTTAAAAAATCTC
1 AAAAATTTAAAAAAATCTC
* * *
10375284 -AAAATTAAAAAAAAACCC
1 AAAAATTTAAAAAAATCTC
* *
10375302 AAAAATTTGAAAATAATTTC
1 AAAAATTT-AAAAAAATCTC
10375322 AAAAA
1 AAAAA
10375327 ATTCAAAAAC
Statistics
Matches: 32, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
18 14 0.44
19 6 0.19
20 12 0.38
ACGTcount: A:0.65, C:0.10, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAAATTTAAAAAAATCTC
Found at i:10375439 original size:27 final size:26
Alignment explanation
Indices: 10375401--10375459 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
10375391 TAAAAATGAT
**
10375401 AAAAATAAAAAATCTAAAATTTTTTCA
1 AAAAATAAAAAATCTAAAAAATTTT-A
* *
10375428 AAAAATATAAAATTTAAAAAATTTTA
1 AAAAATAAAAAATCTAAAAAATTTTA
10375454 AAAAAT
1 AAAAAT
10375460 TCTAAGAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.32
Consensus pattern (26 bp):
AAAAATAAAAAATCTAAAAAATTTTA
Found at i:10375612 original size:18 final size:18
Alignment explanation
Indices: 10375591--10375642 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
10375581 TTTATGTTAT
*
10375591 GAATTTTTTAATTTTTTA
1 GAATTTTTTAATTTTTGA
* *
10375609 GAATGTTTTAGAATTTTGA
1 GAATTTTTTA-ATTTTTGA
*
10375628 -AATTATTTAATTTTT
1 GAATTTTTTAATTTTT
10375643 CAAAAATTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
17 5 0.19
18 16 0.59
19 6 0.22
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.60
Consensus pattern (18 bp):
GAATTTTTTAATTTTTGA
Found at i:10375853 original size:19 final size:20
Alignment explanation
Indices: 10375816--10375856 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
10375806 TAATTTTTAG
10375816 ATTTTTTGAAGTTTTCAAAA
1 ATTTTTTGAAGTTTTCAAAA
*
10375836 ATTTTTT-AA-TTTTCCAAA
1 ATTTTTTGAAGTTTTCAAAA
10375854 ATT
1 ATT
10375857 ATCATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 2 0.10
20 7 0.35
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTTTGAAGTTTTCAAAA
Found at i:10375973 original size:18 final size:19
Alignment explanation
Indices: 10375941--10375976 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
10375931 TTGTAGATTT
10375941 TTTTTAACTTATTAAAATG
1 TTTTTAACTTATTAAAATG
*
10375960 TTTTTAA-TTTTTAAAAT
1 TTTTTAACTTATTAAAAT
10375977 ATTTAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (19 bp):
TTTTTAACTTATTAAAATG
Found at i:10376026 original size:22 final size:21
Alignment explanation
Indices: 10375988--10376042 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
10375978 TTTAAAAATA
*
10375988 TTTTTAATTTTTGAAAATTCTTT
1 TTTTTAATTTTT-AAAA-ACTTT
10376011 TTTTTAA-TTTTAAAAACTTT
1 TTTTTAATTTTTAAAAACTTT
**
10376031 TTTAGAATTTTT
1 TTTTTAATTTTT
10376043 TTAATTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 9 0.32
21 8 0.29
22 4 0.14
23 7 0.25
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTTTAATTTTTAAAAACTTT
Found at i:10376039 original size:20 final size:19
Alignment explanation
Indices: 10375967--10376041 Score: 53
Period size: 20 Copynumber: 3.7 Consensus size: 19
10375957 ATGTTTTTAA
*
10375967 TTTTTAAAATATTTAAAAA-
1 TTTTTTAAAT-TTTAAAAAC
* *
10375986 TATTTTTAATTTTTGAAAATTC
1 T-TTTTTAAATTTT-AAAA-AC
*
10376008 TTTTTTTTAATTTTAAAAAC
1 -TTTTTTAAATTTTAAAAAC
10376028 TTTTTTAGAATTTT
1 TTTTTTA-AATTTT
10376042 TTTAATTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
19 10 0.23
20 18 0.42
21 4 0.09
22 10 0.23
23 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTTTTAAATTTTAAAAAC
Found at i:10376042 original size:21 final size:20
Alignment explanation
Indices: 10375967--10376042 Score: 50
Period size: 19 Copynumber: 3.7 Consensus size: 20
10375957 ATGTTTTTAA
* *
10375967 TTTTTAAAATATTTAAAAA-
1 TTTTTTAAATTTTTAAAAAC
*
10375986 TATTTTT-AATTTTTGAAAATTC
1 T-TTTTTAAATTTTT-AAAA-AC
*
10376008 TTTTTTTTAA-TTTTAAAAAC
1 -TTTTTTAAATTTTTAAAAAC
10376028 TTTTTTAGAATTTTT
1 TTTTTTA-AATTTTT
10376043 TTAATTTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
19 13 0.30
20 11 0.25
21 8 0.18
22 9 0.20
23 3 0.07
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTTTAAATTTTTAAAAAC
Found at i:10376061 original size:29 final size:28
Alignment explanation
Indices: 10376009--10376069 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
10375999 TGAAAATTCT
** *
10376009 TTTTTTTAATTTTAAAAACTTTTTTAGAA
1 TTTTTTTAATTTTAAAAA-AATTTTAAAA
10376038 TTTTTTTAA-TTTAAAGAAAATTTTAAAA
1 TTTTTTTAATTTTAAA-AAAATTTTAAAA
10376066 TTTT
1 TTTT
10376070 ATAGTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 17 0.61
29 11 0.39
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (28 bp):
TTTTTTTAATTTTAAAAAAATTTTAAAA
Found at i:10376983 original size:12 final size:12
Alignment explanation
Indices: 10376966--10376991 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10376956 ATAAACATTG
10376966 TTTTTCCTTATA
1 TTTTTCCTTATA
10376978 TTTTTCCTTATA
1 TTTTTCCTTATA
10376990 TT
1 TT
10376992 ACTTGAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTCCTTATA
Found at i:10379318 original size:22 final size:22
Alignment explanation
Indices: 10379290--10379333 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
10379280 AGCATATGAC
10379290 TTTTCTAAAACTACTGTAAGAG
1 TTTTCTAAAACTACTGTAAGAG
10379312 TTTTCTAAAACTACTGTAAGAG
1 TTTTCTAAAACTACTGTAAGAG
10379334 AAGACTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (22 bp):
TTTTCTAAAACTACTGTAAGAG
Found at i:10380047 original size:2 final size:2
Alignment explanation
Indices: 10380040--10380075 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
10380030 GATAAGTAAA
10380040 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10380076 TACTAACGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10380450 original size:21 final size:21
Alignment explanation
Indices: 10380402--10380478 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 21
10380392 CATTCAATAC
*
10380402 AATTTTGGTAACCTT-CGATAT
1 AATTTTGGTAA-CTTATGATAT
* *
10380423 TAGTTTGGTAACTTATGATAT
1 AATTTTGGTAACTTATGATAT
** * *
10380444 AATTTTGAAAAC-CATTGATAC
1 AATTTTGGTAACTTA-TGATAT
10380465 AATTTTGGTAACTT
1 AATTTTGGTAACTT
10380479 CTTTATGCAA
Statistics
Matches: 41, Mismatches: 12, Indels: 5
0.71 0.21 0.09
Matches are distributed among these distances:
20 4 0.10
21 37 0.90
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.43
Consensus pattern (21 bp):
AATTTTGGTAACTTATGATAT
Found at i:10380921 original size:3 final size:3
Alignment explanation
Indices: 10380909--10380974 Score: 100
Period size: 3 Copynumber: 22.3 Consensus size: 3
10380899 TTTAAAGTTG
10380909 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
10380956 ATT ATT -TCA ATT ATT ATT A
1 ATT ATT AT-T ATT ATT ATT A
10380975 ATTTTTTGTT
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 3 0.05
3 54 0.93
4 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:10381003 original size:11 final size:12
Alignment explanation
Indices: 10380976--10381005 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
10380966 TTATTATTAA
10380976 TTTTTTGTTCTC
1 TTTTTTGTTCTC
*
10380988 TTTTTTGTTTTC
1 TTTTTTGTTCTC
10381000 TTTTTT
1 TTTTTT
10381006 TCCTTTACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (12 bp):
TTTTTTGTTCTC
Found at i:10381355 original size:20 final size:21
Alignment explanation
Indices: 10381326--10381369 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
10381316 ATAGTTTTGG
* *
10381326 GGTG-ATTTTAGGTTTCAGAA
1 GGTGAATTTAAGGTTGCAGAA
10381346 GGTGAATTTAAGGTTGCAGAA
1 GGTGAATTTAAGGTTGCAGAA
10381367 GGT
1 GGT
10381370 TTGGGGAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.27, C:0.05, G:0.34, T:0.34
Consensus pattern (21 bp):
GGTGAATTTAAGGTTGCAGAA
Found at i:10385220 original size:16 final size:16
Alignment explanation
Indices: 10385201--10385231 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10385191 GGGCAAATAT
*
10385201 TTTTTTTTCTTTTCTA
1 TTTTTTTTCTATTCTA
10385217 TTTTTTTTCTATTCT
1 TTTTTTTTCTATTCT
10385232 TTCCATGTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTTTCTATTCTA
Found at i:10393451 original size:89 final size:88
Alignment explanation
Indices: 10393294--10393556 Score: 278
Period size: 89 Copynumber: 2.9 Consensus size: 88
10393284 TTTGTCCCGA
* * * * * * *
10393294 TCACATGGTTCATGGTTTCATCCTGATCACTTATTTTTGACATCGATTTGGTCTTTGTTGCTTAA
1 TCACATGATTCATGGTTTCATCTTGATCACTTATTTTTGACCTCGA-TTAGTC-CTGTCGCTTTA
10393359 TTTTGACTCGTGATTTCATCA-TGG
64 TTTTGACTCGTGATTTCATCATTGG
* * *
10393383 TCACATGATTCTTGGTTTTATCTTGATCATTTATTTTTGACCTCGATTCAGTCCTGATCGCTTTA
1 TCACATGATTCATGGTTTCATCTTGATCACTTATTTTTGACCTCGATT-AGTCCTG-TCGCTTTA
* * *
10393448 TTTTGACTTGTAATTTTAT-ATTGG
64 TTTTGACTCGTGATTTCATCATTGG
* * * *
10393472 TCACATGATTCGTGGTTTCATCTTAATCACTTATTTATGACCTCGACTTAATCCTGGTCGCTTTA
1 TCACATGATTCATGGTTTCATCTTGATCACTTATTTTTGACCTCGA-TTAGTCCT-GTCGCTTTA
* * *
10393537 TTTTGATTCATGGTTTCATC
64 TTTTGACTCGTGATTTCATC
10393557 TCAACACTTA
Statistics
Matches: 143, Mismatches: 25, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
88 5 0.03
89 135 0.94
90 3 0.02
ACGTcount: A:0.19, C:0.18, G:0.16, T:0.47
Consensus pattern (88 bp):
TCACATGATTCATGGTTTCATCTTGATCACTTATTTTTGACCTCGATTAGTCCTGTCGCTTTATT
TTGACTCGTGATTTCATCATTGG
Found at i:10394000 original size:26 final size:26
Alignment explanation
Indices: 10393968--10394036 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
10393958 CCGATTCCAG
*
10393968 ACCCGATTAGGTCCATTGACATCC-GA
1 ACCCGATTAGGCCCATTGACA-CCTGA
*
10393994 ACTCGATTAGGCCCATTGACACCTGA
1 ACCCGATTAGGCCCATTGACACCTGA
*
10394020 GCCCGATTAGGCCCATT
1 ACCCGATTAGGCCCATT
10394037 AGAGTCTAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
25 2 0.05
26 36 0.95
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (26 bp):
ACCCGATTAGGCCCATTGACACCTGA
Found at i:10394121 original size:3 final size:3
Alignment explanation
Indices: 10394113--10394140 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
10394103 TATTATATCA
10394113 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
10394141 TGTTCTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:10394156 original size:8 final size:8
Alignment explanation
Indices: 10394143--10394167 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
10394133 TTATTATTTG
10394143 TTCTCTTT
1 TTCTCTTT
10394151 TTCTCTTT
1 TTCTCTTT
10394159 TTCTCTTT
1 TTCTCTTT
10394167 T
1 T
10394168 CTTATTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTCTTT
Found at i:10394175 original size:16 final size:15
Alignment explanation
Indices: 10394136--10394178 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
10394126 ATTATTATTA
10394136 TTATTTGTTCTCTTTT
1 TTATTT-TTCTCTTTT
*
10394152 TCTCTTTTTCTCTTTT
1 T-TATTTTTCTCTTTT
10394168 CTTATTTTTCT
1 -TTATTTTTCT
10394179 TTATTGCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.74
Consensus pattern (15 bp):
TTATTTTTCTCTTTT
Found at i:10395087 original size:15 final size:16
Alignment explanation
Indices: 10395067--10395108 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
10395057 TTCTATTACC
10395067 AAAAAAAAAAG-TAAA
1 AAAAAAAAAAGTTAAA
**
10395082 AAAAAATGAAGTTAAA
1 AAAAAAAAAAGTTAAA
10395098 AAAATAAAAAA
1 AAAA-AAAAAA
10395109 AAGAAAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 9 0.43
16 8 0.38
17 4 0.19
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (16 bp):
AAAAAAAAAAGTTAAA
Found at i:10395851 original size:22 final size:22
Alignment explanation
Indices: 10395733--10395858 Score: 92
Period size: 22 Copynumber: 5.7 Consensus size: 22
10395723 CTAAGCTATA
* * * *
10395733 AATGATATACTGCTAAATTATT
1 AATGATTTACTACTAAATTGTG
* *
10395755 AATGATTTACTATTAAATT-AG
1 AATGATTTACTACTAAATTGTG
* * *
10395776 CATTACTTTACTACTAATTTGTG
1 AATGA-TTTACTACTAAATTGTG
* * *
10395799 AATGTTTTACTACTAAGTTATG
1 AATGATTTACTACTAAATTGTG
* *
10395821 AATAATTTACTACTAAATTGTT
1 AATGATTTACTACTAAATTGTG
* *
10395843 AATGGTTTATTACTAA
1 AATGATTTACTACTAA
10395859 GTTACTGATG
Statistics
Matches: 79, Mismatches: 23, Indels: 4
0.75 0.22 0.04
Matches are distributed among these distances:
21 3 0.04
22 73 0.92
23 3 0.04
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.44
Consensus pattern (22 bp):
AATGATTTACTACTAAATTGTG
Found at i:10395859 original size:44 final size:44
Alignment explanation
Indices: 10395711--10395862 Score: 144
Period size: 44 Copynumber: 3.5 Consensus size: 44
10395701 TTGTATTATC
* * * * * * *
10395711 AATGATTTATTACTAAGCTATAAATGATATACTGCTAAATTATT
1 AATGATTTACTACTAAGTTATGAATAATTTACTACTAAATTGTT
* * * * * *
10395755 AATGATTTACTATTAAATTA-GCATTACTTTACTACTAATTTGTG
1 AATGATTTACTACTAAGTTATG-AATAATTTACTACTAAATTGTT
*
10395799 AATGTTTTACTACTAAGTTATGAATAATTTACTACTAAATTGTT
1 AATGATTTACTACTAAGTTATGAATAATTTACTACTAAATTGTT
* *
10395843 AATGGTTTATTACTAAGTTA
1 AATGATTTACTACTAAGTTA
10395863 CTGATGATTT
Statistics
Matches: 84, Mismatches: 22, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
44 83 0.99
45 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (44 bp):
AATGATTTACTACTAAGTTATGAATAATTTACTACTAAATTGTT
Found at i:10395876 original size:22 final size:21
Alignment explanation
Indices: 10395712--10395873 Score: 74
Period size: 22 Copynumber: 7.4 Consensus size: 21
10395702 TGTATTATCA
* * *
10395712 ATGATTTATTACTAAGCTATAA
1 ATGATTTACTACTAAGTTAT-G
* * * *
10395734 ATGATATACTGCTAAATTATTA
1 ATGATTTACTACTAAGTTA-TG
* *
10395756 ATGATTTACTATTAAATTA-G
1 ATGATTTACTACTAAGTTATG
* * *
10395776 CATTACTTTACTACTAATTTGTG
1 -ATGA-TTTACTACTAAGTTATG
*
10395799 AATGTTTTACTACTAAGTTATG
1 -ATGATTTACTACTAAGTTATG
* * * *
10395821 AATAATTTACTACTAAATTGTTA
1 -ATGATTTACTACTAAGTT-ATG
* *
10395844 ATGGTTTATTACTAAGTTACTG
1 ATGATTTACTACTAAGTTA-TG
10395866 ATGATTTA
1 ATGATTTA
10395874 TTATAAAGTT
Statistics
Matches: 104, Mismatches: 30, Indels: 12
0.71 0.21 0.08
Matches are distributed among these distances:
21 3 0.03
22 96 0.92
23 5 0.05
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.44
Consensus pattern (21 bp):
ATGATTTACTACTAAGTTATG
Found at i:10395969 original size:22 final size:22
Alignment explanation
Indices: 10395944--10395994 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
10395934 GATTAATTAA
*
10395944 TTACTACTAAA-TTATTGTTGAT
1 TTACTACTAAAGTTATAG-TGAT
*
10395966 TTACAAC-AAAGTTATAGTGAT
1 TTACTACTAAAGTTATAGTGAT
10395987 TTACTACT
1 TTACTACT
10395995 GCTGAGCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (22 bp):
TTACTACTAAAGTTATAGTGAT
Found at i:10396102 original size:22 final size:22
Alignment explanation
Indices: 10396030--10396083 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
10396020 AAATTATTAA
10396030 TGATTTACTATTATGTTA-GTAT
1 TGATTTACTATTATGTTATG-AT
**
10396052 ACATTTACTATTATGTTATGAT
1 TGATTTACTATTATGTTATGAT
10396074 TGATTTACTA
1 TGATTTACTA
10396084 CTTAATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 26 0.96
23 1 0.04
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.52
Consensus pattern (22 bp):
TGATTTACTATTATGTTATGAT
Found at i:10396133 original size:22 final size:21
Alignment explanation
Indices: 10396098--10396200 Score: 75
Period size: 22 Copynumber: 4.8 Consensus size: 21
10396088 ATTTTTGATT
**
10396098 ATTTATTACAAAATTATCACA
1 ATTTATTATTAAATTATCACA
*
10396119 GATTTATTATTAAATTAAC-CA
1 -ATTTATTATTAAATTATCACA
* * *
10396140 TGATTCATTATCAAGTTATCACTA
1 --ATTTATTATTAAATTATCAC-A
*
10396164 ATTTA-TATTAAATTATCATA
1 ATTTATTATTAAATTATCACA
* *
10396184 ATTTACTATTAAGTTAT
1 ATTTATTATTAAATTAT
10396201 TTAGCTATTA
Statistics
Matches: 65, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
20 6 0.09
21 23 0.35
22 34 0.52
23 1 0.02
24 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.45
Consensus pattern (21 bp):
ATTTATTATTAAATTATCACA
Found at i:10396179 original size:21 final size:21
Alignment explanation
Indices: 10396108--10396200 Score: 71
Period size: 21 Copynumber: 4.3 Consensus size: 21
10396098 ATTTATTACA
* *
10396108 AAATTATCACAGATTTATTATT
1 AAATTATCATA-ATTTACTATT
* * * * *
10396130 AAATTAACCATGATTCATTATC
1 AAATT-ATCATAATTTACTATT
*
10396152 AAGTTATCACTAATTTA-TATT
1 AAATTATCA-TAATTTACTATT
10396173 AAATTATCATAATTTACTATT
1 AAATTATCATAATTTACTATT
*
10396194 AAGTTAT
1 AAATTAT
10396201 TTAGCTATTA
Statistics
Matches: 56, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
20 7 0.12
21 24 0.43
22 22 0.39
23 3 0.05
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (21 bp):
AAATTATCATAATTTACTATT
Found at i:10396208 original size:16 final size:15
Alignment explanation
Indices: 10396184--10396217 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
10396174 AATTATCATA
10396184 ATTTACTATTAAGTT
1 ATTTACTATTAAGTT
10396199 ATTTAGCTATTAAGTT
1 ATTTA-CTATTAAGTT
10396215 ATT
1 ATT
10396218 GATAATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (15 bp):
ATTTACTATTAAGTT
Found at i:10396258 original size:21 final size:22
Alignment explanation
Indices: 10396227--10396418 Score: 104
Period size: 22 Copynumber: 8.8 Consensus size: 22
10396217 TGATAATTAA
*
10396227 TTACTACTAAGTTAT-ATTGAT
1 TTACTATTAAGTTATCATTGAT
* *
10396248 TTACTTTTAAGTT-TCAATGAT
1 TTACTATTAAGTTATCATTGAT
* * *
10396269 TAACTATTAAATTATCATTTAT
1 TTACTATTAAGTTATCATTGAT
* * *
10396291 TTACTACTAAGTTAT-TTATAAT
1 TTACTATTAAGTTATCAT-TGAT
* *
10396313 TTACTACTAAGTTTATCAATT-AA
1 TTACTATTAAG-TTATC-ATTGAT
* ** ** * *
10396336 TTACTTTTAAACTAAAACTAAT
1 TTACTATTAAGTTATCATTGAT
* * *
10396358 TTACTATTAAGTTATTACTAAT
1 TTACTATTAAGTTATCATTGAT
* * *
10396380 TTATTATTAAGTTATCAATGAC
1 TTACTATTAAGTTATCATTGAT
*
10396402 TAACTATTAAGTTATCA
1 TTACTATTAAGTTATCA
10396419 CTTATCATTG
Statistics
Matches: 129, Mismatches: 35, Indels: 13
0.73 0.20 0.07
Matches are distributed among these distances:
20 1 0.01
21 29 0.22
22 84 0.65
23 13 0.10
24 1 0.01
25 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.47
Consensus pattern (22 bp):
TTACTATTAAGTTATCATTGAT
Found at i:10396332 original size:67 final size:66
Alignment explanation
Indices: 10396227--10396423 Score: 204
Period size: 67 Copynumber: 3.0 Consensus size: 66
10396217 TGATAATTAA
* * * *
10396227 TTACTACTAAGTTATAT-TGATTTACTTTTAAGTT-TCAATGATTAACTATTAAATTATCATTTA
1 TTACTACTAAGTTATTTATAATTTACTATTAAGTTATCAATGATTAACTATTAAATTATCACTTA
10396290 T
66 T
* * * * **
10396291 TTACTACTAAGTTATTTATAATTTACTACTAAGTTTATCAATTAATT-ACTTTTAAACTAAAACT
1 TTACTACTAAGTTATTTATAATTTACTATTAAG-TTATCAA-TGATTAACTATTAAATTATCACT
*
10396355 AAT
64 TAT
* * * *
10396358 TTACTATTAAGTTA-TTACTAATTTATTATTAAGTTATCAATGACTAACTATTAAGTTATCACTT
1 TTACTACTAAGTTATTTA-TAATTTACTATTAAGTTATCAATGATTAACTATTAAATTATCACTT
10396422 AT
65 AT
10396424 CATTGATTTG
Statistics
Matches: 105, Mismatches: 22, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
64 16 0.15
65 15 0.14
66 26 0.25
67 44 0.42
68 4 0.04
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (66 bp):
TTACTACTAAGTTATTTATAATTTACTATTAAGTTATCAATGATTAACTATTAAATTATCACTTA
T
Found at i:10396377 original size:22 final size:22
Alignment explanation
Indices: 10396199--10396394 Score: 96
Period size: 22 Copynumber: 8.8 Consensus size: 22
10396189 CTATTAAGTT
10396199 ATTTAGCTATTAAGTTATTGA-TA
1 ATTTA-CTATTAAGTTATT-ATTA
* *
10396222 ATTAATTACTACTAAGTTA-TATTG
1 A-T--TTACTATTAAGTTATTATTA
* * * *
10396246 ATTTACTTTTAAGTT-TCAATG
1 ATTTACTATTAAGTTATTATTA
* * * *
10396267 ATTAACTATTAAATTATCATTT
1 ATTTACTATTAAGTTATTATTA
*
10396289 ATTTACTACTAAGTTATT-TATA
1 ATTTACTATTAAGTTATTAT-TA
* *
10396311 ATTTACTACTAAGTTTATCAATTA
1 ATTTACTATTAAG-TTAT-TATTA
* ** ** *
10396335 A-TTACTTTTAAACTAAAACTA
1 ATTTACTATTAAGTTATTATTA
*
10396356 ATTTACTATTAAGTTATTACTA
1 ATTTACTATTAAGTTATTATTA
*
10396378 ATTTATTATTAAGTTAT
1 ATTTACTATTAAGTTAT
10396395 CAATGACTAA
Statistics
Matches: 133, Mismatches: 29, Indels: 23
0.72 0.16 0.12
Matches are distributed among these distances:
21 32 0.24
22 65 0.49
23 15 0.11
24 7 0.05
25 11 0.08
26 3 0.02
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (22 bp):
ATTTACTATTAAGTTATTATTA
Found at i:10403787 original size:62 final size:62
Alignment explanation
Indices: 10403711--10403835 Score: 232
Period size: 62 Copynumber: 2.0 Consensus size: 62
10403701 GTGTTTTATT
10403711 AAATATACTGATTATGATTCATAGTAACTATCATCTATCTTCCTAGTTTAATTTTTGTTAGG
1 AAATATACTGATTATGATTCATAGTAACTATCATCTATCTTCCTAGTTTAATTTTTGTTAGG
* *
10403773 AAATATACTGATTATGATTCCTATTAACTATCATCTATCTTCCTAGTTTAATTTTTGTTAGG
1 AAATATACTGATTATGATTCATAGTAACTATCATCTATCTTCCTAGTTTAATTTTTGTTAGG
10403835 A
1 A
10403836 CCAGCATTGG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (62 bp):
AAATATACTGATTATGATTCATAGTAACTATCATCTATCTTCCTAGTTTAATTTTTGTTAGG
Found at i:10406775 original size:35 final size:35
Alignment explanation
Indices: 10406729--10406800 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
10406719 ATTATATATG
10406729 TGAAGTCAATTGTAAGTTTATG-CCTAGAAAACATT
1 TGAAGTCAATTGTAAGTTTATGTCC-AGAAAACATT
* *
10406764 TGAAGTTAATTGTAGGTTTATGTCCAGAAAACATT
1 TGAAGTCAATTGTAAGTTTATGTCCAGAAAACATT
10406799 TG
1 TG
10406801 GTTTATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 32 0.94
36 2 0.06
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (35 bp):
TGAAGTCAATTGTAAGTTTATGTCCAGAAAACATT
Found at i:10410041 original size:13 final size:13
Alignment explanation
Indices: 10410007--10410055 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 13
10409997 AACTACTTAA
10410007 AAACACCATTCAG
1 AAACACCATTCAG
* *
10410020 CAA-ACCATTTAG
1 AAACACCATTCAG
10410032 AAACACCATTCAG
1 AAACACCATTCAG
*
10410045 TAA-ACCATTCA
1 AAACACCATTCA
10410056 ACATATGATT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 18 0.60
13 12 0.40
ACGTcount: A:0.45, C:0.29, G:0.06, T:0.20
Consensus pattern (13 bp):
AAACACCATTCAG
Found at i:10410052 original size:25 final size:25
Alignment explanation
Indices: 10409978--10410053 Score: 98
Period size: 25 Copynumber: 3.0 Consensus size: 25
10409968 AGCAATGTGC
* * * *
10409978 TTAGATACACCTTTCAGCAAACTAC
1 TTAGAAACACCATTCAGCAAACCAT
*
10410003 TTAAAAACACCATTCAGCAAACCAT
1 TTAGAAACACCATTCAGCAAACCAT
*
10410028 TTAGAAACACCATTCAGTAAACCAT
1 TTAGAAACACCATTCAGCAAACCAT
10410053 T
1 T
10410054 CAACATATGA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.42, C:0.26, G:0.07, T:0.25
Consensus pattern (25 bp):
TTAGAAACACCATTCAGCAAACCAT
Found at i:10410182 original size:80 final size:80
Alignment explanation
Indices: 10410046--10410201 Score: 242
Period size: 80 Copynumber: 1.9 Consensus size: 80
10410036 ACCATTCAGT
* * * *
10410046 AAACCATTCAACATATGATTTAGCCCCCCAATATCATATAATACCATTTAGAAAAACAATATCAG
1 AAACCATTCAACATACGATTCAGCCCCCCAATATCATACAATACCATTCAGAAAAACAATATCAG
10410111 ACAACAAGGTTCAAC
66 ACAACAAGGTTCAAC
* *
10410126 AAACCATTCAGCATACGATTCAGCCCCCTAATATCATACAATACCATTCA-ACAAAACAATATCA
1 AAACCATTCAACATACGATTCAGCCCCCCAATATCATACAATACCATTCAGA-AAAACAATATCA
10410190 GACAACAAGGTT
65 GACAACAAGGTT
10410202 TAGCAAATAA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
79 1 0.01
80 68 0.99
ACGTcount: A:0.44, C:0.26, G:0.08, T:0.22
Consensus pattern (80 bp):
AAACCATTCAACATACGATTCAGCCCCCCAATATCATACAATACCATTCAGAAAAACAATATCAG
ACAACAAGGTTCAAC
Found at i:10422568 original size:8 final size:8
Alignment explanation
Indices: 10422555--10422583 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
10422545 ACTTGTGGAA
10422555 TTAAAATT
1 TTAAAATT
10422563 TTAAAATT
1 TTAAAATT
10422571 TTAAAATT
1 TTAAAATT
10422579 TTAAA
1 TTAAA
10422584 TAGTTTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
TTAAAATT
Found at i:10422685 original size:20 final size:21
Alignment explanation
Indices: 10422649--10422689 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
10422639 AAATAAATTG
10422649 ATAAATATTATATATTTAAAA
1 ATAAATATTATATATTTAAAA
10422670 ATAAAT-TTAT-TAATTTAAAA
1 ATAAATATTATAT-ATTTAAAA
10422690 TTTTATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.05
20 12 0.63
21 6 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAAATATTATATATTTAAAA
Found at i:10426383 original size:2 final size:2
Alignment explanation
Indices: 10426340--10426370 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
10426330 TGTATGTGTC
*
10426340 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10426371 TACTAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10427840 original size:15 final size:14
Alignment explanation
Indices: 10427816--10427857 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
10427806 CATGGCGCCT
10427816 CTTTCTTTTTTCTC
1 CTTTCTTTTTTCTC
10427830 CTTTCCTTTTTTCT-
1 CTTT-CTTTTTTCTC
10427844 -TTT-TTTTTTCTC
1 CTTTCTTTTTTCTC
10427856 CT
1 CT
10427858 CTTTTTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
11 8 0.32
13 4 0.16
14 4 0.16
15 9 0.36
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
CTTTCTTTTTTCTC
Found at i:10430315 original size:14 final size:12
Alignment explanation
Indices: 10430296--10430333 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 12
10430286 ATCGTAGGCC
10430296 TTTTTTCTTTCTT
1 TTTTTTCTTT-TT
10430309 TTCTTTTCTTTTT
1 TT-TTTTCTTTTT
10430322 TTTTTT-TTTTT
1 TTTTTTCTTTTT
10430333 T
1 T
10430334 GGCTGGGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.25
12 4 0.17
13 6 0.25
14 8 0.33
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:10430333 original size:10 final size:10
Alignment explanation
Indices: 10430295--10430333 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
10430285 CATCGTAGGC
10430295 CTTTTTTCTTT
1 CTTTTTT-TTT
*
10430306 CTTTTCTTTT
1 CTTTTTTTTT
10430316 CTTTTTTTTT
1 CTTTTTTTTT
10430326 -TTTTTTTT
1 CTTTTTTTT
10430334 GGCTGGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 8 0.31
10 12 0.46
11 6 0.23
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:10430625 original size:11 final size:12
Alignment explanation
Indices: 10430600--10430635 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
10430590 ATACGATATG
10430600 AATATAATATTAA
1 AATATAATA-TAA
10430613 AATATAATA-AA
1 AATATAATATAA
10430624 AATATAATATAA
1 AATATAATATAA
10430636 TTTAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.50
12 2 0.09
13 9 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AATATAATATAA
Found at i:10430628 original size:24 final size:24
Alignment explanation
Indices: 10430600--10430676 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 24
10430590 ATACGATATG
10430600 AATATAATATTAAAATATAATAAA
1 AATATAATATTAAAATATAATAAA
*
10430624 AATATAATATAATTTAAAATTATAATAAT
1 AATAT-A-AT-A-TTAAAA-TATAATAAA
*
10430653 AAT-T-ATATATAAAATTTAATAAA
1 AATATAATAT-TAAAATATAATAAA
10430676 A
1 A
10430677 TAAAAAATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
23 9 0.20
24 11 0.25
25 3 0.07
26 2 0.05
27 1 0.02
28 7 0.16
29 11 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AATATAATATTAAAATATAATAAA
Found at i:10430632 original size:16 final size:16
Alignment explanation
Indices: 10430613--10430655 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 16
10430603 ATAATATTAA
10430613 AATATAATAAAAATAT
1 AATATAATAAAAATAT
*
10430629 AATATAATTTAAAATTAT
1 AATATAA--TAAAAATAT
10430647 AATAATAAT
1 AAT-ATAAT
10430656 TATATATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 7 0.30
17 1 0.04
18 11 0.48
19 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AATATAATAAAAATAT
Found at i:10430647 original size:29 final size:29
Alignment explanation
Indices: 10430573--10430671 Score: 94
Period size: 31 Copynumber: 3.3 Consensus size: 29
10430563 ATTAGATATA
* * *
10430573 ATAATTTAAAATAT-GTGATACGATATGAAT
1 ATAATTTAAAATATAATAATA-AATAT-AAT
10430603 ATAATATTAAAATATAATAA-AAATATAAT
1 ATAAT-TTAAAATATAATAATAAATATAAT
*
10430632 ATAATTTAAAATTATAATAATAATTATATAT
1 ATAATTTAAAA-TATAATAATAAATATA-AT
*
10430663 AAAATTTAA
1 ATAATTTAA
10430672 TAAAATAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
28 6 0.10
29 16 0.27
30 15 0.25
31 20 0.34
32 2 0.03
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (29 bp):
ATAATTTAAAATATAATAATAAATATAAT
Found at i:10430674 original size:10 final size:11
Alignment explanation
Indices: 10430610--10430677 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
10430600 AATATAATAT
10430610 TAAAA-TATAA
1 TAAAATTATAA
*
10430620 TAAAAATATAA
1 TAAAATTATAA
*
10430631 TATAA-T-T--
1 TAAAATTATAA
10430638 TAAAATTATAA
1 TAAAATTATAA
10430649 TAATAATTATATA
1 TAA-AATTATA-A
10430662 TAAAATT-TAA
1 TAAAATTATAA
10430672 TAAAAT
1 TAAAAT
10430678 AAAAAATTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
7 4 0.08
8 1 0.02
9 2 0.04
10 13 0.27
11 14 0.29
12 11 0.22
13 4 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAAATTATAA
Found at i:10430799 original size:32 final size:32
Alignment explanation
Indices: 10430738--10430800 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
10430728 TTCGTATAAA
* *
10430738 ATATAATATAAATACATAAATTTTAATATTTT
1 ATATAAAATAAATACATAAATTATAATATTTT
*
10430770 ATATAAAATAAATACATAAATTATCATATTT
1 ATATAAAATAAATACATAAATTATAATATTT
10430801 ATTTGGACCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (32 bp):
ATATAAAATAAATACATAAATTATAATATTTT
Found at i:10431353 original size:21 final size:21
Alignment explanation
Indices: 10431329--10431393 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
10431319 ATTACTCTAA
10431329 ATAAAGAGTATTATTTTATAT
1 ATAAAGAGTATTATTTTATAT
* * * *
10431350 AT-AACA-T-TGACTTTTAAAA
1 ATAAAGAGTATTA-TTTTATAT
10431369 ATAAAGAGTATTATTTTATAT
1 ATAAAGAGTATTATTTTATAT
10431390 ATAA
1 ATAA
10431394 CATTGGAAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
18 2 0.06
19 9 0.28
20 6 0.19
21 13 0.41
22 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (21 bp):
ATAAAGAGTATTATTTTATAT
Found at i:10431408 original size:40 final size:40
Alignment explanation
Indices: 10431327--10431408 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 40
10431317 TCATTACTCT
***
10431327 AAATAAAGAGTATTATTTTATATATAACATTGACTTTTAA
1 AAATAAAGAGTATTATTTTATATATAACATTGACAAATAA
10431367 AAATAAAGAGTATTATTTTATATATAACATTGGA-AAATAA
1 AAATAAAGAGTATTATTTTATATATAACATT-GACAAATAA
10431407 AA
1 AA
10431409 GGGGTAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 36 0.95
41 2 0.05
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.38
Consensus pattern (40 bp):
AAATAAAGAGTATTATTTTATATATAACATTGACAAATAA
Found at i:10431636 original size:24 final size:25
Alignment explanation
Indices: 10431598--10431645 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
10431588 ACTTATCTAA
**
10431598 TAATAAAAATTTTA-TCAAAATATT
1 TAATAAAAAACTTATTCAAAATATT
*
10431622 TAATAAAAAACTTATTTAAAATAT
1 TAATAAAAAACTTATTCAAAATAT
10431646 ATGAAAACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (25 bp):
TAATAAAAAACTTATTCAAAATATT
Found at i:10434736 original size:21 final size:20
Alignment explanation
Indices: 10434712--10434750 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
10434702 ATGAAAAGTG
10434712 AATTTCATATAAATTTTAATA
1 AATTTCATAT-AATTTTAATA
10434733 AATTTCATATAATTTTAA
1 AATTTCATATAATTTTAA
10434751 ATTATAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTTCATATAATTTTAATA
Found at i:10434744 original size:11 final size:11
Alignment explanation
Indices: 10434712--10434744 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
10434702 ATGAAAAGTG
10434712 AATTTCATATA
1 AATTTCATATA
*
10434723 AATTTTA-ATA
1 AATTTCATATA
10434733 AATTTCATATA
1 AATTTCATATA
10434744 A
1 A
10434745 TTTTAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (11 bp):
AATTTCATATA
Found at i:10440188 original size:8 final size:10
Alignment explanation
Indices: 10440162--10440189 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
10440152 CATTAATTTT
10440162 TTTTATATAG
1 TTTTATATAG
10440172 TTTTATATAG
1 TTTTATATAG
10440182 TTTTATAT
1 TTTTATAT
10440190 TGGGTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (10 bp):
TTTTATATAG
Found at i:10443865 original size:20 final size:21
Alignment explanation
Indices: 10443831--10443870 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
10443821 AACAAGGGCA
*
10443831 GGAAAAAACTAGAAA-GAAAT
1 GGAAAAAAATAGAAATGAAAT
*
10443851 GGAAAAAAATGGAAATGAAA
1 GGAAAAAAATAGAAATGAAA
10443871 AACTGCCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.65, C:0.03, G:0.23, T:0.10
Consensus pattern (21 bp):
GGAAAAAAATAGAAATGAAAT
Found at i:10443905 original size:20 final size:20
Alignment explanation
Indices: 10443880--10443918 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
10443870 AAACTGCCCA
10443880 TTCGTCCACACAGCAAGGAT
1 TTCGTCCACACAGCAAGGAT
*
10443900 TTCGTCCACACCGCAAGGA
1 TTCGTCCACACAGCAAGGA
10443919 AAAGATGGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.21, T:0.18
Consensus pattern (20 bp):
TTCGTCCACACAGCAAGGAT
Found at i:10445090 original size:23 final size:23
Alignment explanation
Indices: 10445047--10445090 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
10445037 TTTTTGTTAA
*
10445047 AAAAATTAAAAATTTTATTTTTT
1 AAAAATTAAAAATATTATTTTTT
*
10445070 AAAATTTAATAAATATT-TTTT
1 AAAAATTAA-AAATATTATTTT
10445091 AAAGATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AAAAATTAAAAATATTATTTTTT
Found at i:10445158 original size:25 final size:26
Alignment explanation
Indices: 10445125--10445176 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
10445115 TAAAAAATAA
* *
10445125 TATTTTAAAAAAT-AAAATATATTTT
1 TATTGTAAAAAATAAAAAAATATTTT
* *
10445150 TATTGTAAATATTAAAAAAATATTTT
1 TATTGTAAAAAATAAAAAAATATTTT
10445176 T
1 T
10445177 TAGAATTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
TATTGTAAAAAATAAAAAAATATTTT
Found at i:10445331 original size:28 final size:32
Alignment explanation
Indices: 10445295--10445366 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 32
10445285 AATAATTATT
*
10445295 TAATTTAAAATTAAA-TATT-T-TAATTTAT-A
1 TAATATAAAATTAAATTATTATCT-ATTTATAA
*
10445324 TAA-ATAAAACTAAATTATTATCTATTTATAA
1 TAATATAAAATTAAATTATTATCTATTTATAA
10445355 TAATATAAAATT
1 TAATATAAAATT
10445367 TTCTTTAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
28 9 0.26
29 7 0.20
30 7 0.20
31 5 0.14
32 7 0.20
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (32 bp):
TAATATAAAATTAAATTATTATCTATTTATAA
Found at i:10446773 original size:1 final size:1
Alignment explanation
Indices: 10446767--10446800 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
10446757 TGTCTTTCGG
10446767 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
10446801 ACATTTTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:10446964 original size:22 final size:21
Alignment explanation
Indices: 10446939--10446997 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 21
10446929 TAAAAACATG
10446939 AAAAATATATTTTTAAAATTAAA
1 AAAAATATATTTTTAAAA-T-AA
10446962 AAAAATAATATTTTT-AAAT-A
1 AAAAAT-ATATTTTTAAAATAA
10446982 AAAAATATAATTTTTA
1 AAAAATAT-ATTTTTA
10446998 TTGAAAACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
19 2 0.06
20 13 0.39
22 1 0.03
23 9 0.27
24 8 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAAATATATTTTTAAAATAA
Found at i:10446994 original size:70 final size:71
Alignment explanation
Indices: 10446909--10447074 Score: 212
Period size: 70 Copynumber: 2.3 Consensus size: 71
10446899 ACATTTAATC
* * *
10446909 GATAAAAATGTAATTTTTGTTAAAAACATGAAAAATAT-ATTTTTAAAA-TTAAAAAAAATAATA
1 GATAAAAATATAATTTTT-TTAAAAACATGAAAAATATAATTTTCAAAATTTAAAAAAAATAACA
*
10446972 TTTTTAA
65 TTTCTAA
* * *
10446979 -ATAAAAAATATAATTTTTATTGAAAACATGAAAAATATAATTTTCAAAATTTAATAAAAATGAC
1 GAT-AAAAATATAATTTTT-TTAAAAACATGAAAAATATAATTTTCAAAATTTAAAAAAAATAAC
10447043 ATTTCTAA
64 ATTTCTAA
*
10447051 GATAAAAATATAAATTTTTTAAAA
1 GATAAAAATATAATTTTTTTAAAA
10447075 GGATGATTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
69 2 0.02
70 32 0.39
71 14 0.17
72 32 0.39
73 2 0.02
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (71 bp):
GATAAAAATATAATTTTTTTAAAAACATGAAAAATATAATTTTCAAAATTTAAAAAAAATAACAT
TTCTAA
Found at i:10448001 original size:20 final size:21
Alignment explanation
Indices: 10447965--10448016 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
10447955 TCCGAAATTA
10447965 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
10447987 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
10448008 AT-AAATATT
1 ATAAAATATT
10448017 TAAAAATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:10448007 original size:21 final size:22
Alignment explanation
Indices: 10447965--10448016 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
10447955 TCCGAAATTA
10447965 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
10447987 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
10448008 AT-AAATATT
1 ATAAAATATT
10448017 TAAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:10448024 original size:30 final size:30
Alignment explanation
Indices: 10447989--10448045 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
10447979 TTTAAAATAT
* * *
10447989 AAAATATTATTTTTTAAATATAAATATTTA
1 AAAATATCATTATATAAATATAAATATTTA
*
10448019 AAAATATCATTATATAAATATATATAT
1 AAAATATCATTATATAAATATAAATAT
10448046 AAATAATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (30 bp):
AAAATATCATTATATAAATATAAATATTTA
Found at i:10450850 original size:34 final size:34
Alignment explanation
Indices: 10450812--10450877 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
10450802 TTTCAAATAT
*
10450812 TAATTCATATTTTAATCGTGGTTAAGAATGATAG
1 TAATTCATATTTTAATCGTGGTTAAAAATGATAG
*
10450846 TAATTCGTATTTTAATCGTGGTTAAAAATGAT
1 TAATTCATATTTTAATCGTGGTTAAAAATGAT
10450878 CTACTATCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (34 bp):
TAATTCATATTTTAATCGTGGTTAAAAATGATAG
Found at i:10451986 original size:15 final size:15
Alignment explanation
Indices: 10451962--10451993 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
10451952 TTTTTTACCA
10451962 AAAAAAATCTTAAAT
1 AAAAAAATCTTAAAT
*
10451977 AAAAACATCTTAAAT
1 AAAAAAATCTTAAAT
10451992 AA
1 AA
10451994 TCCCTTAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAAAAATCTTAAAT
Found at i:10452730 original size:34 final size:34
Alignment explanation
Indices: 10452692--10452762 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
10452682 TTTCTTGCAT
*
10452692 TTGGGTCAAATCCCTAAACTT-CATGTCTGATTTG
1 TTGGGTCAAATCCCTAAACTTGCA-ATCTGATTTG
*
10452726 TTGGGTTAAATCCCTAAACTTGCAATCTGATTTG
1 TTGGGTCAAATCCCTAAACTTGCAATCTGATTTG
10452760 TTG
1 TTG
10452763 TGTTTCTACC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 32 0.94
35 2 0.06
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (34 bp):
TTGGGTCAAATCCCTAAACTTGCAATCTGATTTG
Done.