Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold258
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: 5730937
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 25
Found at i:2010484 original size:20 final size:21
Alignment explanation
Indices: 2010459--2010518 Score: 56
Period size: 20 Copynumber: 2.9 Consensus size: 21
2010449 TTTTATATAA
2010459 ATATAATCATAT-TAA-AATTT
1 ATATAAT-ATATATAATAATTT
2010479 ATATAA-ATATATAATAATTT
1 ATATAATATATATAATAATTT
*
2010499 AAATAAT-TATAATAAATAAT
1 ATATAATATAT-AT-AATAAT
2010519 ATAAATATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 4 0.12
19 3 0.09
20 19 0.56
21 2 0.06
22 6 0.18
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATAATATATATAATAATTT
Found at i:2010488 original size:18 final size:18
Alignment explanation
Indices: 2010474--2010528 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
2010464 ATCATATTAA
2010474 AATTTATATAAATATATAAT
1 AATTTATAT-AA-ATATAAT
* *
2010494 AATTTAAATAATTATAAT
1 AATTTATATAAATATAAT
* *
2010512 AAATAATATAAATATAA
1 AATTTATATAAATATAA
2010529 AATCAAATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
18 19 0.66
19 2 0.07
20 8 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTTATATAAATATAAT
Found at i:2010492 original size:28 final size:28
Alignment explanation
Indices: 2010450--2010522 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
2010440 TTATTAATGT
*
2010450 TTTATAT-AA-ATATAATCATATTAAA-A
1 TTTATATAAATATATAATAAT-TTAAATA
2010476 TTTATATAAATATATAATAATTTAAATA
1 TTTATATAAATATATAATAATTTAAATA
*
2010504 ATTATAATAAATAATATAA
1 TTTAT-ATAAAT-ATATAA
2010523 ATATAAAATC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
26 7 0.17
27 7 0.17
28 14 0.35
29 6 0.15
30 6 0.15
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (28 bp):
TTTATATAAATATATAATAATTTAAATA
Found at i:2010502 original size:26 final size:25
Alignment explanation
Indices: 2010450--2010531 Score: 76
Period size: 26 Copynumber: 3.0 Consensus size: 25
2010440 TTATTAATGT
*
2010450 TTTATATAAATATAATCATATTAAAA
1 TTTATATAAATAT-ATAATATTAAAA
2010476 TTTATATAAATATATAATAATTTAAATA
1 TTTATATAAATATATAAT-A-TTAAA-A
*
2010504 ATTATAATAAATAATATAA-ATATAAAA
1 TTTAT-ATAAAT-ATATAATAT-TAAAA
2010531 T
1 T
2010532 CAAATAAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
25 4 0.09
26 14 0.30
27 7 0.15
28 10 0.21
29 6 0.13
30 6 0.13
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (25 bp):
TTTATATAAATATATAATATTAAAA
Found at i:2015447 original size:2 final size:2
Alignment explanation
Indices: 2015440--2015474 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2015430 AAGCACATCT
2015440 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2015475 ATATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2018382 original size:2 final size:2
Alignment explanation
Indices: 2018377--2018410 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2018367 GGGAAAAAAC
2018377 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
2018411 GCGCATGTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2028214 original size:17 final size:18
Alignment explanation
Indices: 2028187--2028234 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
2028177 TGCCTTCAGG
*
2028187 ATAAAAGAA-AAGTTATA
1 ATAAAAAAACAAGTTATA
2028204 ATAAAAAAAAACTAAGTTATA
1 AT--AAAAAAAC-AAGTTATA
2028225 ATAAAAAAAC
1 ATAAAAAAAC
2028235 TAAGGCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 2 0.08
19 14 0.54
21 10 0.38
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (18 bp):
ATAAAAAAACAAGTTATA
Found at i:2028230 original size:19 final size:20
Alignment explanation
Indices: 2028196--2028238 Score: 70
Period size: 19 Copynumber: 2.1 Consensus size: 20
2028186 GATAAAAGAA
2028196 AAGTTATAATAAAAAAAAACT
1 AAGTTATAAT-AAAAAAAACT
2028217 AAGTTATAAT-AAAAAAACT
1 AAGTTATAATAAAAAAAACT
2028236 AAG
1 AAG
2028239 GCAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 12 0.55
21 10 0.45
ACGTcount: A:0.65, C:0.05, G:0.07, T:0.23
Consensus pattern (20 bp):
AAGTTATAATAAAAAAAACT
Found at i:2028249 original size:19 final size:19
Alignment explanation
Indices: 2028206--2028252 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
2028196 AAGTTATAAT
** *
2028206 AAAAAAAAACTAAGTTATA
1 AAAAAAAAACTAAGGCAAA
*
2028225 ATAAAAAAACTAAGGCAAA
1 AAAAAAAAACTAAGGCAAA
2028244 AAAAAAAAA
1 AAAAAAAAA
2028253 AAGCTGATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.13
Consensus pattern (19 bp):
AAAAAAAAACTAAGGCAAA
Found at i:2029179 original size:26 final size:28
Alignment explanation
Indices: 2029119--2029180 Score: 92
Period size: 26 Copynumber: 2.3 Consensus size: 28
2029109 TTCACTATTT
**
2029119 ATAAATCTCATGCTATATCAAACTTTTG
1 ATAAATCTCATGCTATATCAAAAGTTTG
2029147 ATAAATCTCAT-CTATAT-AAAAGTTTG
1 ATAAATCTCATGCTATATCAAAAGTTTG
2029173 ATAAATCT
1 ATAAATCT
2029181 TACTTAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 15 0.47
27 6 0.19
28 11 0.34
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.39
Consensus pattern (28 bp):
ATAAATCTCATGCTATATCAAAAGTTTG
Found at i:2041188 original size:66 final size:66
Alignment explanation
Indices: 2041078--2041210 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
2041068 GATGCACATG
* * *
2041078 AGTAATTGATGTGATAGAAGGCATTCCACATCAATTAAACATCATTGCGGTGGAAAATATTAGCC
1 AGTAATTAATGTGATAGAAGGCATTCCACATCAATTAAACATCATTGCAGTGGAAAACATTAGCC
2041143 A
66 A
*
2041144 AGTAATTAATGTGATAGAAGGCATTCCACATCAATTAAATATCATTGCAGTGGAAAACATTAGCC
1 AGTAATTAATGTGATAGAAGGCATTCCACATCAATTAAACATCATTGCAGTGGAAAACATTAGCC
2041209 A
66 A
2041210 A
1 A
2041211 ATTCACTCTT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (66 bp):
AGTAATTAATGTGATAGAAGGCATTCCACATCAATTAAACATCATTGCAGTGGAAAACATTAGCC
A
Found at i:2045279 original size:18 final size:17
Alignment explanation
Indices: 2045237--2045288 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
2045227 ATTTTTAATA
2045237 AATTATAATT-TTATTAT
1 AATTATAATTATT-TTAT
* *
2045254 TATAATAATTAATTTTAT
1 AATTATAATT-ATTTTAT
2045272 AATTATAATTGATTTTA
1 AATTATAATT-ATTTTA
2045289 ATTTTACCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 8 0.29
18 18 0.64
19 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
AATTATAATTATTTTAT
Found at i:2046164 original size:4 final size:4
Alignment explanation
Indices: 2046157--2046191 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
2046147 TATATATATA
*
2046157 TATG TATG TATG TATG TCTG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
2046192 TTTTCCTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.23, C:0.03, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:2050442 original size:19 final size:18
Alignment explanation
Indices: 2050418--2050461 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
2050408 GTAGAAGATC
2050418 AAAAAAACAATAATCAAGT
1 AAAAAAACAATAATC-AGT
* * *
2050437 AAAAAAGCAATTATCATT
1 AAAAAAACAATAATCAGT
2050455 AAAAAAA
1 AAAAAAA
2050462 TTAAGAAAGC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.68, C:0.09, G:0.05, T:0.18
Consensus pattern (18 bp):
AAAAAAACAATAATCAGT
Found at i:2051982 original size:18 final size:18
Alignment explanation
Indices: 2051947--2051985 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2051937 TAATTTTATT
*
2051947 TATTAAATAAATTAATCA
1 TATTAAATAAATGAATCA
* *
2051965 TATTAAATGAATGCATCA
1 TATTAAATAAATGAATCA
2051983 TAT
1 TAT
2051986 AACTTGATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (18 bp):
TATTAAATAAATGAATCA
Found at i:2053444 original size:8 final size:7
Alignment explanation
Indices: 2053413--2053440 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
2053403 TCTCACCTTT
2053413 TTTTCCC
1 TTTTCCC
2053420 TTTTCCC
1 TTTTCCC
2053427 TTTTCCC
1 TTTTCCC
2053434 TTTTCCC
1 TTTTCCC
2053441 CTTTATTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (7 bp):
TTTTCCC
Found at i:2056958 original size:66 final size:66
Alignment explanation
Indices: 2056852--2056982 Score: 253
Period size: 66 Copynumber: 2.0 Consensus size: 66
2056842 AGGTATGCGT
*
2056852 CATGAACATAGAGTTCCATAGTATGCCATTTGCATCGCTGTATTTATGTATTTTAATTTAAACTT
1 CATGAACATAGAGTTCCATAGTATGCCATTTGCATAGCTGTATTTATGTATTTTAATTTAAACTT
2056917 G
66 G
2056918 CATGAACATAGAGTTCCATAGTATGCCATTTGCATAGCTGTATTTATGTATTTTAATTTAAACTT
1 CATGAACATAGAGTTCCATAGTATGCCATTTGCATAGCTGTATTTATGTATTTTAATTTAAACTT
2056983 TCCATTGATA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (66 bp):
CATGAACATAGAGTTCCATAGTATGCCATTTGCATAGCTGTATTTATGTATTTTAATTTAAACTT
G
Found at i:2063789 original size:2 final size:2
Alignment explanation
Indices: 2063784--2063816 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2063774 AAACAAAAAG
2063784 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2063817 AAAGAACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2067899 original size:28 final size:26
Alignment explanation
Indices: 2067872--2067960 Score: 63
Period size: 28 Copynumber: 3.2 Consensus size: 26
2067862 CAATCAAAAT
2067872 TATTATTTAATTATAAAAATATATAAA
1 TATTATTTAATTAT-AAAATATATAAA
* * **
2067899 TATTAATATAATTTTTTTTAATA-ACTAATA
1 TATT-ATTTAA--TTATAAAATATA-TAA-A
*
2067929 TTATCATTTAATTATAAAATATATAAA
1 -TATTATTTAATTATAAAATATATAAA
2067956 TATTA
1 TATTA
2067961 ATGTAAAATA
Statistics
Matches: 45, Mismatches: 10, Indels: 15
0.64 0.14 0.21
Matches are distributed among these distances:
26 4 0.09
27 5 0.11
28 16 0.36
29 8 0.18
30 9 0.20
31 3 0.07
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
TATTATTTAATTATAAAATATATAAA
Found at i:2068875 original size:2 final size:2
Alignment explanation
Indices: 2068870--2068902 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2068860 ACACTTACAG
2068870 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2068903 AAATATGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2082506 original size:21 final size:23
Alignment explanation
Indices: 2082482--2082523 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
2082472 CAATATTTAT
2082482 ATAATTTAA-T-ATTAAATAAAA
1 ATAATTTAATTAATTAAATAAAA
2082503 ATAATTTAATTAATTAAATAA
1 ATAATTTAATTAATTAAATAA
2082524 TATTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 1 0.05
23 9 0.47
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
ATAATTTAATTAATTAAATAAAA
Found at i:2082716 original size:2 final size:2
Alignment explanation
Indices: 2082709--2082746 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2082699 CTATCACCAT
* *
2082709 CA CA CA CA CA CA CA CA CA CG CG CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2082747 TATATATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.50, G:0.05, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2082751 original size:2 final size:2
Alignment explanation
Indices: 2082746--2082788 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2082736 ACACACACAC
2082746 AT AT AT 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 AT AT AT
2082788 A
1 A
2082789 AAGGAATGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2083141 original size:10 final size:9
Alignment explanation
Indices: 2083116--2083143 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2083106 CAATAAATTT
2083116 AAATTTTTA
1 AAATTTTTA
2083125 AAATTTTTA
1 AAATTTTTA
2083134 AAATTTTTA
1 AAATTTTTA
2083143 A
1 A
2083144 TTACAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
AAATTTTTA
Found at i:2083630 original size:10 final size:10
Alignment explanation
Indices: 2083602--2083631 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2083592 AAACATGTGC
*
2083602 ATATATATAT
1 ATATATATGT
2083612 ATATATATGT
1 ATATATATGT
2083622 ATATATATGT
1 ATATATATGT
2083632 GTGTGTGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (10 bp):
ATATATATGT
Found at i:2085042 original size:13 final size:13
Alignment explanation
Indices: 2085026--2085054 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2085016 TTTTTTTCCA
2085026 TTTTTTCCATTTT
1 TTTTTTCCATTTT
2085039 TTTTTTCCATTTT
1 TTTTTTCCATTTT
2085052 TTT
1 TTT
2085055 CTTCATGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTCCATTTT
Found at i:2088959 original size:52 final size:52
Alignment explanation
Indices: 2088896--2089001 Score: 176
Period size: 52 Copynumber: 2.0 Consensus size: 52
2088886 AAGAAAGCCA
* * *
2088896 TGTTGCGGAAATCCAGTTGCGATACTATAGCAAAAGCAATGTTGTATATGAT
1 TGTTGCAGAAATCCACTTGCAATACTATAGCAAAAGCAATGTTGTATATGAT
*
2088948 TGTTGCAGAAATCCACTTGCAATACTATAGCAAAAGCAATGTTGTTTATGAT
1 TGTTGCAGAAATCCACTTGCAATACTATAGCAAAAGCAATGTTGTATATGAT
2089000 TG
1 TG
2089002 GTGGGCATCC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (52 bp):
TGTTGCAGAAATCCACTTGCAATACTATAGCAAAAGCAATGTTGTATATGAT
Found at i:2089682 original size:2 final size:2
Alignment explanation
Indices: 2089675--2089713 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2089665 AGATACATAC
2089675 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2089714 GAGGACTAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2091473 original size:12 final size:13
Alignment explanation
Indices: 2091429--2091476 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 13
2091419 CGGATATCAT
*
2091429 ATTTATATATTGA
1 ATTTATATATTTA
*
2091442 ATTTA-AAATTT-
1 ATTTATATATTTA
2091453 ATTTATATATTTA
1 ATTTATATATTTA
2091466 ATTT-TATATTT
1 ATTTATATATTT
2091477 TTATTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 5 0.17
12 16 0.53
13 9 0.30
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (13 bp):
ATTTATATATTTA
Found at i:2091951 original size:12 final size:12
Alignment explanation
Indices: 2091934--2091959 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2091924 TCAGAATGAA
2091934 ATAGAAAATAAT
1 ATAGAAAATAAT
2091946 ATAGAAAATAAT
1 ATAGAAAATAAT
2091958 AT
1 AT
2091960 GGAACTAGTT
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:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (12 bp):
ATAGAAAATAAT
Found at i:2092467 original size:26 final size:26
Alignment explanation
Indices: 2092448--2092505 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
2092438 TTATAATACT
*
2092448 TTTTGATATAGATATTTTATAAAATA
1 TTTTGATATAAATATTTTATAAAATA
*
2092474 TTTTGATATAAATATTTTGATACTAATA
1 TTTTGATATAAATATTTT-ATA-AAATA
2092502 TTTT
1 TTTT
2092506 TTTCAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 17 0.61
27 3 0.11
28 8 0.29
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (26 bp):
TTTTGATATAAATATTTTATAAAATA
Found at i:2092488 original size:14 final size:14
Alignment explanation
Indices: 2092448--2092505 Score: 77
Period size: 14 Copynumber: 4.3 Consensus size: 14
2092438 TTATAATACT
*
2092448 TTTTGATATAGATA
1 TTTTGATATAAATA
2092462 TTTT-ATA-AAATA
1 TTTTGATATAAATA
2092474 TTTTGATATAAATA
1 TTTTGATATAAATA
2092488 TTTTGATACT-AATA
1 TTTTGATA-TAAATA
2092502 TTTT
1 TTTT
2092506 TTTCAAAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
12 8 0.20
13 6 0.15
14 25 0.62
15 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (14 bp):
TTTTGATATAAATA
Found at i:2095054 original size:67 final size:66
Alignment explanation
Indices: 2094965--2095280 Score: 260
Period size: 67 Copynumber: 4.7 Consensus size: 66
2094955 CTCCCCAATG
* * * * *
2094965 CAAGTACTATTAAT-AAAGAAGTCGACTGTTGTGATCTCCTGCGGCACTCCCATCACTCTCTCAT
1 CAAGTACTCTTAATGGAA-AAGTCGA-TGTTGTGGTCTCATGCGCCACTCCCATCACTCTCTCAT
2095029 TTA
64 TTA
* * * *
2095032 CAAGTATTCTTAATGGAAAAGTCGATTGTTGTGGTCTCATGCACCACTCCCGTCACTCTTTCATT
1 CAAGTACTCTTAATGGAAAAGTCGA-TGTTGTGGTCTCATGCGCCACTCCCATCACTCTCTCATT
*
2095097 TG
65 TA
* * * * *
2095099 CAAGTAGTCTTAATGGAGAAGTTGATCGTTGTGGTCTCTTACGCCACTCCCATCACTCTCTCATT
1 CAAGTACTCTTAATGGAAAAGTCGAT-GTTGTGGTCTCATGCGCCACTCCCATCACTCTCTCATT
2095164 TA
65 TA
* * * * * * * * *
2095166 CAAATACACTTAATGGATAAGTCAGCCT-TTATGGTCTCATGCACCATTCCCTTCACTCTCTTAT
1 CAAGTACTCTTAATGGAAAAGTC-G-ATGTTGTGGTCTCATGCGCCACTCCCATCACTCTCTCAT
2095230 TTA
64 TTA
* * * ** * *
2095233 CAAATGCAT-TTAATGGAGAAGTCGACCATTGTGGTTTCATGTGCCACT
1 CAAGTAC-TCTTAATGGAAAAGTCGA-TGTTGTGGTCTCATGCGCCACT
2095281 TCTGTCACTC
Statistics
Matches: 199, Mismatches: 43, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
66 2 0.01
67 193 0.97
68 3 0.02
69 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (66 bp):
CAAGTACTCTTAATGGAAAAGTCGATGTTGTGGTCTCATGCGCCACTCCCATCACTCTCTCATTT
A
Found at i:2095265 original size:134 final size:134
Alignment explanation
Indices: 2094981--2095267 Score: 339
Period size: 134 Copynumber: 2.1 Consensus size: 134
2094971 CTATTAATAA
* * * * * **
2094981 AGAAGTCGACTGTTGTGATCTCCTGCGGCACTCCCATCACTCTCTCATTTACAAGTATTCTTAAT
1 AGAAGTCGACCGTTGTGGTCTCCTACGCCACTCCCATCACTCTCTCATTTACAAATACACTTAAT
* * * *
2095046 GGAAAAGTCGATTGTTGTGGTCTCATGCACCACTCCCGTCACTCTTTCATTTGCAAGTAGTCTTA
66 GGAAAAGTCGACTGTTATGGTCTCATGCACCACTCCCGTCACTCTTTCATTTACAAGCAGTCTTA
2095111 ATGG
131 ATGG
* * *
2095115 AGAAGTTGATCGTTGTGGTCTCTTACGCCACTCCCATCACTCTCTCATTTACAAATACACTTAAT
1 AGAAGTCGACCGTTGTGGTCTCCTACGCCACTCCCATCACTCTCTCATTTACAAATACACTTAAT
* * * *
2095180 GGATAAGTCAGCCT-TTATGGTCTCATGCACCATTCCCTTCACTCTCTT-ATTTACAAATGCA-T
66 GGAAAAGTC-GACTGTTATGGTCTCATGCACCACTCCCGTCACTCT-TTCATTTAC-AA-GCAGT
2095242 -TTAATGG
127 CTTAATGG
*
2095249 AGAAGTCGACCATTGTGGT
1 AGAAGTCGACCGTTGTGGT
2095268 TTCATGTGCC
Statistics
Matches: 128, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
134 119 0.93
135 7 0.05
136 2 0.02
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (134 bp):
AGAAGTCGACCGTTGTGGTCTCCTACGCCACTCCCATCACTCTCTCATTTACAAATACACTTAAT
GGAAAAGTCGACTGTTATGGTCTCATGCACCACTCCCGTCACTCTTTCATTTACAAGCAGTCTTA
ATGG
Found at i:2095427 original size:64 final size:64
Alignment explanation
Indices: 2095352--2095498 Score: 152
Period size: 66 Copynumber: 2.3 Consensus size: 64
2095342 CGACATTTCC
* * * * * * * *
2095352 GTCATTCTCTTTAATACAAGTATTCTTATTAGAGAAG-ATTGTTATGGTCATGTGCGTCACTTCT
1 GTCACTCTCTTTAATACAAATACTATTAAT-GAGAAGAACTGTTATGGTCATGTACGCCACTTCT
* * * *
2095416 GTCACTTTCTTTATTACAAATACTATTAATGAGAAGTCAACTGTTATGGTCTTGTACGCCACTTT
1 GTCACTCTCTTTAATACAAATACTATTAATGAGAAG--AACTGTTATGGTCATGTACGCCACTTC
2095481 T
64 T
2095482 GTCACTCTCTTTAATAC
1 GTCACTCTCTTTAATAC
2095499 TGTTATGGTC
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
63 6 0.09
64 23 0.35
66 37 0.56
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.41
Consensus pattern (64 bp):
GTCACTCTCTTTAATACAAATACTATTAATGAGAAGAACTGTTATGGTCATGTACGCCACTTCT
Found at i:2106036 original size:3 final size:3
Alignment explanation
Indices: 2106028--2106061 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2106018 CCTGCCTCCC
2106028 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
2106062 CCTGCTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:2108763 original size:5 final size:5
Alignment explanation
Indices: 2108753--2108794 Score: 57
Period size: 5 Copynumber: 8.0 Consensus size: 5
2108743 CATTATCCGA
*
2108753 TAAAT TAAAT TAAAT TAAAT TAAATT TATAT TAAATT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAA-T TAAAT TAAA-T TAAAT
2108795 ATTAATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 24 0.73
6 9 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (5 bp):
TAAAT
Found at i:2108787 original size:11 final size:11
Alignment explanation
Indices: 2108753--2108794 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
2108743 CATTATCCGA
2108753 TAAA-TTAAAT
1 TAAATTTAAAT
2108763 TAAA-TTAAAT
1 TAAATTTAAAT
*
2108773 TAAATTTATAT
1 TAAATTTAAAT
2108784 TAAATTTAAAT
1 TAAATTTAAAT
2108795 ATTAATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
10 14 0.48
11 15 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TAAATTTAAAT
Found at i:2109007 original size:3 final size:3
Alignment explanation
Indices: 2109001--2109029 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2108991 ATTATAGCAT
2109001 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2109030 TAAACGAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2122640 original size:3 final size:3
Alignment explanation
Indices: 2122632--2122663 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2122622 GCAAATGAAA
*
2122632 AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2122664 ATATGAGACA
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:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2130637 original size:6 final size:6
Alignment explanation
Indices: 2130626--2130668 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
2130616 ACCAAATTCT
*
2130626 TTACAA TTACAA TTACAA TTACAA TTACAA TTATAA TTA-AA TT
1 TTACAA TTACAA TTACAA TTACAA TTACAA TTACAA TTACAA TT
2130669 GCATTTAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
5 4 0.11
6 32 0.89
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.40
Consensus pattern (6 bp):
TTACAA
Found at i:2134319 original size:18 final size:18
Alignment explanation
Indices: 2134296--2134342 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
2134286 AATTATTATT
*
2134296 TAATATATATATAATATA
1 TAATATATATATAATAAA
* *
2134314 TAATATTTTTATAATAAA
1 TAATATATATATAATAAA
2134332 TAATATATATA
1 TAATATATATA
2134343 AAAAACTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATATATATATAATAAA
Found at i:2134320 original size:25 final size:25
Alignment explanation
Indices: 2134274--2134340 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
2134264 TATATTAAAA
* *
2134274 ATAATAAATAA-AAATTATTATTTA-
1 ATAATAAATAATATA-TAATATTTAT
* *
2134298 ATATATATATAATATATAATATTTTT
1 ATA-ATAAATAATATATAATATTTAT
2134324 ATAATAAATAATATATA
1 ATAATAAATAATATATA
2134341 TAAAAAACTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
24 3 0.09
25 27 0.77
26 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
ATAATAAATAATATATAATATTTAT
Found at i:2134561 original size:16 final size:16
Alignment explanation
Indices: 2134540--2134585 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
2134530 AATTATTATT
2134540 TAATATATATATAATA
1 TAATATATATATAATA
* *
2134556 TAATATTTTTATAATA
1 TAATATATATATAATA
2134572 -AATAATATATATAA
1 TAAT-ATATATATAA
2134586 AAAACTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 3 0.12
16 22 0.88
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAATATATATATAATA
Found at i:2134576 original size:23 final size:26
Alignment explanation
Indices: 2134517--2134580 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 26
2134507 ATATATTAAA
2134517 AATAATAAATAA-A-AATTATTATTT
1 AATAATAAATAATATAATTATTATTT
*
2134541 AATATATATATAATATAA-TATT-TTT
1 AATA-ATAAATAATATAATTATTATTT
2134566 -ATAATAAATAATATA
1 AATAATAAATAATATA
2134581 TATAAAAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
23 11 0.31
24 7 0.20
25 10 0.29
26 5 0.14
27 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AATAATAAATAATATAATTATTATTT
Found at i:2134648 original size:242 final size:244
Alignment explanation
Indices: 2134221--2134711 Score: 959
Period size: 242 Copynumber: 2.0 Consensus size: 244
2134211 AGTGTCTTAA
2134221 AATTATTTTTGTAGGATTATTATTTAGTAATATTTTTATTTAATATATTAAAAATAATAAATAAA
1 AATTATTTTTGTAGGATTATTATTTAGTAATATTTTTATTTAATATATTAAAAATAATAAATAAA
2134286 AATTATTATTTAATATATATATAATATATAATATTTTTATAATAAATAATATATATAAAAAACTT
66 AATTATTATTTAATATATATATAATATATAATATTTTTATAATAAATAATATATATAAAAAACTT
2134351 TAAAAAAATATCCTAAAAACAATTACTGACAAATGCCTATATATAATATACCATTCAGTATCATA
131 TAAAAAAATATCCTAAAAACAATTACTGACAAATGCCTATATATAATATACCATTCAGTATCATA
2134416 CGATTATATTATTATTTGTACCATCCAAATTAACATATGTCATGCTTTG
196 CGATTATATTATTATTTGTACCATCCAAATTAACATATGTCATGCTTTG
2134465 AATTATTTTTGTAGGATTATTATTTAGTAATATTTTTATTTAATATATTAAAAATAATAAATAAA
1 AATTATTTTTGTAGGATTATTATTTAGTAATATTTTTATTTAATATATTAAAAATAATAAATAAA
2134530 AATTATTATTTAATATATATAT-A-ATATAATATTTTTATAATAAATAATATATATAAAAAACTT
66 AATTATTATTTAATATATATATAATATATAATATTTTTATAATAAATAATATATATAAAAAACTT
*
2134593 TAAAAATATATCCTAAAAACAATTACTGACAAATGCCTATATATAATATACCATTCAGTATCATA
131 TAAAAAAATATCCTAAAAACAATTACTGACAAATGCCTATATATAATATACCATTCAGTATCATA
2134658 CGATTATATTATTATTTGTACCATCCAAATTAACATATGTCATGCTTTG
196 CGATTATATTATTATTTGTACCATCCAAATTAACATATGTCATGCTTTG
2134707 AATTA
1 AATTA
2134712 CTCCAACAAC
Statistics
Matches: 246, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
242 158 0.64
243 1 0.00
244 87 0.35
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (244 bp):
AATTATTTTTGTAGGATTATTATTTAGTAATATTTTTATTTAATATATTAAAAATAATAAATAAA
AATTATTATTTAATATATATATAATATATAATATTTTTATAATAAATAATATATATAAAAAACTT
TAAAAAAATATCCTAAAAACAATTACTGACAAATGCCTATATATAATATACCATTCAGTATCATA
CGATTATATTATTATTTGTACCATCCAAATTAACATATGTCATGCTTTG
Found at i:2139312 original size:50 final size:50
Alignment explanation
Indices: 2139209--2139519 Score: 417
Period size: 50 Copynumber: 6.2 Consensus size: 50
2139199 CAAGTGGGAG
* * **
2139209 AATTGTTGACTATTCTTCACCAACCTTTGACAATTGAGAGAGATGGTCAT
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCAT
* * *
2139259 AATTGTTGACTATTCTTCACCAA-CTTTCGACGATCGAGAAAGGTGACCGT
1 AATTGTTGACTATTCTTCACCAACCTTT-GACAATCGAGAGAGGTGACCAT
* * * *
2139309 AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAAAGATGGCCAT
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCAT
*
2139359 AATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGT
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCAT
* * ***
2139409 AATTGTTGACTATTCTTTACCAATCTTTGACAATCGAGAGAGGTGGTTAT
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCAT
* * * *
2139459 AATTGTTGACTATTCTTTACCAACTTTTGAAAATCGAGAGAGGTGACCGT
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCAT
2139509 AATTGTTGACT
1 AATTGTTGACT
2139520 TTAAGCAACT
Statistics
Matches: 229, Mismatches: 30, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
49 4 0.02
50 221 0.97
51 4 0.02
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (50 bp):
AATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCAT
Found at i:2139382 original size:100 final size:99
Alignment explanation
Indices: 2139209--2139519 Score: 487
Period size: 100 Copynumber: 3.1 Consensus size: 99
2139199 CAAGTGGGAG
*
2139209 AATTGTTGACTATTCTTCACCAACCTTTGACAATTGAGAGAGATGGTCATAATTGTTGACTATTC
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGATGGTCATAATTGTTGACTATTC
* *
2139274 TTCACCAACTTTCGACGATCGAGAAAGGTGACCGT
66 TTCACCAACTTT-GACAATCGAGAGAGGTGACCGT
* *
2139309 AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAAAGATGGCCATAATTGTTGACTATTC
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGATGGTCATAATTGTTGACTATTC
2139374 TTCACCAACCTTTGACAATCGAGAGAGGTGACCGT
66 TTCACCAA-CTTTGACAATCGAGAGAGGTGACCGT
* * * * *
2139409 AATTGTTGACTATTCTTTACCAATCTTTGACAATCGAGAGAGGTGGTTATAATTGTTGACTATTC
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGATGGTCATAATTGTTGACTATTC
* *
2139474 TTTACCAACTTTTGAAAATCGAGAGAGGTGACCGT
66 TTCACCAAC-TTTGACAATCGAGAGAGGTGACCGT
2139509 AATTGTTGACT
1 AATTGTTGACT
2139520 TTAAGCAACT
Statistics
Matches: 195, Mismatches: 14, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
99 1 0.01
100 190 0.97
101 4 0.02
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (99 bp):
AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGATGGTCATAATTGTTGACTATTC
TTCACCAACTTTGACAATCGAGAGAGGTGACCGT
Found at i:2139836 original size:2 final size:2
Alignment explanation
Indices: 2139829--2139860 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2139819 TGGCTTTGGC
2139829 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
2139861 TTGTTTGTTT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2140577 original size:23 final size:22
Alignment explanation
Indices: 2140512--2140583 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 22
2140502 TTATTATTTA
2140512 ATTATAAA-AATATA-AATAATT
1 ATTA-AAATAATATATAATAATT
*
2140533 ATTAAAATAAT-TATTATTTAATT
1 ATTAAAATAATATA-TA-ATAATT
* *
2140556 ATTACATATAATATATAATAATA
1 ATTA-AAATAATATATAATAATT
2140579 ATTAA
1 ATTAA
2140584 CATTCTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
20 5 0.12
21 7 0.17
22 2 0.05
23 17 0.41
24 8 0.20
25 2 0.05
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTAAAATAATATATAATAATT
Found at i:2141132 original size:19 final size:19
Alignment explanation
Indices: 2141108--2141147 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2141098 ATGTCTTATT
*
2141108 TTTTTAAT-TAATTTTAAAA
1 TTTTTAATAT-ATTCTAAAA
2141127 TTTTTAATATATTCTAAAA
1 TTTTTAATATATTCTAAAA
2141146 TT
1 TT
2141148 ATGTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTTAATATATTCTAAAA
Found at i:2142034 original size:23 final size:23
Alignment explanation
Indices: 2142008--2142057 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2141998 AAAATTTAAA
* *
2142008 ATTTATTATTTATATAT-TTTTTT
1 ATTTATAAATTATAT-TATTTTTT
*
2142031 ATTTGTAAATTATATTATTTTTT
1 ATTTATAAATTATATTATTTTTT
2142054 ATTT
1 ATTT
2142058 CGAGAAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (23 bp):
ATTTATAAATTATATTATTTTTT
Found at i:2142048 original size:16 final size:15
Alignment explanation
Indices: 2141980--2142050 Score: 63
Period size: 16 Copynumber: 4.6 Consensus size: 15
2141970 CTTAAAAAAA
2141980 TTATTATTTAATAAAT
1 TTATTATTT-ATAAAT
**
2141996 TTAAAATTTA-AAAT
1 TTATTATTTATAAAT
*
2142010 TTATTATTTATATATT
1 TTATTATTTATA-AAT
* *
2142026 TTTTTATTTGTAAAT
1 TTATTATTTATAAAT
2142041 TATATTATTT
1 T-TATTATTT
2142051 TTTATTTCGA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
14 12 0.28
15 5 0.12
16 26 0.60
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (15 bp):
TTATTATTTATAAAT
Found at i:2148270 original size:42 final size:42
Alignment explanation
Indices: 2148075--2148260 Score: 266
Period size: 42 Copynumber: 4.4 Consensus size: 42
2148065 TCATTGCCAT
* * *
2148075 CTTCTCCGGCCAAG-CAAGTGGCAACTATTGGCTCTGTTCCTA
1 CTTCTCCGGCCAAGAC-AGTGGCAACTACTGCCTCTGTTCCAA
*
2148117 CTTCTCCGGCAAAGACAGTGGCAACTACTGCCTCTGTTCCAA
1 CTTCTCCGGCCAAGACAGTGGCAACTACTGCCTCTGTTCCAA
*
2148159 CTTCTCCGGTCAAGACAGTGGCAACTACTGCCTCTGTTCCAA
1 CTTCTCCGGCCAAGACAGTGGCAACTACTGCCTCTGTTCCAA
* * * *
2148201 CTTCTCCGGCCAAGACGGTGGCAACTACTGTCTCTGTACCCA
1 CTTCTCCGGCCAAGACAGTGGCAACTACTGCCTCTGTTCCAA
*
2148243 CTTCTCCAGCCAAGACAG
1 CTTCTCCGGCCAAGACAG
2148261 CCCCAACTAC
Statistics
Matches: 130, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
42 129 0.99
43 1 0.01
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.25
Consensus pattern (42 bp):
CTTCTCCGGCCAAGACAGTGGCAACTACTGCCTCTGTTCCAA
Found at i:2159264 original size:7 final size:7
Alignment explanation
Indices: 2159242--2159296 Score: 56
Period size: 7 Copynumber: 7.7 Consensus size: 7
2159232 TCAATTGATA
*
2159242 TTTTACT
1 TTTTATT
*
2159249 TTGTATT
1 TTTTATT
2159256 TTTTATT
1 TTTTATT
2159263 TTTTATT
1 TTTTATT
*
2159270 TATTTAGT
1 T-TTTATT
*
2159278 TTTTACT
1 TTTTATT
*
2159285 TTTCATT
1 TTTTATT
2159292 TTTTA
1 TTTTA
2159297 AAAATAAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
7 33 0.85
8 6 0.15
ACGTcount: A:0.16, C:0.05, G:0.04, T:0.75
Consensus pattern (7 bp):
TTTTATT
Found at i:2159287 original size:22 final size:21
Alignment explanation
Indices: 2159255--2159296 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2159245 TACTTTGTAT
* *
2159255 TTTTTATTTTTTATTTATTTAG
1 TTTTTACTTTTCATTT-TTTAG
2159277 TTTTTACTTTTCATTTTTTA
1 TTTTTACTTTTCATTTTTTA
2159297 AAAATAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTTACTTTTCATTTTTTAG
Found at i:2160012 original size:2 final size:2
Alignment explanation
Indices: 2159999--2160053 Score: 101
Period size: 2 Copynumber: 27.0 Consensus size: 2
2159989 AGAGATTCCC
2159999 AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2160042 AT AT AT AT AT AT
1 AT AT AT AT AT AT
2160054 TATGAAAACT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 50 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2160420 original size:2 final size:2
Alignment explanation
Indices: 2160413--2160452 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2160403 TGGGTATATG
2160413 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2160453 ATATATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2164641 original size:25 final size:22
Alignment explanation
Indices: 2164610--2164687 Score: 66
Period size: 24 Copynumber: 3.3 Consensus size: 22
2164600 TAAAATAATT
*
2164610 TTAAAATTAATAAATAAATTATA
1 TTAAAAATAATAAATAAA-TATA
*
2164633 TCTATAAATAATAAAAATAAATATA
1 T-TAAAAATAAT--AAATAAATATA
* *
2164658 TTAAAAAATAATAAATCGAATATC
1 TT-AAAAATAATAAAT-AAATATA
2164682 TTAAAA
1 TTAAAA
2164688 TCGGTTTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
23 9 0.20
24 16 0.36
25 13 0.29
26 7 0.16
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (22 bp):
TTAAAAATAATAAATAAATATA
Found at i:2165445 original size:2 final size:2
Alignment explanation
Indices: 2165433--2165484 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
2165423 TTGCCTTGCA
*
2165433 AT AT GT 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 AT AT AT
2165475 AT AT AT AT AT
1 AT AT AT AT AT
2165485 TACTAAATAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2165558 original size:3 final size:3
Alignment explanation
Indices: 2165550--2165583 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2165540 TTCTTATAAA
2165550 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2165584 TTACATAGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2165660 original size:19 final size:18
Alignment explanation
Indices: 2165638--2165680 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
2165628 TCAAATTTTT
* *
2165638 ATTTAATTTCAAGATTTAA
1 ATTTAATTT-AAAATATAA
2165657 ATTTAAATTTAAAATATAA
1 ATTT-AATTTAAAATATAA
2165676 ATTTA
1 ATTTA
2165681 CGATGAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 15 0.71
20 5 0.24
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTTAATTTAAAATATAA
Found at i:2167288 original size:3 final size:3
Alignment explanation
Indices: 2167280--2167318 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2167270 TGATATAGAT
2167280 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2167319 AAAAATGACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2171508 original size:3 final size:3
Alignment explanation
Indices: 2171502--2171527 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2171492 CCTAAATAAT
2171502 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
2171528 TAATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:2171532 original size:3 final size:3
Alignment explanation
Indices: 2171526--2171561 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2171516 CAACAACAAC
2171526 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2171562 GTTAATGTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2172275 original size:3 final size:3
Alignment explanation
Indices: 2172269--2172294 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2172259 TATTATTATT
2172269 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
2172295 TCGGAATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2179932 original size:2 final size:2
Alignment explanation
Indices: 2179925--2179967 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2179915 TACAACCAAC
2179925 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2179967 T
1 T
2179968 CCTTGTTTCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2183472 original size:2 final size:2
Alignment explanation
Indices: 2183465--2183502 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2183455 CTGTCTGCCC
2183465 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2183503 GTCCAGACCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2184725 original size:33 final size:32
Alignment explanation
Indices: 2184662--2184722 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
2184652 AAAAATTTTG
* *
2184662 AAAATAATATTTATTTAAATATTATTAAATTA
1 AAAATAAGATTAATTTAAATATTATTAAATTA
*
2184694 AAAATAAGATTAATTTTTAATATT-TTAAA
1 AAAATAAGATTAA-TTTAAATATTATTAAA
2184723 ATTTAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 16 0.64
33 9 0.36
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (32 bp):
AAAATAAGATTAATTTAAATATTATTAAATTA
Found at i:2185223 original size:23 final size:24
Alignment explanation
Indices: 2185180--2185228 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
2185170 TTAGTATATA
2185180 TTAATTG-TATTTTTCTATTTTGT
1 TTAATTGTTATTTTTCTATTTTGT
* *
2185203 TTAATTGATT-TTTTTTTTTTTTGT
1 TTAATTG-TTATTTTTCTATTTTGT
2185227 TT
1 TT
2185229 TAGTGAGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 7 0.32
24 14 0.64
25 1 0.05
ACGTcount: A:0.14, C:0.02, G:0.08, T:0.76
Consensus pattern (24 bp):
TTAATTGTTATTTTTCTATTTTGT
Found at i:2186185 original size:22 final size:21
Alignment explanation
Indices: 2186148--2186191 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
2186138 TTACTTTTAC
* *
2186148 AAAATTAATTAATAAATTATA
1 AAAATTAACTAATAAATAATA
2186169 AAAATTATACTAATAAATAATA
1 AAAATTA-ACTAATAAATAATA
2186191 A
1 A
2186192 TTAAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAATTAACTAATAAATAATA
Found at i:2186698 original size:25 final size:24
Alignment explanation
Indices: 2186670--2186718 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2186660 ATAATCAACT
*
2186670 TCTATATATTTTAAATTTTTTATAC
1 TCTATATA-ATTAAATTTTTTATAC
*
2186695 TCTATCTAATTAAATTTTTTATAC
1 TCTATATAATTAAATTTTTTATAC
2186719 AAATCAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (24 bp):
TCTATATAATTAAATTTTTTATAC
Found at i:2190597 original size:2 final size:2
Alignment explanation
Indices: 2190590--2190631 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2190580 AAATATAAAG
2190590 AT AT AT 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 AT AT AT
2190632 TTCTTTTGGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2191729 original size:101 final size:101
Alignment explanation
Indices: 2191554--2191749 Score: 254
Period size: 101 Copynumber: 1.9 Consensus size: 101
2191544 AGGGCCGTGC
* * * * *
2191554 TTTGATGAATTCTTGAAGCCCTAAGTCCACATTTTTCTCTAGAATGATTGATCTGTTTTGCGTAT
1 TTTGATGAATTCTTGAAGCCCTAAGTCCACAATTTTCCCTAGAATGATTGACCTCTTTTACGTAT
*
2191619 AGCTTTGACC-AAGACTCCCAAAAAGTTTTAGCCACG
66 AGCATTGACCAAAGACT-CCAAAAAGTTTTAGCCACG
* * *
2191655 TTTGATGAATTCTTGAAGCCCTAAAG-CCACAATTTTCCCTAGAATGGTTGGCCTCTTTTATGTA
1 TTTGATGAATTCTTGAAGCCCT-AAGTCCACAATTTTCCCTAGAATGATTGACCTCTTTTACGTA
*
2191719 TAAG-ATTGACCAAAGACTCCAAAACGTTTTA
65 T-AGCATTGACCAAAGACTCCAAAAAGTTTTA
2191750 ATGCATTTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
101 71 0.87
102 11 0.13
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (101 bp):
TTTGATGAATTCTTGAAGCCCTAAGTCCACAATTTTCCCTAGAATGATTGACCTCTTTTACGTAT
AGCATTGACCAAAGACTCCAAAAAGTTTTAGCCACG
Found at i:2197477 original size:15 final size:14
Alignment explanation
Indices: 2197455--2197499 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
2197445 AATTATCATA
2197455 TATT-TTATTTTTT
1 TATTATTATTTTTT
2197468 TATTAATTATTTTTT
1 TATT-ATTATTTTTT
*
2197483 TATTTTTAATTTTTT
1 TATTATT-ATTTTTT
2197498 TA
1 TA
2197500 AGGGGTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 4 0.14
14 2 0.07
15 22 0.79
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TATTATTATTTTTT
Found at i:2206048 original size:25 final size:25
Alignment explanation
Indices: 2206015--2206082 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
2206005 TATTTTATAT
* *
2206015 TTAAATTAAAAAATTAATTATAAAA-
1 TTAATTTAAAAAATTAATCA-AAAAC
*
2206040 TTAATTTAAAAAATTTATCAAAAAC
1 TTAATTTAAAAAATTAATCAAAAAC
2206065 TTAATTTAAATAAATTAA
1 TTAATTTAAA-AAATTAA
2206083 ATTTATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 4 0.11
25 27 0.73
26 6 0.16
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (25 bp):
TTAATTTAAAAAATTAATCAAAAAC
Found at i:2206052 original size:13 final size:13
Alignment explanation
Indices: 2206015--2206087 Score: 69
Period size: 12 Copynumber: 5.6 Consensus size: 13
2206005 TATTTTATAT
*
2206015 TTAAATTAAAAAA
1 TTAATTTAAAAAA
*
2206028 TTAA-TTATAAAA
1 TTAATTTAAAAAA
2206040 TTAATTTAAAAAA
1 TTAATTTAAAAAA
* * *
2206053 TTTA-TCAAAAAC
1 TTAATTTAAAAAA
2206065 TTAATTTAAATAAA
1 TTAATTTAAA-AAA
2206079 TTAAATTTA
1 TT-AATTTA
2206088 TTAAATTAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
12 20 0.42
13 18 0.38
14 4 0.08
15 6 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.40
Consensus pattern (13 bp):
TTAATTTAAAAAA
Found at i:2206377 original size:19 final size:17
Alignment explanation
Indices: 2206353--2206400 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 17
2206343 CTTTGGTAAA
2206353 AATATAATTAATAAATAAT
1 AATATAATTAATAAAT--T
*
2206372 AATATAATTATTAAATT
1 AATATAATTAATAAATT
2206389 AATTATAATTAA
1 AA-TATAATTAA
2206401 AATTATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 3 0.12
18 8 0.31
19 15 0.58
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATATAATTAATAAATT
Found at i:2206927 original size:2 final size:2
Alignment explanation
Indices: 2206920--2206959 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2206910 TGTTCCATTG
2206920 AT AT 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 AT AT
2206960 CGGGAAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2207862 original size:2 final size:2
Alignment explanation
Indices: 2207855--2207883 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2207845 AAAACCTAAT
2207855 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
2207884 GAAAGGATGC
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:2209177 original size:2 final size:2
Alignment explanation
Indices: 2209170--2209206 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2209160 ATTTCTTTAC
2209170 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2209207 GCTTGAGTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2212196 original size:2 final size:2
Alignment explanation
Indices: 2212189--2212220 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2212179 CCACAAATTG
*
2212189 AT AT AT AT AT AC 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
2212221 CAACTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2212710 original size:17 final size:17
Alignment explanation
Indices: 2212669--2212712 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2212659 ATAGAAATAT
* * *
2212669 AATTTTTTAATTTATTA
1 AATTATTTATTTTATAA
2212686 AA-TATTTATTTTATAA
1 AATTATTTATTTTATAA
2212702 AATTATTTATT
1 AATTATTTATT
2212713 ATAATTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTATTTATTTTATAA
Found at i:2212710 original size:28 final size:28
Alignment explanation
Indices: 2212678--2212733 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
2212668 TAATTTTTTA
2212678 ATTTATTA-AATATTTATTTTATAAAATT
1 ATTTATTATAAT-TTTATTTTATAAAATT
*
2212706 ATTTATTATAATTTTATTTTGTAAAATT
1 ATTTATTATAATTTTATTTTATAAAATT
2212734 TTAAAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (28 bp):
ATTTATTATAATTTTATTTTATAAAATT
Found at i:2212749 original size:28 final size:29
Alignment explanation
Indices: 2212686--2212749 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
2212676 TAATTTATTA
**
2212686 AATATTTATTTTATAAAATTATTTATTAT
1 AATATTTATTTTATAAAATTATTTAAAAT
*
2212715 AAT-TTTATTTTGTAAAA-T-TTTAAAAT
1 AATATTTATTTTATAAAATTATTTAAAAT
2212741 AATTATTTA
1 AA-TATTTA
2212750 GTGTTTTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 8 0.27
27 2 0.07
28 17 0.57
29 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (29 bp):
AATATTTATTTTATAAAATTATTTAAAAT
Found at i:2212830 original size:21 final size:20
Alignment explanation
Indices: 2212781--2212841 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
2212771 TATTTTGATC
*
2212781 TTATAAAAAATATAAAATTATT
1 TTAT-AAAAATTTAAAATT-TT
2212803 TTA-AAAAATTTAAAATTTT
1 TTATAAAAATTTAAAATTTT
2212822 TTATCAAAAATTT-AAATTTT
1 TTAT-AAAAATTTAAAATTTT
2212842 ATAATATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 5 0.14
20 20 0.56
21 8 0.22
22 3 0.08
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
TTATAAAAATTTAAAATTTT
Found at i:2213732 original size:19 final size:18
Alignment explanation
Indices: 2213695--2213739 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
2213685 TAATTTTTTT
2213695 AATTATAATTTTTACAAA
1 AATTATAATTTTTACAAA
*
2213713 AATTAATAACTTTTTAAAAAA
1 AATT-ATAA-TTTTT-ACAAA
2213734 AATTAT
1 AATTAT
2213740 CTACTTGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 7 0.30
21 8 0.35
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTATAATTTTTACAAA
Found at i:2213738 original size:21 final size:19
Alignment explanation
Indices: 2213695--2213734 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
2213685 TAATTTTTTT
*
2213695 AATT-ATAATTTTTACAAA
1 AATTAATAATTTTTAAAAA
2213713 AATTAATAACTTTTTAAAAA
1 AATTAATAA-TTTTTAAAAA
2213733 AA
1 AA
2213735 ATTATCTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 4 0.21
20 11 0.58
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTAATAATTTTTAAAAA
Found at i:2213796 original size:41 final size:41
Alignment explanation
Indices: 2213751--2213830 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
2213741 TACTTGTTTG
*
2213751 AAAAATTACTACT-CGCAAGAAAATATTTTTAGTTTTTTTAA
1 AAAAATTACTA-TACGCAAGAAAATATTTTTACTTTTTTTAA
*
2213792 AAAAATTACTATACGTAAGAAAATATTTTTACTTTTTTT
1 AAAAATTACTATACGCAAGAAAATATTTTTACTTTTTTT
2213831 TCTAAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 1 0.03
41 35 0.97
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (41 bp):
AAAAATTACTATACGCAAGAAAATATTTTTACTTTTTTTAA
Found at i:2218890 original size:2 final size:2
Alignment explanation
Indices: 2218883--2218921 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2218873 GTTTATGCCT
2218883 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2218922 AAGATTATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2219140 original size:2 final size:2
Alignment explanation
Indices: 2219133--2219185 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
2219123 GGGACAAGAC
2219133 AT AT AT 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 AT AT AT
2219175 AT AT AT AT AT A
1 AT AT AT AT AT A
2219186 GCTTTCTTGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2220333 original size:20 final size:20
Alignment explanation
Indices: 2220310--2220389 Score: 67
Period size: 22 Copynumber: 4.0 Consensus size: 20
2220300 TCATATATAA
2220310 AATATTTTTATATAAATTTT
1 AATATTTTTATATAAATTTT
2220330 AATATATTTCTAT-TATAATTTT
1 AATAT-TTT-TATATA-AATTTT
* * * *
2220352 TATTTTTTTATAT-TATATT
1 AATATTTTTATATAAATTTT
2220371 -ATATTTTTATATAATATTT
1 AATATTTTTATATAA-ATTT
2220390 ATATTATAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
18 11 0.23
19 4 0.09
20 11 0.23
21 9 0.19
22 12 0.26
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (20 bp):
AATATTTTTATATAAATTTT
Found at i:2220372 original size:18 final size:18
Alignment explanation
Indices: 2220311--2220394 Score: 69
Period size: 18 Copynumber: 4.3 Consensus size: 18
2220301 CATATATAAA
*
2220311 ATATTTTTATATAAATTTT
1 ATATTTTTATAT-AATATT
*
2220330 AATATATTTCTATTATAATTTTT
1 -ATAT-TTT-TA-TATAA-TATT
* *
2220353 ATTTTTTTATATTATATT
1 ATATTTTTATATAATATT
2220371 ATATTTTTATATAATATTT
1 ATATTTTTATATAATA-TT
2220390 ATATT
1 ATATT
2220395 ATAAAATTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
18 17 0.31
19 11 0.20
20 6 0.11
21 6 0.11
22 7 0.13
23 7 0.13
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (18 bp):
ATATTTTTATATAATATT
Found at i:2221475 original size:21 final size:21
Alignment explanation
Indices: 2221451--2221491 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2221441 CAATTAACAT
2221451 AAAAAAACAAAGAAAAAAAAC
1 AAAAAAACAAAGAAAAAAAAC
* * *
2221472 AAAAAGAGAAAGAAACAAAA
1 AAAAAAACAAAGAAAAAAAA
2221492 GATAAGTACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (21 bp):
AAAAAAACAAAGAAAAAAAAC
Found at i:2221477 original size:15 final size:16
Alignment explanation
Indices: 2221451--2221491 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
2221441 CAATTAACAT
2221451 AAAAAAAC--AAAGA-
1 AAAAAAACAAAAAGAG
2221464 AAAAAAACAAAAAGAG
1 AAAAAAACAAAAAGAG
*
2221480 AAAGAAACAAAA
1 AAAAAAACAAAA
2221492 GATAAGTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 8 0.33
15 5 0.21
16 11 0.46
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAAAACAAAAAGAG
Found at i:2221492 original size:15 final size:14
Alignment explanation
Indices: 2221451--2221493 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
2221441 CAATTAACAT
2221451 AAAAAAAC-AAAGA
1 AAAAAAACAAAAGA
2221464 AAAAAAACAAAAAGA
1 AAAAAAAC-AAAAGA
*
2221479 GAAAGAAACAAAAGA
1 -AAAAAAACAAAAGA
2221494 TAAGTACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 8 0.31
15 11 0.42
16 7 0.27
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAAAACAAAAGA
Found at i:2222539 original size:50 final size:50
Alignment explanation
Indices: 2222484--2222687 Score: 227
Period size: 50 Copynumber: 4.1 Consensus size: 50
2222474 GTTGTCATTA
** *
2222484 TTGACTATTCTTCATTAACCTTTGACAATCAAGAAAGGTAGTCGTAATTA
1 TTGACTATTCTTCACCAACCTTTGACAATCAAGAAAGGTAGTCGTAATTG
* *
2222534 TTGACTATTCTTCACCAACCTTTGACAATCAAGAAATGTGGTCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCAAGAAAGGTAGTCGTAATTG
* ** * *
2222584 TT-AATGATTCTTCACCAACCTTTGACAATTGAGATAA-GT-GACCATAATTG
1 TTGACT-ATTCTTCACCAACCTTTGACAATCAAGA-AAGGTAG-TCGTAATTG
* * *
2222634 TTGACTATTCTTCACCAACTTTTGATAAT-AGAGAGAGGTAGTCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCA-AGAAAGGTAGTCGTAATTG
2222684 TTGA
1 TTGA
2222688 TTTTAAGCAA
Statistics
Matches: 130, Mismatches: 17, Indels: 14
0.81 0.11 0.09
Matches are distributed among these distances:
49 4 0.03
50 121 0.93
51 5 0.04
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (50 bp):
TTGACTATTCTTCACCAACCTTTGACAATCAAGAAAGGTAGTCGTAATTG
Found at i:2227135 original size:50 final size:50
Alignment explanation
Indices: 2227081--2227336 Score: 316
Period size: 50 Copynumber: 5.1 Consensus size: 50
2227071 AGGTGTTGCC
* * *
2227081 ATTGTTGATTATTCTTTACCAACTTTTGACAATCAAGAGAGGTGGTCGTA
1 ATTGTTGACTATTCTTTACCAACCTTTGACAATCGAGAGAGGTGGTCGTA
* * **
2227131 ATTGTTGACTATTCTTCACCAACTTTTGACAATCGAGAGAGGTGGTTATA
1 ATTGTTGACTATTCTTTACCAACCTTTGACAATCGAGAGAGGTGGTCGTA
* * * *
2227181 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGCGATTGTA
1 ATTGTTGACTATTCTTTACCAACCTTTGACAATCGAGAGAGGTGGTCGTA
* * * * *
2227231 ATTGTTGACGATTCTTTACCAACGTTTGACAATTGAGAGAGGTGGCCATA
1 ATTGTTGACTATTCTTTACCAACCTTTGACAATCGAGAGAGGTGGTCGTA
* * * *
2227281 ATTGTTGATTATT-TTTCACCAACCTTTGATAATAGAAAGAGGTGGTCGTA
1 ATTGTTGACTATTCTTT-ACCAACCTTTGACAATCGAGAGAGGTGGTCGTA
2227331 ATTGTT
1 ATTGTT
2227337 AACTCTAAGC
Statistics
Matches: 179, Mismatches: 26, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
49 3 0.02
50 176 0.98
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (50 bp):
ATTGTTGACTATTCTTTACCAACCTTTGACAATCGAGAGAGGTGGTCGTA
Found at i:2227259 original size:100 final size:100
Alignment explanation
Indices: 2227081--2227336 Score: 359
Period size: 100 Copynumber: 2.6 Consensus size: 100
2227071 AGGTGTTGCC
* * * *
2227081 ATTGTTGATTATTCTTTACCAACTTTTGACAATCAAGAGAGGTGGTCGTAATTGTTGACTATTCT
1 ATTGTTGATTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTAATTGTTGACGATTCT
* **
2227146 TCACCAACTTTTGACAATCGAGAGAGGTGGTTATA
66 TCACCAACGTTTGACAATCGAGAGAGGTGGCCATA
* * * *
2227181 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGCGATTGTAATTGTTGACGATTCT
1 ATTGTTGATTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTAATTGTTGACGATTCT
* *
2227246 TTACCAACGTTTGACAATTGAGAGAGGTGGCCATA
66 TCACCAACGTTTGACAATCGAGAGAGGTGGCCATA
* * * *
2227281 ATTGTTGATTATTTTTCACCAACCTTTGATAATAGAAAGAGGTGGTCGTAATTGTT
1 ATTGTTGATTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTAATTGTT
2227337 AACTCTAAGC
Statistics
Matches: 135, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
100 135 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (100 bp):
ATTGTTGATTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTAATTGTTGACGATTCT
TCACCAACGTTTGACAATCGAGAGAGGTGGCCATA
Found at i:2229057 original size:2 final size:2
Alignment explanation
Indices: 2229050--2229105 Score: 60
Period size: 2 Copynumber: 28.0 Consensus size: 2
2229040 AGAAACTCTT
* * *
2229050 TA TA TA TA TA TA TA TA TG TA TA TA AA TA TA CTT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
*
2229093 TA TA -A TA TT TA TA
1 TA TA TA TA TA TA TA
2229106 AGACCGGAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
1 1 0.02
2 42 0.95
3 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2229374 original size:2 final size:2
Alignment explanation
Indices: 2229369--2229397 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2229359 TATATATATA
2229369 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2229398 ACGTATTATA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2235980 original size:1 final size:1
Alignment explanation
Indices: 2235976--2236000 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2235966 TTTTTTTTTT
2235976 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
2236001 TTAAAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:2236908 original size:2 final size:2
Alignment explanation
Indices: 2236876--2236900 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2236866 GTACTTTCCT
2236876 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 T
2236901 GCATATATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2247985 original size:22 final size:23
Alignment explanation
Indices: 2247960--2248013 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
2247950 TTTTAATATA
* *
2247960 ATATTTAATTTTAATTAAA-ATT
1 ATATTTAATGTTAATTAAATAAT
*
2247982 ATATCATAA-GTTAATTAAATAAT
1 ATAT-TTAATGTTAATTAAATAAT
2248005 ATATTTAAT
1 ATATTTAAT
2248014 AATAAAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
ATATTTAATGTTAATTAAATAAT
Found at i:2249055 original size:27 final size:26
Alignment explanation
Indices: 2248999--2249049 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 26
2248989 TATATTGATA
2248999 TAAATTATAATATAAATATTAAAAAG
1 TAAATTATAATATAAATATTAAAAAG
2249025 TAAATTA-AATATTAATATATTAAAA
1 TAAATTATAATA-TAA-ATATTAAAA
2249050 TTTAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.17
26 10 0.43
27 9 0.39
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (26 bp):
TAAATTATAATATAAATATTAAAAAG
Found at i:2250689 original size:15 final size:16
Alignment explanation
Indices: 2250669--2250699 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2250659 TGGGGACAAG
2250669 TTTATT-TTTTATTTT
1 TTTATTATTTTATTTT
2250684 TTTATTATTTTATTTT
1 TTTATTATTTTATTTT
2250700 CGTAAGTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTATTATTTTATTTT
Found at i:2251536 original size:7 final size:7
Alignment explanation
Indices: 2251524--2251561 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
2251514 ATCAATTGAG
2251524 TTAGACT
1 TTAGACT
2251531 TTAGACT
1 TTAGACT
2251538 TTAGACT
1 TTAGACT
*
2251545 TTAAACT
1 TTAGACT
*
2251552 TTAAACT
1 TTAGACT
2251559 TTA
1 TTA
2251562 AATGTAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (7 bp):
TTAGACT
Found at i:2252675 original size:2 final size:2
Alignment explanation
Indices: 2252670--2252703 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2252660 ACCCACACAA
*
2252670 AT AT AT CT 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
2252704 GGATTTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2253463 original size:2 final size:2
Alignment explanation
Indices: 2253456--2253480 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2253446 TCTACTCCAT
2253456 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 T
2253481 TAAAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2259511 original size:86 final size:86
Alignment explanation
Indices: 2259366--2259712 Score: 667
Period size: 86 Copynumber: 4.0 Consensus size: 86
2259356 ATATCTTTGG
* *
2259366 AACCATGTAGACAGCTTAACTTGTTTTGTTACTCCAATTGGAAGCCATTTCCAAACAAGGTAATT
1 AACCATGCAGACAGCTTAACTTGTTTTGTCACTCCAATTGGAAGCCATTTCCAAACAAGGTAATT
2259431 AAAAGGAAATTTATAAGAATT
66 AAAAGGAAATTTATAAGAATT
2259452 AACCATGCAGACAGCTTAACTTGTTTTGTCACTCCAATTGGAAGCCATTTCCAAACAAGGTAATT
1 AACCATGCAGACAGCTTAACTTGTTTTGTCACTCCAATTGGAAGCCATTTCCAAACAAGGTAATT
2259517 AAAAGGAAATTTATAAGAATT
66 AAAAGGAAATTTATAAGAATT
2259538 AACCATGCAGACAGCTTAACTTGTTTTGTCACTCCAATTGGAAGCCATTTCCAAACAAGGTAATT
1 AACCATGCAGACAGCTTAACTTGTTTTGTCACTCCAATTGGAAGCCATTTCCAAACAAGGTAATT
2259603 AAAAGGAAATTTATAAGAATT
66 AAAAGGAAATTTATAAGAATT
2259624 AACCATGCAGACAGCTTAACTTGTTTTGTCACTCCAATTGGAAGCCATTTCCAAACAAGGTAATT
1 AACCATGCAGACAGCTTAACTTGTTTTGTCACTCCAATTGGAAGCCATTTCCAAACAAGGTAATT
2259689 AAAAAGGAAATTTATAAGAATT
66 -AAAAGGAAATTTATAAGAATT
2259711 AA
1 AA
2259713 GTAATTGAAG
Statistics
Matches: 258, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
86 235 0.91
87 23 0.09
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (86 bp):
AACCATGCAGACAGCTTAACTTGTTTTGTCACTCCAATTGGAAGCCATTTCCAAACAAGGTAATT
AAAAGGAAATTTATAAGAATT
Found at i:2265129 original size:31 final size:31
Alignment explanation
Indices: 2265094--2265192 Score: 80
Period size: 31 Copynumber: 3.2 Consensus size: 31
2265084 GTAAGTAAAT
2265094 GTACTTAACAGTTTTAGATCATGTTTCTATG
1 GTACTTAACAGTTTTAGATCATGTTTCTATG
* * * *
2265125 GTAC-TGA-AGTATGAGATTGCATGTAAGTT-AAT-
1 GTACTTAACAGTTTTAGA-T-CATGT---TTCTATG
*
2265157 GTACATAACAGTTTTAGATCATGTTTCTATG
1 GTACTTAACAGTTTTAGATCATGTTTCTATG
2265188 GTACT
1 GTACT
2265193 GAAGTTTGAG
Statistics
Matches: 50, Mismatches: 9, Indels: 18
0.65 0.12 0.23
Matches are distributed among these distances:
29 9 0.18
30 5 0.10
31 13 0.26
32 9 0.18
33 5 0.10
34 9 0.18
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.40
Consensus pattern (31 bp):
GTACTTAACAGTTTTAGATCATGTTTCTATG
Found at i:2265150 original size:63 final size:63
Alignment explanation
Indices: 2265072--2265202 Score: 235
Period size: 63 Copynumber: 2.1 Consensus size: 63
2265062 TGATTTTGGC
*
2265072 ATGAGATTGCATGTAAGTAAATGTACTTAACAGTTTTAGATCATGTTTCTATGGTACTGAAGT
1 ATGAGATTGCATGTAAGTAAATGTACATAACAGTTTTAGATCATGTTTCTATGGTACTGAAGT
*
2265135 ATGAGATTGCATGTAAGTTAATGTACATAACAGTTTTAGATCATGTTTCTATGGTACTGAAGT
1 ATGAGATTGCATGTAAGTAAATGTACATAACAGTTTTAGATCATGTTTCTATGGTACTGAAGT
*
2265198 TTGAG
1 ATGAG
2265203 TTCAAGGAGA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.38
Consensus pattern (63 bp):
ATGAGATTGCATGTAAGTAAATGTACATAACAGTTTTAGATCATGTTTCTATGGTACTGAAGT
Found at i:2265199 original size:29 final size:29
Alignment explanation
Indices: 2265103--2265199 Score: 81
Period size: 29 Copynumber: 3.2 Consensus size: 29
2265093 TGTACTTAAC
2265103 AGTTTTAGATCATGTTTCTATGGTACTGA
1 AGTTTTAGATCATGTTTCTATGGTACTGA
* * * *
2265132 AGTATGAGATTGCATGTAAGTT-AAT-GTACATAA
1 AGTTTTAGA-T-CATGT---TTCTATGGTAC-TGA
2265165 CAGTTTTAGATCATGTTTCTATGGTACTGA
1 -AGTTTTAGATCATGTTTCTATGGTACTGA
2265195 AGTTT
1 AGTTT
2265200 GAGTTCAAGG
Statistics
Matches: 51, Mismatches: 8, Indels: 18
0.66 0.10 0.23
Matches are distributed among these distances:
29 14 0.27
30 5 0.10
31 9 0.18
32 9 0.18
33 5 0.10
34 9 0.18
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (29 bp):
AGTTTTAGATCATGTTTCTATGGTACTGA
Found at i:2269893 original size:17 final size:18
Alignment explanation
Indices: 2269867--2269900 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2269857 TAAATAAAAT
2269867 ATTATATTAAAAATTTAA
1 ATTATATTAAAAATTTAA
*
2269885 ATTAT-TTAATAATTTA
1 ATTATATTAAAAATTTA
2269901 TTATATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTATATTAAAAATTTAA
Found at i:2281934 original size:29 final size:29
Alignment explanation
Indices: 2281901--2281966 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
2281891 TTACTTATTC
**
2281901 TTAAATACATTTTTATATTTTTA-TTGTAT
1 TTAAATA-ATTTTTATATTTAAATTTGTAT
* *
2281930 TTAAATAATTTTTTTCTTTAAATTTGTAT
1 TTAAATAATTTTTATATTTAAATTTGTAT
2281959 TTAAATAA
1 TTAAATAA
2281967 ACTCTTATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 11 0.34
29 21 0.66
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (29 bp):
TTAAATAATTTTTATATTTAAATTTGTAT
Found at i:2290510 original size:24 final size:23
Alignment explanation
Indices: 2290483--2290533 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
2290473 ATATAAGATT
2290483 AGAAAATTATACAAT-TTATCATA
1 AGAAAATTATACAATATTA-CATA
2290506 GAGAAAATTATACAATATTACATA
1 -AGAAAATTATACAATATTACATA
2290530 AGAA
1 AGAA
2290534 TATCTACAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 4 0.15
24 19 0.73
25 3 0.12
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (23 bp):
AGAAAATTATACAATATTACATA
Found at i:2293268 original size:2 final size:2
Alignment explanation
Indices: 2293261--2293288 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2293251 AAAGATAAGA
2293261 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
2293289 GGGAACAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2303734 original size:18 final size:18
Alignment explanation
Indices: 2303711--2303748 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
2303701 AAATTTTATT
2303711 ATTGATTTAAC-AAAGTAA
1 ATTGA-TTAACTAAAGTAA
2303729 ATTGATTAACTTAAAGTAA
1 ATTGATTAAC-TAAAGTAA
2303748 A
1 A
2303749 AATAAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 5 0.28
19 8 0.44
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (18 bp):
ATTGATTAACTAAAGTAA
Found at i:2305579 original size:964 final size:961
Alignment explanation
Indices: 2303469--2306193 Score: 3410
Period size: 987 Copynumber: 2.8 Consensus size: 961
2303459 TTCACCTTTC
* * * *
2303469 TTTTTT-GAGTTTATTTTAAAAGCAAATATTTTT-AAAAATTGTCTTGCGCCGTTTTA-TTTTTC
1 TTTTTTCGAGTTTATCTTAAAAGCAAATATTTTTGAAAAATAG-ATTGCGCC-TTTTATTTTTTT
* * * **
2303531 CTGCTTTCTCGTATGTATTTATAGCCAAATGTGTCGATCATTTTTGTTTTTGAAACCCATCAATA
64 C-GCTTTCTCATATGTATTTATAGCCAAATGTGTTGGTCATTTTTGTTTTTGAAACCCATCGGTA
* * * * * *
2303596 GTTTTATGAATAGCTAATAGGTAAGTTACATGAAAGTTTTCGATATATATTTATGTACAATATAT
128 GCTTTATGAATAGCTAATAGGTAGGTTATATGAAAATTTTCTATATATATTTATGTACAATGTAT
2303661 TGATTTAAATTTTATAAAAAAGTAAAATAAAAATAAAAT--A-AAATT-TTATTAT-TGATTTAA
193 TGATTTAAATTTTAT--AAAAGTAAAAT-AAAATAAAATAAATAAATTATTATTATATGATTTAA
2303721 CAAAGTAAATTGATTAACTTAAAGTAAAAATAAATTGATTAAGAAAATTTTATCAAATATTATTT
255 CAAAGTAAATTGATTAACTTAAA-TAAAAATAAATTGATTAAG---------T-AAAT-TTA--T
* * *
2303786 TATAAAACTATTTGTA--TTAAAAGTT--AGATATTTAATATAATTAATTATTATAATATTTTAT
306 TATAAAACTACTTGTATTTTAAAAGTTAAAGATCTTTAACATAATTAATTATTATAATATTTTAT
* *
2303847 TTTGAAAAAAAATTAAATTATTTTTATATTAT-ATTTAGCTGATATAATTTAATTTTAGTAGCAT
371 TTTGAAAAAAAATTAAATTATTTTTATATT-TCATTTAGTTGATATAATTTAATTTTAGTCGCAT
* * * **
2303911 ATTTTTTCAAAATTCAAGATTAACTTATTTGATAGAGCTTTTGATAGTAGTACTGCCTAAACCAG
435 ATTTTTTCAAAATTCAAGATTAACTTACTTGATAGAGCTTTTGATAGTAGTTCTTCC-AAGTCAG
* * *
2303976 GTTTAAGTTATCATGGTATAAATTTTAATATTTTATAAATATCAAAAAATGATTGTAATTTTTAT
499 GTTTAAATTATCATAGTATAAATTTTAA-ATTTTATAAATATCAAAAAATTATTGTAATTTTTAT
* *
2304041 ATTAAGTAATATTTTTAAGGTTTAAATCCCAATGATATAATATTTTTAAATATTAATAAAATAAT
563 ATTAAGTAATATTTTTAAGGTTTAAATCCCGATGGTATAATATTTTTAAATATTAATAAAATAAT
* * *
2304106 TA-TTCTTTTTTTAAATTTTAATTTTAG-TTTTTTTCATTATGTAAAAATAAAATTAATTATTAA
628 TATTTC-TTTTTAAAATTTTAATTTTAGTTTTTTTTTATTATGTAAAAGTAAAATTAATTATT--
* * * *
2304169 AATCAAAATTAAAAAATATTTATACCTTATAATATTCAAGAACAACCCAACTCTATTCGTTACGC
690 -ATCAAAATTAAAAAATATTTATACCTTATAAAATTCAAGAACAATCAAACTTTATTCGTTACGC
* * * * * *
2304234 AAGATCATGAGATGCCATCTTTAGAAGCTCGACTAAATTCAAATGTTAAAGATCGAGTTGATTTT
754 AAGATCATGAGATGCCATTTTTTGAAGCTCGA-TTAATTTAAATGTTAAAAATCGAGTTGAATTT
* * *
2304299 ATTTAGAGAGTAACTTTGATTTGAGAATCTTAAAATTCTCAAACATTTGAACATTCGAGGGATAA
818 ATTTAGAGAGTAACTTTGATTTGAGAATCCTAAAATTCTCAAACATTCGAACATTCGAGGCATAA
2304364 CATTCAAATGAATAATCATGACTCAAAGAAATAAACTTTAAAAGTGTCGATACTTAATAAGAAAT
883 CATTCAAATGAATAATCATGACTCAAAGAAATAAACTTTAAAA--G--G-------AT-----AT
*
2304429 TTACTTTAATCGAAAGCTTTCTCTACTTAT
932 TTACCTTAATCGAAAGCTTTCTCTACTTAT
* * *
2304459 TTTCTCCGAGTTTATCTTAAAAGCAAATATTTTTGAAAAATAGATTGCGCCCTTTATTTTTTTCG
1 TTTTTTCGAGTTTATCTTAAAAGCAAATATTTTTGAAAAATAGATTGCGCCTTTTATTTTTTTCG
*
2304524 CTTTCTCATGTGTATTTATAGCCAAATGTGTTGGTCATTTTTGTTTTTGAAACCCATCGGTAGCT
66 CTTTCTCATATGTATTTATAGCCAAATGTGTTGGTCATTTTTGTTTTTGAAACCCATCGGTAGCT
2304589 TTATGAATAGCTAATAGGTAGGTTATATGAAAATTTTCTATATATATTTATGTACAATGTATTGA
131 TTATGAATAGCTAATAGGTAGGTTATATGAAAATTTTCTATATATATTTATGTACAATGTATTGA
2304654 TTTAAATTTTATAAAAGTAAAATAAAATAAAATAAAGTAAATTTTATTATTATAGTGATTTAACA
196 TTTAAATTTTATAAAAGTAAAATAAAATAAAATAAA-TAAA--TTATTATTATA-TGATTTAACA
*
2304719 AAGTAAATTGATTAACTTAAACTAAAAATAAATTGATTAAGTAAATTTATTATAAAACTACTCGT
257 AAGTAAATTGATTAACTTAAA-TAAAAATAAATTGATTAAGTAAATTTATTATAAAACTACTTGT
2304784 ATTTTAAAAGTTAAAGATCTTTAACATAATTAATTATTATAATATTTTATTTTGAAAAAAAATTA
321 ATTTTAAAAGTTAAAGATCTTTAACATAATTAATTATTATAATATTTTATTTTGAAAAAAAATTA
* *
2304849 AATTATTTTTATATTTCATGTAGTTAATATAATTTAATTTTAGTCGCATATTTTTTCAAAATTCA
386 AATTATTTTTATATTTCATTTAGTTGATATAATTTAATTTTAGTCGCATATTTTTTCAAAATTCA
2304914 AGATTAACTTACTTGATAGAGCTTTTGATAGTAGTTCTATCCAAGTCAGGTTTAAATTATCATAG
451 AGATTAACTTACTTGATAGAGCTTTTGATAGTAGTTCT-TCCAAGTCAGGTTTAAATTATCATAG
2304979 TATAAATTTTAACATTTTATAAATATCAAAAAATTATTGTAATTTTTATATTAAGTAATATTTTT
515 TATAAATTTTAA-ATTTTATAAATATCAAAAAATTATTGTAATTTTTATATTAAGTAATATTTTT
2305044 AAGGTTTAAATCCCGATGGTATAATATTTTTAAATATTAATAAAATAATTATTTCTTTTTAAAAT
579 AAGGTTTAAATCCCGATGGTATAATATTTTTAAATATTAATAAAATAATTATTTCTTTTTAAAAT
2305109 TTTAATTTTAGTTTTTTTTTATTATGTAAAAGTAAAATTAATTA-T-T-AAAATTAAAAAATATT
644 TTTAATTTTAGTTTTTTTTTATTATGTAAAAGTAAAATTAATTATTATCAAAATTAAAAAATATT
* *
2305171 TATTCCTTATAAAATTCAAGAACAATCAAACTTTATTCGTTACGCAATATCATGAGATGCCATTT
709 TATACCTTATAAAATTCAAGAACAATCAAACTTTATTCGTTACGCAAGATCATGAGATGCCATTT
*
2305236 TTTGAAGCTCGATTAATTTAAATGTTAAAAA-CTGAGTTGAATTTATTT-GAAGGGTAACTTTGA
774 TTTGAAGCTCGATTAATTTAAATGTTAAAAATC-GAGTTGAATTTATTTAG-AGAGTAACTTTGA
* * * * *
2305299 TTTGAATTAATCCTAAAATTCTTAGACATTCGAACATTCTATGCATAACATTCAAATGAATAATC
837 TTTG-A-GAATCCTAAAATTCTCAAACATTCGAACATTCGAGGCATAACATTCAAATGAATAATC
*
2305364 ATGACTTAAAGAAATAAACTTTAAAA-G-T-TTTACCTTAATCGAAAGCTTTCTCTA-TCTAT
900 ATGACTCAAAGAAATAAACTTTAAAAGGATATTTACCTTAATCGAAAGCTTTCTCTACT-TAT
* * * *
2305423 TTTTTTCGAGTTTGTCTTAAAAGCAAATATTTTTGAAAAAGAGATTGAGCCTTTTATTTTTTTCA
1 TTTTTTCGAGTTTATCTTAAAAGCAAATATTTTTGAAAAATAGATTGCGCCTTTTATTTTTTTCG
*
2305488 CTTTCTCATATGTATTTATAACCAAATGTGTTGGTCATTTTTGTTTTTGAAACCCATCGGTAGCT
66 CTTTCTCATATGTATTTATAGCCAAATGTGTTGGTCATTTTTGTTTTTGAAACCCATCGGTAGCT
* * *
2305553 TTATGAATAGCTAATAGGTTGGTTATATGAACATTTTTTTATATATATTTATGTACAATGTATTG
131 TTATGAATAGCTAATAGGTAGGTTATATGAA-AATTTTCTATATATATTTATGTACAATGTATTG
* * * *
2305618 ATTTGAATTTTATAAAAGTAAAATAAAA-ATAAA-AAA-AAA-TA-AATTTTATGA-TTAGC---
195 ATTTAAATTTTATAAAAGTAAAATAAAATA-AAATAAATAAATTATTATTATATGATTTAACAAA
* *
2305674 G-----TGA-T---TT-AAT-AAAGTAAATTGATGAAGTAAATTTTATTATAAAACTACTTGTAT
259 GTAAATTGATTAACTTAAATAAAAATAAATTGATTAAGTAAA-TTTATTATAAAACTACTTGTAT
** *
2305728 TTTAAAAGTTAAAGATCTTTAACATAATTAATTATTATAATATTTTATTTTGAAAAAATTTTTAA
323 TTTAAAAGTTAAAGATCTTTAACATAATTAATTATTATAATATTTTATTTTGAAAAAAAATTAAA
2305793 TTATTTTTATATTTCATTTAGTTGATATAATTTAATTTTAGTCGCATATTTTTTTCAAAATTCAA
388 TTATTTTTATATTTCATTTAGTTGATATAATTTAATTTTAGTCGCATA-TTTTTTCAAAATTCAA
* * ** * *
2305858 AATTAACTCACTTGATA-AAATCTTTG---GTAGTTCTGTTCAAGTCAGGTTTAAATCA-C-TA-
452 GATTAACTTACTTGATAGAGCT-TTTGATAGTAGTTCT-TCCAAGTCAGGTTTAAATTATCATAG
* *
2305916 TGAT--A---TAAATTTTA-AAA-AT-----GATTA---TAATTTTTATATTGAGTAATATTTTT
515 T-ATAAATTTTAAATTTTATAAATATCAAAAAATTATTGTAATTTTTATATTAAGTAATATTTTT
** * *
2305966 AAGGTTTAAAT-ATGATAGTATAATATTTTTAAATATTAATAAAATAATTATTT-TTGTTTGAAA
579 AAGGTTTAAATCCCGATGGTATAATATTTTTAAATATTAATAAAATAATTATTTCTT-TTTAAAA
* *
2306029 TTTTAATTTTAGTATTTTTTTATTAGGTAAAAGTAAAATTAATTATTAAAATCAAAATTAAAAAA
643 TTTTAATTTTAGTTTTTTTTTATTATGTAAAAGTAAAATTAATTATT---ATCAAAATTAAAAAA
* * * * * * * **
2306094 TATTTATACCTTATAAAATTCAAGAAGAATAAAACTTTATTCATGACACAAGATTATGAAATGTT
705 TATTTATACCTTATAAAATTCAAGAACAATCAAACTTTATTCGTTACGCAAGATCATGAGATGCC
*
2306159 A-TTTTTGAAAGCTCGACTAAGTTTAAATGTTAAAA
770 ATTTTTTG-AAGCTCGATTAA-TTTAAATGTTAAAA
2306194 TACAATAAAA
Statistics
Matches: 1579, Mismatches: 116, Indels: 142
0.86 0.06 0.08
Matches are distributed among these distances:
920 2 0.00
921 88 0.06
922 37 0.02
925 4 0.00
926 7 0.00
927 78 0.05
928 14 0.01
930 2 0.00
931 3 0.00
932 6 0.00
933 3 0.00
936 1 0.00
937 1 0.00
938 4 0.00
939 1 0.00
940 26 0.02
941 19 0.01
942 132 0.08
943 37 0.02
944 2 0.00
947 1 0.00
948 3 0.00
953 1 0.00
956 4 0.00
957 3 0.00
958 5 0.00
959 2 0.00
962 3 0.00
963 1 0.00
964 183 0.12
965 61 0.04
970 1 0.00
978 1 0.00
980 2 0.00
981 46 0.03
982 86 0.05
983 91 0.06
985 12 0.01
986 5 0.00
987 307 0.19
988 46 0.03
989 1 0.00
990 139 0.09
991 42 0.03
992 7 0.00
993 2 0.00
994 7 0.00
996 50 0.03
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (961 bp):
TTTTTTCGAGTTTATCTTAAAAGCAAATATTTTTGAAAAATAGATTGCGCCTTTTATTTTTTTCG
CTTTCTCATATGTATTTATAGCCAAATGTGTTGGTCATTTTTGTTTTTGAAACCCATCGGTAGCT
TTATGAATAGCTAATAGGTAGGTTATATGAAAATTTTCTATATATATTTATGTACAATGTATTGA
TTTAAATTTTATAAAAGTAAAATAAAATAAAATAAATAAATTATTATTATATGATTTAACAAAGT
AAATTGATTAACTTAAATAAAAATAAATTGATTAAGTAAATTTATTATAAAACTACTTGTATTTT
AAAAGTTAAAGATCTTTAACATAATTAATTATTATAATATTTTATTTTGAAAAAAAATTAAATTA
TTTTTATATTTCATTTAGTTGATATAATTTAATTTTAGTCGCATATTTTTTCAAAATTCAAGATT
AACTTACTTGATAGAGCTTTTGATAGTAGTTCTTCCAAGTCAGGTTTAAATTATCATAGTATAAA
TTTTAAATTTTATAAATATCAAAAAATTATTGTAATTTTTATATTAAGTAATATTTTTAAGGTTT
AAATCCCGATGGTATAATATTTTTAAATATTAATAAAATAATTATTTCTTTTTAAAATTTTAATT
TTAGTTTTTTTTTATTATGTAAAAGTAAAATTAATTATTATCAAAATTAAAAAATATTTATACCT
TATAAAATTCAAGAACAATCAAACTTTATTCGTTACGCAAGATCATGAGATGCCATTTTTTGAAG
CTCGATTAATTTAAATGTTAAAAATCGAGTTGAATTTATTTAGAGAGTAACTTTGATTTGAGAAT
CCTAAAATTCTCAAACATTCGAACATTCGAGGCATAACATTCAAATGAATAATCATGACTCAAAG
AAATAAACTTTAAAAGGATATTTACCTTAATCGAAAGCTTTCTCTACTTAT
Found at i:2308137 original size:2 final size:2
Alignment explanation
Indices: 2308078--2308119 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2308068 CGTTGGATTT
*
2308078 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2308120 GAACCAGAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Done.