Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 148 of 168
Found at i:43710060 original size:24 final size:24
Alignment explanation
Indices: 43710003--43710061 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
43709993 GGTTTAATGC
* *
43710003 AAATGGAGATATTTTGGAGAGATG
1 AAATGGATATATTTTGGAAAGATG
*
43710027 AAATGAATATATTTTGGAAAGATG
1 AAATGGATATATTTTGGAAAGATG
43710051 AAATGGATATA
1 AAATGGATATA
43710062 AATGGAGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (24 bp):
AAATGGATATATTTTGGAAAGATG
Found at i:43710133 original size:17 final size:17
Alignment explanation
Indices: 43710111--43710208 Score: 61
Period size: 17 Copynumber: 5.4 Consensus size: 17
43710101 AATTCAAGAC
43710111 TTATGTAATATTTTTAA
1 TTATGTAATATTTTTAA
* ***
43710128 TTATGTAGTGATTCAAAGA
1 TTATGTAAT-ATTTTTA-A
43710147 CTTATGTAATATTTTTAA
1 -TTATGTAATATTTTTAA
* ***
43710165 TTATGTAGTGATTCAAAGA
1 TTATGTAAT-ATTTTTA-A
*
43710184 TTTATGTAATGTTTTTAA
1 -TTATGTAATATTTTTAA
43710202 TTATGTA
1 TTATGTA
43710209 GTGATTTAAT
Statistics
Matches: 58, Mismatches: 17, Indels: 12
0.67 0.20 0.14
Matches are distributed among these distances:
17 23 0.40
18 10 0.17
19 9 0.16
20 16 0.28
ACGTcount: A:0.34, C:0.03, G:0.13, T:0.50
Consensus pattern (17 bp):
TTATGTAATATTTTTAA
Found at i:43710153 original size:20 final size:19
Alignment explanation
Indices: 43710127--43710191 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
43710117 AATATTTTTA
43710127 ATTATGTAGTGATTCAAAG
1 ATTATGTAGTGATTCAAAG
* ***
43710146 ACTTATGTAAT-ATTTTTA-
1 A-TTATGTAGTGATTCAAAG
43710164 ATTATGTAGTGATTCAAAG
1 ATTATGTAGTGATTCAAAG
43710183 ATTTATGTA
1 A-TTATGTA
43710192 ATGTTTTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 7
0.69 0.16 0.14
Matches are distributed among these distances:
17 8 0.24
18 5 0.15
19 6 0.18
20 15 0.44
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (19 bp):
ATTATGTAGTGATTCAAAG
Found at i:43710156 original size:37 final size:37
Alignment explanation
Indices: 43710102--43710214 Score: 201
Period size: 37 Copynumber: 3.1 Consensus size: 37
43710092 TTATGTTTTA
43710102 ATTC-AAGACTTATGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
43710138 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
* *
43710175 ATTCAAAGATTTATGTAATGTTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
43710212 ATT
1 ATT
43710215 TAATTCGGGT
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
36 4 0.05
37 70 0.95
ACGTcount: A:0.34, C:0.04, G:0.14, T:0.48
Consensus pattern (37 bp):
ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
Found at i:43710263 original size:9 final size:9
Alignment explanation
Indices: 43710215--43710360 Score: 184
Period size: 9 Copynumber: 15.6 Consensus size: 9
43710205 TGTAGTGATT
43710215 TAATTCGGG
1 TAATTCGGG
* *
43710224 TAATTTGGA
1 TAATTCGGG
43710233 TAATTTTCGGG
1 TAA--TTCGGG
43710244 TAATTTTCGGG
1 TAA--TTCGGG
43710255 TAATTCGGG
1 TAATTCGGG
*
43710264 TAATTTGGG
1 TAATTCGGG
43710273 TAATTTTCGGG
1 TAA--TTCGGG
43710284 TAATTCGGG
1 TAATTCGGG
43710293 TAATTCGGG
1 TAATTCGGG
43710302 TAATTCGGG
1 TAATTCGGG
*
43710311 TAAGTCGGG
1 TAATTCGGG
43710320 TAATTCGGG
1 TAATTCGGG
*
43710329 TAAGTCGGG
1 TAATTCGGG
43710338 TAATTCGGG
1 TAATTCGGG
*
43710347 TAATTCAGG
1 TAATTCGGG
43710356 TAATT
1 TAATT
43710361 TTTAACCAAA
Statistics
Matches: 122, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
9 96 0.79
11 26 0.21
ACGTcount: A:0.23, C:0.09, G:0.31, T:0.37
Consensus pattern (9 bp):
TAATTCGGG
Found at i:43713367 original size:2 final size:2
Alignment explanation
Indices: 43713360--43713395 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
43713350 TGGATATGTG
43713360 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
43713396 GTAATGACTT
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:43717757 original size:13 final size:13
Alignment explanation
Indices: 43717739--43717802 Score: 83
Period size: 13 Copynumber: 4.9 Consensus size: 13
43717729 AGTTCTTCAT
*
43717739 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
43717752 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
43717765 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
43717778 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
43717791 TACTTTTGAAAA
1 TGCTTTTGAAAA
43717803 TTTTGAGTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:43717997 original size:28 final size:30
Alignment explanation
Indices: 43717965--43718030 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 30
43717955 ATTATAACTT
43717965 ATTTTTAATATTT-TAA-T-ATATAATATTA
1 ATTTTTAATATTTCTAAGTAAT-TAATATTA
*
43717993 ATTTTAAATATTTCTAAGTAATTAATATTA
1 ATTTTTAATATTTCTAAGTAATTAATATTA
43718023 ATTATTTA
1 ATT-TTTA
43718031 TTAAATTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 12 0.38
29 3 0.09
30 12 0.38
31 5 0.16
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (30 bp):
ATTTTTAATATTTCTAAGTAATTAATATTA
Found at i:43718021 original size:30 final size:28
Alignment explanation
Indices: 43717965--43718025 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 28
43717955 ATTATAACTT
*
43717965 ATTTTTAATATTTTAATATATAATATTA
1 ATTTTAAATATTTTAATATATAATATTA
43717993 ATTTTAAATATTTCTAAGTA-ATTAATATTA
1 ATTTTAAATATTT-TAA-TATA-TAATATTA
43718023 ATT
1 ATT
43718026 ATTTATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 12 0.41
29 4 0.14
30 13 0.45
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (28 bp):
ATTTTAAATATTTTAATATATAATATTA
Found at i:43719936 original size:41 final size:41
Alignment explanation
Indices: 43719891--43720009 Score: 96
Period size: 41 Copynumber: 3.1 Consensus size: 41
43719881 AATTTAATAA
43719891 AAATAAGTAGAACATAAATTCAATATCTAAAGACCAAACAT
1 AAATAAGTAGAACATAAATTCAATATCTAAAGACCAAACAT
* * * ** *
43719932 AAATAACT-----ATTAA-T-AA-AACT--AGATTACACAT
1 AAATAAGTAGAACATAAATTCAATATCTAAAGACCAAACAT
* *
43719963 AAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACAT
1 AAATAAGTAGAACATAAATTCAATATCTAAAGACCAAACAT
43720004 AAATAA
1 AAATAA
43720010 CTATTGATAA
Statistics
Matches: 54, Mismatches: 14, Indels: 20
0.61 0.16 0.23
Matches are distributed among these distances:
31 15 0.28
33 3 0.06
34 2 0.04
35 1 0.02
36 8 0.15
37 1 0.02
38 2 0.04
39 2 0.04
41 20 0.37
ACGTcount: A:0.58, C:0.14, G:0.05, T:0.23
Consensus pattern (41 bp):
AAATAAGTAGAACATAAATTCAATATCTAAAGACCAAACAT
Found at i:43719983 original size:72 final size:71
Alignment explanation
Indices: 43719859--43720021 Score: 247
Period size: 72 Copynumber: 2.3 Consensus size: 71
43719849 AAAATCATAT
* * * *
43719859 ATAAACAACTATTGATAAAACTAATTTAATAAAAATAAGTAGAACATAAATTCAATATCTAAAGA
1 ATAAATAACTATTGATAAAACTAATTTAACAAAAATAAGTAGAACATAAATTCAATATCCAAAAA
43719924 CCAAAC
66 CCAAAC
* *
43719930 ATAAATAACTATTAATAAAACTAGA-TTACACATAAATAAGTAGAACATAAATTCAATATCCAAA
1 ATAAATAACTATTGATAAAACTA-ATTTA-ACAAAAATAAGTAGAACATAAATTCAATATCCAAA
43719994 AACCAAAC
64 AACCAAAC
43720002 ATAAATAACTATTGATAAAA
1 ATAAATAACTATTGATAAAA
43720022 TTAGTTTAGC
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
71 24 0.29
72 59 0.71
ACGTcount: A:0.57, C:0.13, G:0.05, T:0.25
Consensus pattern (71 bp):
ATAAATAACTATTGATAAAACTAATTTAACAAAAATAAGTAGAACATAAATTCAATATCCAAAAA
CCAAAC
Found at i:43720475 original size:18 final size:18
Alignment explanation
Indices: 43720454--43720519 Score: 105
Period size: 18 Copynumber: 3.7 Consensus size: 18
43720444 TCCATCAATT
*
43720454 TGAACATCATTTGAGATG
1 TGAACATCATTTGAAATG
*
43720472 TGAAAATCATTTGAAATG
1 TGAACATCATTTGAAATG
*
43720490 TGAACATCATTTAAAATG
1 TGAACATCATTTGAAATG
43720508 TGAACATCATTT
1 TGAACATCATTT
43720520 NNNNNNNNNN
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (18 bp):
TGAACATCATTTGAAATG
Found at i:43722460 original size:23 final size:24
Alignment explanation
Indices: 43722408--43722464 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
43722398 GAAGTGGAGA
43722408 AGAGGAACAAAGAACAAGCACCAGC
1 AGAGGAACAAAGAACAAGCA-CAGC
* *
43722433 AGAGGAACAAAGAACCAGTA-AGC
1 AGAGGAACAAAGAACAAGCACAGC
43722456 AGAGGAACA
1 AGAGGAACA
43722465 CTAGCACAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 12 0.40
25 18 0.60
ACGTcount: A:0.53, C:0.19, G:0.26, T:0.02
Consensus pattern (24 bp):
AGAGGAACAAAGAACAAGCACAGC
Found at i:43723578 original size:22 final size:22
Alignment explanation
Indices: 43723531--43723591 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
43723521 CTCTGATTAT
*
43723531 TAGCACATTAGTGCTCTCCATT
1 TAGCACATTAGTGCTCTCCATA
* **
43723553 TAGCACATTCGTGCTCTCTGTA
1 TAGCACATTAGTGCTCTCCATA
43723575 TAGCA-ATTTAGTGCTCT
1 TAGCACA-TTAGTGCTCT
43723592 TTGTTTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 1 0.03
22 32 0.97
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (22 bp):
TAGCACATTAGTGCTCTCCATA
Found at i:43725279 original size:17 final size:19
Alignment explanation
Indices: 43725248--43725289 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
43725238 AAAATAGATT
43725248 AATAAGATAAAA-TTTTAA
1 AATAAGATAAAATTTTTAA
*
43725266 AATAA-ATAATATTTTTAA
1 AATAAGATAAAATTTTTAA
43725284 AATAAG
1 AATAAG
43725290 TATTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
AATAAGATAAAATTTTTAA
Found at i:43725405 original size:14 final size:16
Alignment explanation
Indices: 43725371--43725408 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
43725361 TTTTTAAGAT
43725371 AAATTTAGCACTTATA
1 AAATTTAGCACTTATA
*
43725387 AAATTTAGTA-TTA-A
1 AAATTTAGCACTTATA
43725401 AAATTTAG
1 AAATTTAG
43725409 AACCTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
15 3 0.14
16 9 0.43
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (16 bp):
AAATTTAGCACTTATA
Found at i:43733716 original size:15 final size:16
Alignment explanation
Indices: 43733690--43733724 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
43733680 ATGACTCATA
*
43733690 AAATCTAATTAAACCT
1 AAATCTAATTAAACCC
43733706 AAATC-AATTAAACCC
1 AAATCTAATTAAACCC
43733721 AAAT
1 AAAT
43733725 AAAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATCTAATTAAACCC
Found at i:43734581 original size:31 final size:30
Alignment explanation
Indices: 43734546--43734615 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 30
43734536 CGACTAAATA
* *
43734546 AAAGTCGGTTCCATTTGATATTTTTTCA-ATT
1 AAAGTCGGTTCAAATT-A-ATTTTTTCATATT
* *
43734577 AAAGTTGG-TCAAATTAATTTTTTCATGTT
1 AAAGTCGGTTCAAATTAATTTTTTCATATT
43734606 AAAGTCGGTT
1 AAAGTCGGTT
43734616 TAAAAAATCA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 9 0.28
29 10 0.31
30 6 0.19
31 7 0.22
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.46
Consensus pattern (30 bp):
AAAGTCGGTTCAAATTAATTTTTTCATATT
Found at i:43738439 original size:22 final size:21
Alignment explanation
Indices: 43738395--43738451 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
43738385 TTTTTTATTT
* **
43738395 TTATTTATTTTTATAAATTTA
1 TTATTTATTTTTAAAAAAATA
43738416 TTATTATATTTTTAAAAAAATA
1 TTATT-TATTTTTAAAAAAATA
*
43738438 TTTATGTATTTTTA
1 -TTATTTATTTTTA
43738452 TATTATAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 5 0.17
22 21 0.70
23 4 0.13
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TTATTTATTTTTAAAAAAATA
Found at i:43739655 original size:121 final size:123
Alignment explanation
Indices: 43739359--43739755 Score: 577
Period size: 121 Copynumber: 3.2 Consensus size: 123
43739349 AAATTGCTCC
* * * * * *
43739359 CACGTGGACGCGTTTTTGATACAATAGGTCCTGGAAAAATAATTTCGAGTTTACGTTTCTAAGCA
1 CACGTGGA-GCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTAACGTTTCTGAGCA
*
43739424 AATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATAAGAAGAATTTCTGAAATCGC-TCT
65 AATAGTAT-AAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTT-TGAAATCGCTTCT
*
43739484 CACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAACATAATTTCGAGTTAACGTTTCTGAGCA
1 CACGTGGA-GCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTAACGTTTCTGAGCA
43739549 AATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTTGAAATCGCTTC-
65 AATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTTGAAATCGCTTCT
* * * *
43739607 CATGTGG-GCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGACGTTTTTGAGCAA
1 CACGTGGAGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTAACGTTTCTGAGCAA
*
43739671 ATAGTATAAAAACGCTTCAAGCAGGATACTTTATCAGAAGAATTTTTGAAATCGC-TCT
66 ATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAA-TTTTGAAATCGCTTCT
* *
43739729 TACGTGAACGCGCTTTTGCTACAGTAG
1 CACGTGGA-GCGCTTTTGCTACAGTAG
43739756 CATGTTTGGC
Statistics
Matches: 250, Mismatches: 17, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
121 96 0.38
122 16 0.06
123 15 0.06
124 57 0.23
125 66 0.26
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (123 bp):
CACGTGGAGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTAACGTTTCTGAGCAA
ATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTTGAAATCGCTTCT
Found at i:43740956 original size:49 final size:49
Alignment explanation
Indices: 43740898--43741018 Score: 215
Period size: 49 Copynumber: 2.5 Consensus size: 49
43740888 TAAGAATATT
43740898 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
* *
43740947 AATTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAATTA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
*
43740996 AACTACTTTGTATTTTATTACAT
1 AACTATTTTGTATTTTATTACAT
43741019 TAATATAAAC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 68 1.00
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (49 bp):
AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
Found at i:43741464 original size:18 final size:18
Alignment explanation
Indices: 43741438--43741480 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
43741428 GACTAGAAAA
* * *
43741438 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
43741456 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
43741474 AGGATAC
1 AGGATAC
43741481 GCACCTGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:43743263 original size:13 final size:12
Alignment explanation
Indices: 43743238--43743272 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
43743228 ATTTTTACGA
43743238 TTTAAAAAAATT
1 TTTAAAAAAATT
43743250 TTTAAAAAATATT
1 TTTAAAAAA-ATT
43743263 TTTAAAAAAA
1 TTTAAAAAAA
43743273 AAATTAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TTTAAAAAAATT
Found at i:43743342 original size:11 final size:11
Alignment explanation
Indices: 43743328--43743390 Score: 60
Period size: 11 Copynumber: 5.7 Consensus size: 11
43743318 TTAAATATGG
43743328 ATTTGAGAGAA
1 ATTTGAGAGAA
43743339 ATTT-AGAAGGAA
1 ATTTGAG-A-GAA
*
43743351 A-TTGAGAGCA
1 ATTTGAGAGAA
43743361 ATTTGAGAGGAA
1 ATTTGAGA-GAA
43743373 A-TTGAGAGAA
1 ATTTGAGAGAA
*
43743383 AATTGAGA
1 ATTTGAGA
43743391 AATGATTAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
10 9 0.20
11 26 0.59
12 9 0.20
ACGTcount: A:0.46, C:0.02, G:0.29, T:0.24
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:43743355 original size:22 final size:22
Alignment explanation
Indices: 43743330--43743390 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
43743320 AAATATGGAT
43743330 TTGAGAGAAATTT-AGAAGGAAA
1 TTGAGAGAAATTTGAG-AGGAAA
*
43743352 TTGAGAGCAATTTGAGAGGAAA
1 TTGAGAGAAATTTGAGAGGAAA
*
43743374 TTGAGAGAAAATTGAGA
1 TTGAGAGAAATTTGAGA
43743391 AATGATTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 33 0.94
23 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.30, T:0.23
Consensus pattern (22 bp):
TTGAGAGAAATTTGAGAGGAAA
Found at i:43743368 original size:33 final size:33
Alignment explanation
Indices: 43743328--43743390 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
43743318 TTAAATATGG
* *
43743328 ATTTGAGA-GAAATTTAGAAGGAAATTGAGAGCA
1 ATTTGAGAGGAAATTGAG-AGAAAATTGAGAGCA
43743361 ATTTGAGAGGAAATTGAGAGAAAATTGAGA
1 ATTTGAGAGGAAATTGAGAGAAAATTGAGA
43743391 AATGATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 19 0.70
34 8 0.30
ACGTcount: A:0.46, C:0.02, G:0.29, T:0.24
Consensus pattern (33 bp):
ATTTGAGAGGAAATTGAGAGAAAATTGAGAGCA
Found at i:43748377 original size:31 final size:31
Alignment explanation
Indices: 43748341--43748419 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
43748331 CAAAAAAATA
*
43748341 AATATAATAATAAATAAGATTTAAATAATTT
1 AATATAATGATAAATAAGATTTAAATAATTT
* * *
43748372 AATATAATGATAAATGATATTTAAGTAATTT
1 AATATAATGATAAATAAGATTTAAATAATTT
*
43748403 AATATAATGATATATAA
1 AATATAATGATAAATAA
43748420 AATATAAAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.39
Consensus pattern (31 bp):
AATATAATGATAAATAAGATTTAAATAATTT
Found at i:43748667 original size:20 final size:21
Alignment explanation
Indices: 43748642--43748682 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
43748632 ATCAAACACC
43748642 TGCAGGTTAG-TTTTTTCCAT
1 TGCAGGTTAGTTTTTTTCCAT
43748662 TGCAGGTTAGTTTTTTTCCAT
1 TGCAGGTTAGTTTTTTTCCAT
43748683 CAAAGCTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.15, C:0.15, G:0.20, T:0.51
Consensus pattern (21 bp):
TGCAGGTTAGTTTTTTTCCAT
Found at i:43761770 original size:50 final size:50
Alignment explanation
Indices: 43761716--43761832 Score: 153
Period size: 50 Copynumber: 2.3 Consensus size: 50
43761706 AGTCTCCCCA
* * * *
43761716 CATGCGTCTGGGAGCAGGGCCTTTATTACTACCTTTCATAAGCCTCTTCC
1 CATGCGTCTGGGAGCAGGGCCTTTATTACCACCTTCCATAAGCCTCCTAC
** **
43761766 CATGCGTCTAAGAGCAATGCCTTTATTACCACCTTCCATAAGCCTCCTAC
1 CATGCGTCTGGGAGCAGGGCCTTTATTACCACCTTCCATAAGCCTCCTAC
*
43761816 CATGCGTCTGGAAGCAG
1 CATGCGTCTGGGAGCAG
43761833 AGTCGCTTTA
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (50 bp):
CATGCGTCTGGGAGCAGGGCCTTTATTACCACCTTCCATAAGCCTCCTAC
Found at i:43783194 original size:8 final size:8
Alignment explanation
Indices: 43783166--43783200 Score: 52
Period size: 9 Copynumber: 4.1 Consensus size: 8
43783156 GACTTTTTAC
43783166 TTTTTAGAA
1 TTTTTA-AA
43783175 TTTTTAATA
1 TTTTTAA-A
43783184 TTTTTAAA
1 TTTTTAAA
43783192 TTTTTAAA
1 TTTTTAAA
43783200 T
1 T
43783201 GAGGATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 11 0.44
9 14 0.56
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (8 bp):
TTTTTAAA
Found at i:43783588 original size:19 final size:18
Alignment explanation
Indices: 43783564--43783620 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
43783554 CGTTTAATTA
43783564 AATTTTAATATTTTAAAAT
1 AATTTTAATATTTT-AAAT
* * *
43783583 ATTTTTTATATTTTTAAT
1 AATTTTAATATTTTAAAT
43783601 AATTTTAATGATTTTTAAAT
1 AATTTTAAT-A-TTTTAAAT
43783621 TTTAAATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 10 0.33
19 13 0.43
20 7 0.23
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
AATTTTAATATTTTAAAT
Found at i:43783595 original size:9 final size:9
Alignment explanation
Indices: 43783566--43783634 Score: 68
Period size: 9 Copynumber: 7.4 Consensus size: 9
43783556 TTTAATTAAA
43783566 TTTTAATAT
1 TTTTAATAT
*
43783575 TTTAAAATAT
1 TTT-TAATAT
*
43783585 TTTTTATAT
1 TTTTAATAT
*
43783594 TTTTAATAA
1 TTTTAATAT
43783603 TTTTAATGAT
1 TTTTAAT-AT
43783613 TTTTAA-AT
1 TTTTAATAT
*
43783621 TTTAAATAT
1 TTTTAATAT
43783630 ATTTT
1 -TTTT
43783635 TTTTGAATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
8 7 0.15
9 23 0.48
10 18 0.38
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (9 bp):
TTTTAATAT
Found at i:43783633 original size:19 final size:20
Alignment explanation
Indices: 43783564--43783635 Score: 57
Period size: 19 Copynumber: 3.9 Consensus size: 20
43783554 CGTTTAATTA
**
43783564 AATTTTAATAT-TTTAAAAT
1 AATTTTAATATATTTTTAAT
*
43783583 -ATTTT-TTATATTTTTAAT
1 AATTTTAATATATTTTTAAT
*
43783601 AATTTTAAT-GATTTTT-A-
1 AATTTTAATATATTTTTAAT
43783618 AATTTTAAATATATTTTT
1 AATTTT-AATATATTTTT
43783636 TTTGAATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
17 9 0.21
18 15 0.36
19 17 0.40
20 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (20 bp):
AATTTTAATATATTTTTAAT
Found at i:43788767 original size:21 final size:22
Alignment explanation
Indices: 43788743--43788799 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
43788733 ATTCAAAAAA
43788743 AATTTTAAATTTAACTTTTTT-
1 AATTTTAAATTTAACTTTTTTG
* * *
43788764 AATTATATATTT-ATTTTTTTG
1 AATTTTAAATTTAACTTTTTTG
43788785 AATTTTTATAATTTA
1 AA-TTTTA-AATTTA
43788800 CATATATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
20 7 0.26
21 12 0.44
22 4 0.15
23 4 0.15
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (22 bp):
AATTTTAAATTTAACTTTTTTG
Found at i:43792647 original size:264 final size:262
Alignment explanation
Indices: 43792147--43792674 Score: 758
Period size: 264 Copynumber: 2.0 Consensus size: 262
43792137 TTACACTATT
* *
43792147 TATGTAACAGCCCGTTTTAAGTGAAATCGAATACCAGTTTTGGGACCACAAATCTGAGTCTGAAA
1 TATGTAACAGCCCGTTTTAAGTGAAATCGAATACCAGTTTCGGGACCACAAATCTGAGTCCGAAA
* ** *
43792212 GAAAATTTATTTTAATATTATTTTATGGTTTGCATTATGATAGGAATATCGTATAAAAATTTCGT
66 GAAAATTTATTTTAATATTATTTTATGATTACCATTATGATAGGAATAACGTATAAAAATTTCGT
* *
43792277 TAAGAAAAAATTACCGATTATATGATTAATTGATAAAAGGACCAAATTGCATAGAATGAAAAAGT
131 TAAGAAAAAATTACCGATTACATGATTAATTGATAAAAGGACCAAATTGCATAAAATGAAAAAGT
* *
43792342 TGAATTCTAGTAGCTAAAAGGATCAAATAGCTATAGAATTCAAAATTGGAGGTCCTTATATGACA
196 TGAATTCTAGTAGCTAAAAGGATCAAATAGCTATAGAATTCAAAATTGAAGGTCCTTATAAGACA
43792407 AA
261 AA
* * ***
43792409 TATGTAACAGCTCGTTTTTAGTGAAATCAGAATAGTGGTTTCGGGACCACAAAT-TCGAGTCCGA
1 TATGTAACAGCCCGTTTTAAGTGAAATC-GAATACCAGTTTCGGGACCACAAATCT-GAGTCCGA
*
43792473 AAGAGAATTTATTTTAATATTA-TTTATGATCTACCA-TATGATAGGAATAACGTATAAAAATTT
64 AAGAAAATTTATTTTAATATTATTTTATGAT-TACCATTATGATAGGAATAACGTATAAAAATTT
* * *
43792536 CGTTAAGAAAAATTTTACCGATTACATGTTTAATTGTTAGAAAGGACCAAATTGCATAAAAT-AC
128 CGTTAAGAAAAA-ATTACCGATTACATGATTAATTGATA-AAAGGACCAAATTGCATAAAATGA-
* * * *
43792600 AAAAGTTGAATTCTAGTAGCTAGAGGGATCAAATAGCTATGGAATTCAAAATTTAAGGTCCTTAT
190 AAAAGTTGAATTCTAGTAGCTAAAAGGATCAAATAGCTATAGAATTCAAAATTGAAGGTCCTTAT
*
43792665 AAGGCAAA
255 AAGACAAA
43792673 TA
1 TA
43792675 GACCACTAAG
Statistics
Matches: 236, Mismatches: 24, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
262 72 0.31
263 75 0.32
264 89 0.38
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (262 bp):
TATGTAACAGCCCGTTTTAAGTGAAATCGAATACCAGTTTCGGGACCACAAATCTGAGTCCGAAA
GAAAATTTATTTTAATATTATTTTATGATTACCATTATGATAGGAATAACGTATAAAAATTTCGT
TAAGAAAAAATTACCGATTACATGATTAATTGATAAAAGGACCAAATTGCATAAAATGAAAAAGT
TGAATTCTAGTAGCTAAAAGGATCAAATAGCTATAGAATTCAAAATTGAAGGTCCTTATAAGACA
AA
Found at i:43792699 original size:29 final size:29
Alignment explanation
Indices: 43792666--43792725 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
43792656 GGTCCTTATA
43792666 AGGCAAATAGACCACTAAGAGGAGTTAGT
1 AGGCAAATAGACCACTAAGAGGAGTTAGT
*
43792695 AGGCAAATAGACCATTAAGAGGAGTTAGT
1 AGGCAAATAGACCACTAAGAGGAGTTAGT
43792724 AG
1 AG
43792726 ATAATTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.12, G:0.28, T:0.18
Consensus pattern (29 bp):
AGGCAAATAGACCACTAAGAGGAGTTAGT
Found at i:43793167 original size:27 final size:28
Alignment explanation
Indices: 43793136--43793189 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
43793126 TTTAGGGGTT
*
43793136 AAATTGTAAA-TATGTAAAATACATGGA
1 AAATTCTAAATTATGTAAAATACATGGA
* *
43793163 AAATTCTAAATTTTGTGAAATACATGG
1 AAATTCTAAATTATGTAAAATACATGG
43793190 GCTGTAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (28 bp):
AAATTCTAAATTATGTAAAATACATGGA
Found at i:43793874 original size:25 final size:26
Alignment explanation
Indices: 43793808--43793875 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
43793798 GTCTCGTTAT
*
43793808 ATGGCTCTTCGTGAGCATCCCGATTA
1 ATGGCTCTTCGTGAGCTTCCCGATTA
*
43793834 AAGGCTCTTCGTGAGCTTCCCG-TTA
1 ATGGCTCTTCGTGAGCTTCCCGATTA
43793859 ATTGGCTCTTCG-GAGCT
1 A-TGGCTCTTCGTGAGCT
43793876 ACCGGTTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 9 0.24
26 29 0.76
ACGTcount: A:0.16, C:0.26, G:0.25, T:0.32
Consensus pattern (26 bp):
ATGGCTCTTCGTGAGCTTCCCGATTA
Found at i:43793883 original size:25 final size:25
Alignment explanation
Indices: 43793803--43793883 Score: 83
Period size: 26 Copynumber: 3.2 Consensus size: 25
43793793 TGAGTGTCTC
*
43793803 GTTATATGGCTCTTCGTGAGCATCCCG
1 GTTA-ATGGCTCTTCGTGAGC-TACCG
* * * *
43793830 ATTAAAGGCTCTTCGTGAGCTTCCC
1 GTTAATGGCTCTTCGTGAGCTACCG
43793855 GTTAATTGGCTCTTCG-GAGCTACCG
1 GTTAA-TGGCTCTTCGTGAGCTACCG
43793880 GTTA
1 GTTA
43793884 TTGACTCACA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
25 18 0.40
26 24 0.53
27 3 0.07
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (25 bp):
GTTAATGGCTCTTCGTGAGCTACCG
Found at i:43796506 original size:25 final size:25
Alignment explanation
Indices: 43796450--43796519 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
43796440 ATGGTTCTTC
*
43796450 GGAGCTTCTCGATAT-TGGCTCGCT
1 GGAGCTTCTCGATATATGGCTAGCT
* * * *
43796474 TGAACTTCCCGATATATGGCTATCT
1 GGAGCTTCTCGATATATGGCTAGCT
43796499 GGAGCTTCTCGAT-TAATGGCT
1 GGAGCTTCTCGATAT-ATGGCT
43796520 CTTCGGAGCT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
24 13 0.36
25 23 0.64
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (25 bp):
GGAGCTTCTCGATATATGGCTAGCT
Found at i:43796513 original size:74 final size:73
Alignment explanation
Indices: 43796426--43796567 Score: 189
Period size: 74 Copynumber: 1.9 Consensus size: 73
43796416 GGCTCTTTGT
* * *
43796426 GAGCTTCCTGATTAATGGTTCTTCGGAGCTTCTCGATATTGGCTCGCT-TGAACTTCCCGATATA
1 GAGCTTCCTGATTAATGGCTCTTCGGAGCTACCCGATATTGGCTCG-TATGAACTTCCCGA-ATA
43796490 TGGCTATCTG
64 TGGCTATCTG
* * *
43796500 GAGCTT-CTCGATTAATGGCTCTTCGGAGCTACCCGTTATTGGCTCGTATGAGCTTCCTGAATAT
1 GAGCTTCCT-GATTAATGGCTCTTCGGAGCTACCCGATATTGGCTCGTATGAACTTCCCGAATAT
43796564 GGCT
65 GGCT
43796568 CTTATGAGCT
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
73 11 0.18
74 49 0.82
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (73 bp):
GAGCTTCCTGATTAATGGCTCTTCGGAGCTACCCGATATTGGCTCGTATGAACTTCCCGAATATG
GCTATCTG
Found at i:43796527 original size:25 final size:25
Alignment explanation
Indices: 43796400--43796580 Score: 106
Period size: 24 Copynumber: 7.3 Consensus size: 25
43796390 GACTCTTCAT
* *
43796400 GAGCTTCCCGATTAAAGGCTCTTTG
1 GAGCTTCCCGATTAATGGCTCTTCG
* *
43796425 TGAGCTTCCTGATTAATGGTTCTTCG
1 -GAGCTTCCCGATTAATGGCTCTTCG
* *
43796451 GAGCTTCTCGA-TATTGGCTCGCTT--
1 GAGCTTCCCGATTAATGGCT--CTTCG
* *
43796475 GAACTTCCCGA-TATATGGCT-ATCTG
1 GAGCTTCCCGATTA-ATGGCTCTTC-G
*
43796500 GAGCTTCTCGATTAATGGCTCTTCG
1 GAGCTTCCCGATTAATGGCTCTTCG
* * * **
43796525 GAGCTACCCG-TTATTGGCTCGTAT
1 GAGCTTCCCGATTAATGGCTCTTCG
* * **
43796549 GAGCTTCCTGAAT-ATGGCTCTTAT
1 GAGCTTCCCGATTAATGGCTCTTCG
43796573 GAGCTTCC
1 GAGCTTCC
43796581 TATTATATAG
Statistics
Matches: 120, Mismatches: 26, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
22 1 0.01
24 52 0.43
25 39 0.32
26 28 0.23
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (25 bp):
GAGCTTCCCGATTAATGGCTCTTCG
Found at i:43809816 original size:27 final size:26
Alignment explanation
Indices: 43809786--43809865 Score: 79
Period size: 29 Copynumber: 2.9 Consensus size: 26
43809776 TTTTTTATTT
43809786 AATTTATAATTTTTCAATATTTTTTAC
1 AATTTATAATTTTT-AATATTTTTTAC
* *
43809813 AATTTATTATCATTTTTAATTTTTTTTAG
1 AATTTA-TA--ATTTTTAATATTTTTTAC
**
43809842 AAAATATAATTTTTAATGATTTTT
1 AATTTATAATTTTTAAT-ATTTTT
43809866 GACTAATCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
26 9 0.20
27 11 0.25
28 4 0.09
29 14 0.32
30 6 0.14
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.60
Consensus pattern (26 bp):
AATTTATAATTTTTAATATTTTTTAC
Found at i:43810502 original size:238 final size:239
Alignment explanation
Indices: 43810087--43810666 Score: 711
Period size: 238 Copynumber: 2.4 Consensus size: 239
43810077 TTATTCAAAT
* * * * * * *
43810087 TCTTCATCTAGGAGAAGAAAGAGTCTCGATAGGTCCAGTTCTA-TAATAAACACTGCTGCAGCTG
1 TCTTCTTCTAGGAGAAGAAAGAGTCTTGACAGGTCCAGTTCTATTAGT-AAGACTACTGCAGCTA
* ** *
43810151 TAGTGGTTGAGATGGATGAAATGAAA-TGAGTTTCTAATGCAAAGGTCTCTCCTGCAACTGTTTA
65 TAGAGGTCCAGATGGATGAAATGAAATTG-GTTTCTAATGCAAAGGTCTCTCCTGCAACTGTTGA
** * * *
43810215 TTATGTCAAAGGACCTAAGCTTGATGTGCTAGATATTGATTCCAACTCCAATTCTTTGAGGGGTG
129 TTACATCAAAGGACCTAAGCTCGATGTGCTAGATAGTGATTCCAACTCCAATTCTTTGAGGGATG
* * *
43810280 AATCACTTCCCGGAGATCCAACTCAAACAAGGGATTATTATTTTGAT
194 AATCACTGCCCGGAGAGCCAACTCAAACAA-GGATTATTATTTTGAA
* **
43810327 TCTTCTTCTAGGAGAAG-AA-AGTCTTGACAGGTCCAGTTCTATTGGTAAGTTTACTGCAGCTAT
1 TCTTCTTCTAGGAGAAGAAAGAGTCTTGACAGGTCCAGTTCTATTAGTAAGACTACTGCAGCTAT
* *
43810390 AGTAGG-CCAGATGGATGAATTGAAATTGGTTTCTAATGCAAAGGTCTTTCCTGCAACTGTTGAT
66 AG-AGGTCCAGATGGATGAAATGAAATTGGTTTCTAATGCAAAGGTCTCTCCTGCAACTGTTGAT
* * * * * *
43810454 TACATCAATGGATCTAAGCTCGGTGTTCTAGATGGTGATTCTAACTCCAATTCTTTGAGGGATGA
130 TACATCAAAGGACCTAAGCTCGATGTGCTAGATAGTGATTCCAACTCCAATTCTTTGAGGGATGA
* * * **
43810519 ATCACTGCCTGGAGGGCTAACTCGGACAAGGATTATTATTTTGAA
195 ATCACTGCCCGGAGAGCCAACTCAAACAAGGATTATTATTTTGAA
* ** *
43810564 TCTTCTTCTAGGAGAAGAAAGAGTCTTGACATGTCCAGTTCTATTAGTAAGACTGTTGCAGCTGT
1 TCTTCTTCTAGGAGAAGAAAGAGTCTTGACAGGTCCAGTTCTATTAGTAAGACTACTGCAGCTAT
* **
43810629 AGCGGTTGAGATGGATGAAATGAAATTGGTTTCTAATG
66 AGAGGTCCAGATGGATGAAATGAAATTGGTTTCTAATG
43810667 TTGATTACAT
Statistics
Matches: 288, Mismatches: 46, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
237 32 0.11
238 164 0.57
239 76 0.26
240 16 0.06
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.32
Consensus pattern (239 bp):
TCTTCTTCTAGGAGAAGAAAGAGTCTTGACAGGTCCAGTTCTATTAGTAAGACTACTGCAGCTAT
AGAGGTCCAGATGGATGAAATGAAATTGGTTTCTAATGCAAAGGTCTCTCCTGCAACTGTTGATT
ACATCAAAGGACCTAAGCTCGATGTGCTAGATAGTGATTCCAACTCCAATTCTTTGAGGGATGAA
TCACTGCCCGGAGAGCCAACTCAAACAAGGATTATTATTTTGAA
Found at i:43810850 original size:212 final size:213
Alignment explanation
Indices: 43810490--43810882 Score: 558
Period size: 212 Copynumber: 1.8 Consensus size: 213
43810480 TCTAGATGGT
* *
43810490 GATTCTAACTCCAATTCTTTGAGGGATGAATCACTGCCTGGAGGGCTAACTCGGACAAGGATTAT
1 GATTCTAACTCCAATTCTTTGAGGGATGAATCACTGCCTGAAGGGCTAACTCAGACAAGGATTAT
* ** * * *
43810555 TATTTTGAATCTTCTTCTAGGAGAAGAAAGAGTCTTGACATGTCCAGTTCTATTAGTAAGACTGT
66 TATTCTGAATCTTCTTCTAGGAGAAGAAAGAGTCGCGACAGGTCCAGTTCTATTAGGAAGACTGC
* * **
43810620 TGCAGCTGTAGCGGTTGAGATGGATGAAATGAAATTGGTTTCTAATGTTGATTACATTCATGGAC
131 GGCAGCTATAGCGGTTGAGACCGATGAAATGAAATTGGTTTCTAATGTTGATTACATTCATGGAC
43810685 CTCGGTGTGCCGGATAGG
196 CTCGGTGTGCCGGATAGG
* * * *
43810703 GATTCTAACTCCCATTCTTTGAGGGATGAATCACTTCCTGAAGGGTCTGA-TCAGACGA-GATTA
1 GATTCTAACTCCAATTCTTTGAGGGATGAATCACTGCCTGAAGGG-CTAACTCAGACAAGGATTA
* * *
43810766 TTATTCT-AATTCTTCTTCTAGGAGACGAAAGAGTCGCGATAGGTCCGGTTCTATTAGGAAGACT
65 TTATTCTGAA-TCTTCTTCTAGGAGAAGAAAGAGTCGCGACAGGTCCAGTTCTATTAGGAAGACT
* *
43810830 GCGGCATCTATAGTGGTTGAGACCGATGAAATGAAATTGGTTTCTAATGTTGA
129 GCGGCAGCTATAGCGGTTGAGACCGATGAAATGAAATTGGTTTCTAATGTTGA
43810883 AGCCTCTCCT
Statistics
Matches: 157, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
211 2 0.01
212 104 0.66
213 48 0.31
214 3 0.02
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (213 bp):
GATTCTAACTCCAATTCTTTGAGGGATGAATCACTGCCTGAAGGGCTAACTCAGACAAGGATTAT
TATTCTGAATCTTCTTCTAGGAGAAGAAAGAGTCGCGACAGGTCCAGTTCTATTAGGAAGACTGC
GGCAGCTATAGCGGTTGAGACCGATGAAATGAAATTGGTTTCTAATGTTGATTACATTCATGGAC
CTCGGTGTGCCGGATAGG
Found at i:43814569 original size:13 final size:13
Alignment explanation
Indices: 43814551--43814575 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43814541 TACTACACAC
43814551 AAAAAATAAAAAT
1 AAAAAATAAAAAT
43814564 AAAAAATAAAAA
1 AAAAAATAAAAA
43814576 ATCTGTAACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:43816142 original size:19 final size:19
Alignment explanation
Indices: 43816115--43816155 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
43816105 AAGAGGATAG
43816115 AAAAAAATA-AAAAAAAGTT
1 AAAAAAATATAAAAAAA-TT
*
43816134 AAAAGAATATAAAAAAATT
1 AAAAAAATATAAAAAAATT
43816153 AAA
1 AAA
43816156 TTGCTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (19 bp):
AAAAAAATATAAAAAAATT
Found at i:43820123 original size:23 final size:22
Alignment explanation
Indices: 43820061--43820123 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 22
43820051 ATATATATTT
*
43820061 AAATAT-TTTTAATA-AAATAA
1 AAATATATTTTAATATAAACAA
*
43820081 AAATTAATATTTT-ATTTAAACAA
1 AAA-T-ATATTTTAATATAAACAA
43820104 AATATATATTTTAATATAAA
1 AA-ATATATTTTAATATAAA
43820124 AATTGATTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
20 3 0.09
21 1 0.03
22 11 0.32
23 18 0.53
24 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATATATTTTAATATAAACAA
Found at i:43821158 original size:22 final size:21
Alignment explanation
Indices: 43821133--43821183 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
43821123 TTTTGAGCAA
*
43821133 TTTATTTTTTCTTTTATGT-TCT
1 TTTATTTTTT-TTTCAT-TCTCT
*
43821155 TTTAACTTTTTTTTCATTCTCT
1 TTT-ATTTTTTTTTCATTCTCT
43821177 TTTATTT
1 TTTATTT
43821184 CTCCCTCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 4 0.17
22 14 0.58
23 6 0.25
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTATTTTTTTTTCATTCTCT
Found at i:43822171 original size:67 final size:66
Alignment explanation
Indices: 43822049--43822188 Score: 176
Period size: 67 Copynumber: 2.1 Consensus size: 66
43822039 TTTGGTGAAA
* * * * *
43822049 TTTT-TTTATAACCCCTTTATTGTTTGTGTTTTTATAATTTATTTTATAACCTTATTATAAATCT
1 TTTTGTTTATAACCCCTTTATTGTTTGAGTTTTTATAATTTAATTTAAAACATTATTACAAATC-
43822113 TT
65 TT
* * *
43822115 TTTTGTTTATAACCCCTTTAATT-TTTGAGTTTTTATAATTTAATTTAAAATATTATTGCAATTC
1 TTTTGTTTATAACCCCTTT-ATTGTTTGAGTTTTTATAATTTAATTTAAAACATTATTACAAATC
43822179 TT
65 TT
43822181 TTTTGTTT
1 TTTTGTTT
43822189 TGCCTATATT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
66 14 0.22
67 47 0.73
68 3 0.05
ACGTcount: A:0.25, C:0.09, G:0.06, T:0.60
Consensus pattern (66 bp):
TTTTGTTTATAACCCCTTTATTGTTTGAGTTTTTATAATTTAATTTAAAACATTATTACAAATCT
T
Found at i:43823095 original size:124 final size:124
Alignment explanation
Indices: 43822875--43823159 Score: 498
Period size: 124 Copynumber: 2.3 Consensus size: 124
43822865 TTTATTAAGG
* * * *
43822875 AAATCGCTCCCACGTGGAAGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGCGTTGACG
1 AAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGATCCTGAAAAAATAAATTTGAGTTGACG
43822940 TTTCTGAGCAAATAGTATAAAAAAGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCTA
66 TTTCTGAGCAAATAGTATAAAAAAGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCTA
* *
43822999 AAATCGCTCCCACTTGGACGTGCTTTTGCTACAGTAGATCCTGAAAAAATAAATTTGAGTTGACG
1 AAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGATCCTGAAAAAATAAATTTGAGTTGACG
*
43823064 TTTCTGAGGAAATAGTATAAAAAAGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCTA
66 TTTCTGAGCAAATAGTATAAAAAAGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCTA
*
43823123 AAATCGCTCCCACGTGGACGCGTTTTTGCTACAGTAG
1 AAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAG
43823160 CATGTTTAGG
Statistics
Matches: 151, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
124 151 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (124 bp):
AAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGATCCTGAAAAAATAAATTTGAGTTGACG
TTTCTGAGCAAATAGTATAAAAAAGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCTA
Found at i:43826377 original size:49 final size:49
Alignment explanation
Indices: 43826317--43826581 Score: 476
Period size: 49 Copynumber: 5.4 Consensus size: 49
43826307 AAAATATTCA
*
43826317 GTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAGCTATTTT
1 GTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTT
43826366 GTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTT
1 GTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTT
*
43826415 GTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTC
1 GTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTT
43826464 GTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTT
1 GTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTT
* *
43826513 GTATTTTATTACATCAAATAATATCAAAATATTCAAAATAAACTATTTT
1 GTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTT
* *
43826562 GTATTTTATTACATCAAATA
1 GTATTTTATTAAATGAAATA
43826582 TTTTGTATAA
Statistics
Matches: 211, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 211 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.41
Consensus pattern (49 bp):
GTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTT
Found at i:43828850 original size:11 final size:11
Alignment explanation
Indices: 43828836--43828922 Score: 51
Period size: 11 Copynumber: 8.3 Consensus size: 11
43828826 GAGAAATTTA
43828836 AGAGGAAATTG
1 AGAGGAAATTG
*
43828847 AGAGCAAATTG
1 AGAGGAAATTG
**
43828858 AGATTAAA-T-
1 AGAGGAAATTG
* *
43828867 A-TGG-ATTTG
1 AGAGGAAATTG
43828876 AGA-GAAAGTTG
1 AGAGGAAA-TTG
43828887 -GCAGGAAATTG
1 AG-AGGAAATTG
* *
43828898 AGAGCAATTTG
1 AGAGGAAATTG
43828909 AGAGGAAATTG
1 AGAGGAAATTG
43828920 AGA
1 AGA
43828923 AAATAATTGA
Statistics
Matches: 55, Mismatches: 13, Indels: 16
0.65 0.15 0.19
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 3 0.05
11 42 0.76
12 5 0.09
ACGTcount: A:0.43, C:0.03, G:0.31, T:0.23
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:43828874 original size:51 final size:51
Alignment explanation
Indices: 43828812--43828911 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
43828802 AAATAATTAA
*
43828812 AAATAGGGATTTAAGAGAAATTTAAG-AGGAAATTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAAGTT-AGCAGGAAATTGAGAGCAAATTGAGATT
* * * *
43828863 AAATATGGATTTGAGAGAAAGTTGGCAGGAAATTGAGAGCAATTTGAGA
1 AAATAGGGATTTAAGAGAAAGTTAGCAGGAAATTGAGAGCAAATTGAGA
43828912 GGAAATTGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 1 0.02
51 42 0.98
ACGTcount: A:0.44, C:0.03, G:0.28, T:0.25
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAAGTTAGCAGGAAATTGAGAGCAAATTGAGATT
Found at i:43828898 original size:22 final size:22
Alignment explanation
Indices: 43828873--43828922 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
43828863 AAATATGGAT
43828873 TTGAGAGAAAGTTG-GCAGGAAA
1 TTGAGAGAAAGTTGAG-AGGAAA
* *
43828895 TTGAGAGCAATTTGAGAGGAAA
1 TTGAGAGAAAGTTGAGAGGAAA
43828917 TTGAGA
1 TTGAGA
43828923 AAATAATTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.34, T:0.22
Consensus pattern (22 bp):
TTGAGAGAAAGTTGAGAGGAAA
Found at i:43834225 original size:23 final size:23
Alignment explanation
Indices: 43834198--43834253 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
43834188 TCAACTCCAA
* * *
43834198 TGCTGATCTTCATGTTGAGCTGC
1 TGCTGATCTCCATGCTGAACTGC
*
43834221 TGCTGGTCTCCATGCTGAACTGC
1 TGCTGATCTCCATGCTGAACTGC
*
43834244 TGCTGGTCTC
1 TGCTGATCTC
43834254 TTGTTGCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.11, C:0.27, G:0.27, T:0.36
Consensus pattern (23 bp):
TGCTGATCTCCATGCTGAACTGC
Found at i:43835286 original size:24 final size:24
Alignment explanation
Indices: 43835259--43835306 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
43835249 AATATATCCC
* *
43835259 TACACATACATACATGCGTACATA
1 TACACACACATACATACGTACATA
*
43835283 TACATACACATACATACGTACATA
1 TACACACACATACATACGTACATA
43835307 CGTGATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (24 bp):
TACACACACATACATACGTACATA
Found at i:43837780 original size:2 final size:2
Alignment explanation
Indices: 43837773--43837806 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
43837763 CTTTAAATTG
43837773 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
43837807 TGTTCGTTTT
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:43840156 original size:20 final size:20
Alignment explanation
Indices: 43840131--43840173 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
43840121 AAATAAGACT
43840131 AAATTAGTTGAATATTCCAA
1 AAATTAGTTGAATATTCCAA
43840151 AAATTAGTTGAATATTCCAA
1 AAATTAGTTGAATATTCCAA
43840171 AAA
1 AAA
43840174 AAAGTTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (20 bp):
AAATTAGTTGAATATTCCAA
Found at i:43840179 original size:20 final size:20
Alignment explanation
Indices: 43840136--43840181 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
43840126 AGACTAAATT
**
43840136 AGTTGAATATTCCAAAAATT
1 AGTTGAATATTCCAAAAAAA
43840156 AGTTGAATATTCCAAAAAAA
1 AGTTGAATATTCCAAAAAAA
43840176 AGTTGA
1 AGTTGA
43840182 TTAACTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (20 bp):
AGTTGAATATTCCAAAAAAA
Found at i:43842393 original size:23 final size:23
Alignment explanation
Indices: 43842367--43842416 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
43842357 TAGTTTCTAA
*
43842367 TTTTCTAATCTACTATATTATGT
1 TTTTCTAATCTACTACATTATGT
* *
43842390 TTTTTTTATCTACTACATTATGT
1 TTTTCTAATCTACTACATTATGT
43842413 TTTT
1 TTTT
43842417 ATATATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.22, C:0.12, G:0.04, T:0.62
Consensus pattern (23 bp):
TTTTCTAATCTACTACATTATGT
Found at i:43842577 original size:20 final size:21
Alignment explanation
Indices: 43842539--43842577 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
43842529 CACTCAACTT
43842539 TTAAAACTTACGTAATAGTCA
1 TTAAAACTTACGTAATAGTCA
43842560 TTAAAA-TTATCG-AATAGT
1 TTAAAACTTA-CGTAATAGT
43842578 TACATTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (21 bp):
TTAAAACTTACGTAATAGTCA
Found at i:43843872 original size:45 final size:45
Alignment explanation
Indices: 43843808--43843896 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
43843798 CTAGAACATT
* *
43843808 GTTTATTTGATATTTGTAAATATTTTCTAAACATTATTTAATATC
1 GTTTATTTGATATTTGTAAATATTTTATAAACATTATTAAATATC
43843853 GTTTATTTGATATTTGTAAATATTTTATAAACATTATTAAATAT
1 GTTTATTTGATATTTGTAAATATTTTATAAACATTATTAAATAT
43843897 TTTTTTCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (45 bp):
GTTTATTTGATATTTGTAAATATTTTATAAACATTATTAAATATC
Found at i:43843895 original size:21 final size:21
Alignment explanation
Indices: 43843824--43843899 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
43843814 TTGATATTTG
*
43843824 TAAATATTTTCTAAACATTAT
1 TAAATATTTTATAAACATTAT
* ** *
43843845 TTAATATCGTTTATTTGATATT-T
1 TAAATAT--TTTA-TAAACATTAT
43843868 GTAAATATTTTATAAACATTAT
1 -TAAATATTTTATAAACATTAT
43843890 TAAATATTTT
1 TAAATATTTT
43843900 TTTCAAAAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
21 21 0.51
22 5 0.12
23 4 0.10
24 11 0.27
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.53
Consensus pattern (21 bp):
TAAATATTTTATAAACATTAT
Found at i:43846768 original size:6 final size:6
Alignment explanation
Indices: 43846757--43846782 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
43846747 CATTACTGCT
43846757 TGTTGC TGTTGC TGTTGC TGTTGC TG
1 TGTTGC TGTTGC TGTTGC TGTTGC TG
43846783 CATGCTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.35, T:0.50
Consensus pattern (6 bp):
TGTTGC
Found at i:43854473 original size:6 final size:6
Alignment explanation
Indices: 43854462--43854492 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
43854452 AAACCCAGCC
43854462 GTCGAG GTCGAG GTCGAG GTCGAG GTCGAG G
1 GTCGAG GTCGAG GTCGAG GTCGAG GTCGAG G
43854493 GTTTTACAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.52, T:0.16
Consensus pattern (6 bp):
GTCGAG
Found at i:43856795 original size:6 final size:6
Alignment explanation
Indices: 43856784--43856808 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
43856774 AGTACTTGAG
43856784 CCTTTT CCTTTT CCTTTT CCTTTT C
1 CCTTTT CCTTTT CCTTTT CCTTTT C
43856809 TTTCATGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (6 bp):
CCTTTT
Found at i:43859684 original size:34 final size:35
Alignment explanation
Indices: 43859640--43859706 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
43859630 CAGTAAAATA
*
43859640 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
43859674 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
43859707 CTGATGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:43867746 original size:27 final size:27
Alignment explanation
Indices: 43867705--43867784 Score: 133
Period size: 27 Copynumber: 3.0 Consensus size: 27
43867695 ACTCCCTGGG
*
43867705 ACAAGGGAACACTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
43867732 ACAAGGGAACCCTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
**
43867759 ACAAGGGTTCCCTGTTGGCGGCACCA
1 ACAAGGGAACCCTGTTGGCGGCACCA
43867785 CTCGTGTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.28, C:0.29, G:0.30, T:0.14
Consensus pattern (27 bp):
ACAAGGGAACCCTGTTGGCGGCACCAA
Found at i:43867949 original size:3 final size:3
Alignment explanation
Indices: 43867941--43867975 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
43867931 AATTTTATAG
43867941 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
43867976 AGATGTTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:43868085 original size:12 final size:12
Alignment explanation
Indices: 43867941--43868085 Score: 55
Period size: 12 Copynumber: 11.8 Consensus size: 12
43867931 AATTTTATAG
*
43867941 TATTATTATTAT
1 TATTATTATTAA
*
43867953 TATTATTATTAT
1 TATTATTATTAA
43867965 TATTATTATTAA
1 TATTATTATTAA
* * *
43867977 GA-TGTTACTTAG
1 TATTATTA-TTAA
* *
43867989 TATTATTGTTAG
1 TATTATTATTAA
* ** *
43868001 TA-AAAAATTAG
1 TATTATTATTAA
*
43868012 TATTATT-TTTA
1 TATTATTATTAA
43868023 TAGTTAGTTATTAA
1 TA-TTA-TTATTAA
*
43868037 TAATT-TTAGTTAG
1 T-ATTATTA-TTAA
*
43868050 TATTATTTTGTATA
1 TATTATTAT-TA-A
**
43868064 TAAAATTATTAA
1 TATTATTATTAA
43868076 TATTATTATT
1 TATTATTATT
43868086 GTGTTAGTTA
Statistics
Matches: 97, Mismatches: 25, Indels: 22
0.67 0.17 0.15
Matches are distributed among these distances:
11 15 0.15
12 54 0.56
13 15 0.15
14 12 0.12
15 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.08, T:0.56
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:43868748 original size:18 final size:18
Alignment explanation
Indices: 43868704--43868748 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
43868694 TTGATATGGT
* *
43868704 TGGTGGTGAAGAAGAATG
1 TGGTGGCGAAGAAGAAGG
* *
43868722 TGATTGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
43868740 TGGTGGCGA
1 TGGTGGCGA
43868749 TCATTGGGAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.04, G:0.44, T:0.20
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:43871483 original size:27 final size:27
Alignment explanation
Indices: 43871445--43871578 Score: 205
Period size: 27 Copynumber: 5.0 Consensus size: 27
43871435 ATAACACGAG
43871445 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAGGGAACCCTTGTT
43871472 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAGGGAACCCTTGTT
43871499 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAGGGAACCCTTGTT
* *** *
43871526 TGGTGCTGCCAACAGGGTTTCATTGTT
1 TGGTGCCGCCAACAGGGAACCCTTGTT
**
43871553 TGGTGCCGCCAACAGGGTTCCCTTGT
1 TGGTGCCGCCAACAGGGAACCCTTGT
43871579 CCGAGGGAGT
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 99 1.00
ACGTcount: A:0.16, C:0.28, G:0.30, T:0.26
Consensus pattern (27 bp):
TGGTGCCGCCAACAGGGAACCCTTGTT
Found at i:43871671 original size:28 final size:29
Alignment explanation
Indices: 43871637--43871706 Score: 108
Period size: 28 Copynumber: 2.5 Consensus size: 29
43871627 TTTTTTTTGG
43871637 ATATATTTTGGTAAAT-AAAAAAAATTAT
1 ATATATTTTGGTAAATAAAAAAAAATTAT
*
43871665 ATATATTTTAGTAAATAAAAAAAAATTAT
1 ATATATTTTGGTAAATAAAAAAAAATTAT
*
43871694 A-ACATTTTGGTAA
1 ATATATTTTGGTAA
43871707 TTTTTAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 25 0.66
29 13 0.34
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (29 bp):
ATATATTTTGGTAAATAAAAAAAAATTAT
Found at i:43877185 original size:18 final size:18
Alignment explanation
Indices: 43877164--43877208 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
43877154 ATATGTAGGT
*
43877164 ATAATAATATATAATA-TA
1 ATAATAATA-ACAATATTA
43877182 ATAATAATAACAATATTA
1 ATAATAATAACAATATTA
43877200 ATAA-AATAA
1 ATAATAATAA
43877209 ACCCCCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAATAATAACAATATTA
Found at i:43879831 original size:13 final size:14
Alignment explanation
Indices: 43879815--43879856 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
43879805 TTTCAATTTT
43879815 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
43879828 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
43879843 ATTTTAAATAATAT
1 ATTTT-AATAATAT
43879857 TCTTCATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:43879841 original size:16 final size:16
Alignment explanation
Indices: 43879819--43879855 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
43879809 AATTTTATTT
43879819 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
43879836 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
43879851 TAATA
1 TAATA
43879856 TTCTTCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:43879906 original size:15 final size:15
Alignment explanation
Indices: 43879874--43879944 Score: 56
Period size: 15 Copynumber: 4.6 Consensus size: 15
43879864 ATATTATTGA
43879874 AAAT-TTTTAAT-AT
1 AAATATTTTAATAAT
*
43879887 TAATATTTTAATAAT
1 AAATATTTTAATAAT
*
43879902 AAATATTTATTAAAATTAT
1 AAATA-TT-TT--AATAAT
*
43879921 AAATATATTAATAAT
1 AAATATTTTAATAAT
*
43879936 AAATGTTTT
1 AAATATTTT
43879945 GTAGTGTAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
13 3 0.07
14 7 0.16
15 18 0.40
16 2 0.04
17 4 0.09
18 1 0.02
19 10 0.22
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (15 bp):
AAATATTTTAATAAT
Found at i:43880789 original size:17 final size:17
Alignment explanation
Indices: 43880769--43880801 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
43880759 CATAAAATAT
43880769 TAAAT-TTTTTAGAAAAA
1 TAAATATTTTTA-AAAAA
43880786 TAAATATTTTTAAAAA
1 TAAATATTTTTAAAAA
43880802 TATTTTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TAAATATTTTTAAAAAA
Found at i:43882169 original size:24 final size:24
Alignment explanation
Indices: 43882116--43882161 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
43882106 TTTTTCTAGA
* *
43882116 ATATTTAGTATTTATTAGTATAAT
1 ATATTTAGCATTTATTAGCATAAT
43882140 ATATTTAGCATTTATTAGCATA
1 ATATTTAGCATTTATTAGCATA
43882162 GTTTATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (24 bp):
ATATTTAGCATTTATTAGCATAAT
Found at i:43882985 original size:41 final size:37
Alignment explanation
Indices: 43882940--43883030 Score: 101
Period size: 40 Copynumber: 2.3 Consensus size: 37
43882930 AACAGGCTTT
43882940 TAGCGGCGTTTGGACAAAAAACGCCACTAAAAATGAAGCAG
1 TAGCGGCGTTTGG---AAAAACGCCACTAAAAAT-AAGCAG
** *
43882981 TAGCGGCGCTTTTGGAAAAACGCTGCTAAAAATAAGCAT
1 TAGCGGCG--TTTGGAAAAACGCCACTAAAAATAAGCAG
43883020 TAGCGGCGTTT
1 TAGCGGCGTTT
43883031 TTTGGAAAGC
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
37 3 0.07
39 13 0.29
40 16 0.36
41 8 0.18
43 5 0.11
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (37 bp):
TAGCGGCGTTTGGAAAAACGCCACTAAAAATAAGCAG
Found at i:43883010 original size:40 final size:40
Alignment explanation
Indices: 43882956--43883038 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
43882946 CGTTTGGACA
43882956 AAAAACGCCACTAAAAATGAAGCAGTAGCGGCG-CTTTTGG
1 AAAAACGCCACTAAAAAT-AAGCAGTAGCGGCGTCTTTTGG
** * *
43882996 AAAAACGCTGCTAAAAATAAGCATTAGCGGCGTTTTTTGG
1 AAAAACGCCACTAAAAATAAGCAGTAGCGGCGTCTTTTGG
43883036 AAA
1 AAA
43883039 GCGCCGCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 13 0.34
40 25 0.66
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.22
Consensus pattern (40 bp):
AAAAACGCCACTAAAAATAAGCAGTAGCGGCGTCTTTTGG
Found at i:43883226 original size:42 final size:42
Alignment explanation
Indices: 43883074--43883226 Score: 181
Period size: 41 Copynumber: 3.7 Consensus size: 42
43883064 GTTTTGGGGT
* * * *
43883074 CTTTAGCGGCATTTTCTGAA-AAGCGCCTCTAATGCT--TAGGT
1 CTTTAGCGGCGTTTTTTGAATAAGCGCCGCTAATGCTCGTA--C
*
43883115 CTTTAGCGGCG-TTTTTGAATAAGTGCCGCTAATGCTCGTAC
1 CTTTAGCGGCGTTTTTTGAATAAGCGCCGCTAATGCTCGTAC
43883156 CTTTAGCGGCGTTTTTT-AATAAGCGCCGCTAATGCTCGTAC
1 CTTTAGCGGCGTTTTTTGAATAAGCGCCGCTAATGCTCGTAC
* **
43883197 CTTTAGCAGCGTTTTTTGAGGAAGCGCCGC
1 CTTTAGCGGCGTTTTTTGAATAAGCGCCGC
43883227 AAAAACATTT
Statistics
Matches: 98, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
40 7 0.07
41 74 0.76
42 15 0.15
43 2 0.02
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTTTGAATAAGCGCCGCTAATGCTCGTAC
Found at i:43884193 original size:18 final size:19
Alignment explanation
Indices: 43884170--43884211 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
43884160 GGACAGGACC
*
43884170 AAAATATAAGAA-AAATAA
1 AAAATATAAAAAGAAATAA
43884188 AAAATATAAAAAGGAAATAA
1 AAAATATAAAAA-GAAATAA
43884208 AAAA
1 AAAA
43884212 CTAAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.52
20 10 0.48
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (19 bp):
AAAATATAAAAAGAAATAA
Found at i:43884242 original size:21 final size:21
Alignment explanation
Indices: 43884218--43884284 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 21
43884208 AAAACTAAAA
43884218 TTTATAATTTTA-TCAAAAACT
1 TTTATAATTTTACT-AAAAACT
* *
43884239 TTTA-AATATTACTTAAAACT
1 TTTATAATTTTACTAAAAACT
*
43884259 TTAATAATTATTTACTAAAAA-T
1 TTTATAA-T-TTTACTAAAAACT
43884281 TTTA
1 TTTA
43884285 ATGAAAATAC
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
20 15 0.42
21 7 0.19
22 5 0.14
23 9 0.25
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTATAATTTTACTAAAAACT
Found at i:43884279 original size:23 final size:22
Alignment explanation
Indices: 43884232--43884286 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
43884222 TAATTTTATC
43884232 AAAAACTTT--TAAATATTACT
1 AAAAACTTTAATAAATATTACT
* *
43884252 TAAAACTTTAATAATTATTTACT
1 AAAAACTTTAATAAATA-TTACT
*
43884275 AAAAATTTTAAT
1 AAAAACTTTAAT
43884287 GAAAATACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 8 0.29
22 5 0.18
23 15 0.54
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAAACTTTAATAAATATTACT
Found at i:43885235 original size:23 final size:23
Alignment explanation
Indices: 43885206--43885249 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
43885196 AAAATAAAAT
43885206 TTTAGGGTTTTGTTTATTTGGGA
1 TTTAGGGTTTTGTTTATTTGGGA
43885229 TTTAGGGTTTTGTTTATTTGG
1 TTTAGGGTTTTGTTTATTTGG
43885250 AATGAATCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.00, G:0.30, T:0.59
Consensus pattern (23 bp):
TTTAGGGTTTTGTTTATTTGGGA
Found at i:43886962 original size:18 final size:16
Alignment explanation
Indices: 43886920--43886952 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
43886910 AAACTTGTAG
43886920 AAATAAGTTTGAAGAT
1 AAATAAGTTTGAAGAT
43886936 AAATAAGTTTGAAGAT
1 AAATAAGTTTGAAGAT
43886952 A
1 A
43886953 TAATTGAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (16 bp):
AAATAAGTTTGAAGAT
Found at i:43887028 original size:9 final size:9
Alignment explanation
Indices: 43887016--43887084 Score: 60
Period size: 9 Copynumber: 8.1 Consensus size: 9
43887006 TTAAAATAGT
43887016 TAACTTACA
1 TAACTTACA
43887025 TAACTTA-A
1 TAACTTACA
43887033 TTAA-TTA-A
1 -TAACTTACA
* *
43887041 T-ATTATATA
1 TAACT-TACA
43887050 TAACTTACA
1 TAACTTACA
43887059 TAACTTAC-
1 TAACTTACA
43887067 -AACTTACA
1 TAACTTACA
43887075 TAACTTACA
1 TAACTTACA
43887084 T
1 T
43887085 TAATATTAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
6 1 0.02
7 9 0.18
8 7 0.14
9 32 0.63
10 2 0.04
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (9 bp):
TAACTTACA
Found at i:43887072 original size:16 final size:16
Alignment explanation
Indices: 43887051--43887083 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
43887041 TATTATATAT
43887051 AACTTACATAACTTAC
1 AACTTACATAACTTAC
43887067 AACTTACATAACTTAC
1 AACTTACATAACTTAC
43887083 A
1 A
43887084 TTAATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:43893637 original size:66 final size:66
Alignment explanation
Indices: 43893498--43893637 Score: 169
Period size: 66 Copynumber: 2.1 Consensus size: 66
43893488 GGCAACATCG
*
43893498 AGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAATTGAAAGCAGATGCAGCAGC
1 AGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAATTGAAAGCAGATGCAGCAAC
*
43893563 C
66 A
* * * *
43893564 AGTGAAGCTGAGGTTCAACGAAAG-TATGAAGAACTCCAGC-AGCAGCTT-AAAGCAGATGCGGC
1 AGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCTA-CA-ATTGAAAGCAGATGCAGC
*
43893626 AATA
63 AACA
43893630 AGAGAAGC
1 AGAGAAGC
43893638 AAAGGCGGCA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
65 1 0.02
66 56 0.89
67 6 0.10
ACGTcount: A:0.41, C:0.18, G:0.26, T:0.15
Consensus pattern (66 bp):
AGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAATTGAAAGCAGATGCAGCAAC
A
Found at i:43893654 original size:21 final size:21
Alignment explanation
Indices: 43893633--43893725 Score: 123
Period size: 21 Copynumber: 4.4 Consensus size: 21
43893623 GGCAATAAGA
* * *
43893633 GAAGCAAAGGCGGCAGCGAGA
1 GAAGCAGAGGCTGCAGCGAGG
* *
43893654 GAAGTACAGGCTGCAGCGAGG
1 GAAGCAGAGGCTGCAGCGAGG
**
43893675 GAAGCAGAGGCTAAAGCGAGG
1 GAAGCAGAGGCTGCAGCGAGG
43893696 GAAGCAGAGGCTGCAGCGAGG
1 GAAGCAGAGGCTGCAGCGAGG
43893717 GAAGCAGAG
1 GAAGCAGAG
43893726 CAGCGTCAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.34, C:0.17, G:0.44, T:0.04
Consensus pattern (21 bp):
GAAGCAGAGGCTGCAGCGAGG
Found at i:43894113 original size:43 final size:43
Alignment explanation
Indices: 43894055--43894282 Score: 174
Period size: 43 Copynumber: 5.3 Consensus size: 43
43894045 TTTTTTTTTA
* * * * * * *
43894055 AAAAACGCCACTAAAGGTGTTGGCCTTTAGTGGCGTTTTTGGT
1 AAAAGCGCCGCTAAAGATGATGGTCTTTAGCGGCGTTTGTGGT
* **
43894098 AAAAGCGCCGCTAAAGAT-AAGGTTCTTTAGCGGCGTTTGTGAA
1 AAAAGCGCCGCTAAAGATGATGG-TCTTTAGCGGCGTTTGTGGT
* * *
43894141 AAAAGCGCCCCTAAAGATGATGGTCTTTCGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGATGATGGTCTTTAGCGGCGTTTGTGGT
* * *
43894184 GAAAGCGCCGCTAAAGATTA-GGTTCTTTA-CTGGAGTTTGTGGT
1 AAAAGCGCCGCTAAAGATGATGG-TCTTTAGC-GGCGTTTGTGGT
** * * ** * * *
43894227 CGAAGTGCCGCTATAGATCTTAGTCTTCAGCGGCGTTTGTGCT
1 AAAAGCGCCGCTAAAGATGATGGTCTTTAGCGGCGTTTGTGGT
*
43894270 AGAAGCGCCGCTA
1 AAAAGCGCCGCTA
43894283 TAGACCAACA
Statistics
Matches: 146, Mismatches: 33, Indels: 12
0.76 0.17 0.06
Matches are distributed among these distances:
42 5 0.03
43 136 0.93
44 5 0.03
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGATGATGGTCTTTAGCGGCGTTTGTGGT
Found at i:43894189 original size:86 final size:85
Alignment explanation
Indices: 43894054--43894212 Score: 219
Period size: 86 Copynumber: 1.9 Consensus size: 85
43894044 GTTTTTTTTT
* * * * *
43894054 AAAAAACGCCACTAAAGGTGTTGGCCTTTAGTGGCGTTTTTGGTAAAAGCGCCGCTAAAGATAAG
1 AAAAAACGCCACTAAAGATGATGGCCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATAAG
43894119 GTTCTTTAGCGGCGTTTGTG
66 GTTCTTTAGCGGCGTTTGTG
* * * * *
43894139 AAAAAAGCGCCCCTAAAGATGATGGTCTTTCGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATTA
1 AAAAAA-CGCCACTAAAGATGATGGCCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATAA
43894204 GGTTCTTTA
65 GGTTCTTTA
43894213 CTGGAGTTTG
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
85 6 0.10
86 57 0.90
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (85 bp):
AAAAAACGCCACTAAAGATGATGGCCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATAAG
GTTCTTTAGCGGCGTTTGTG
Found at i:43894253 original size:86 final size:86
Alignment explanation
Indices: 43894099--43894267 Score: 198
Period size: 86 Copynumber: 2.0 Consensus size: 86
43894089 GTTTTTGGTA
* * *
43894099 AAAGCGCCGCTAAAGATAAGGTTCTTTAGCGGCGTTTGTGAAAAAAGCGCCCCTAAAGATGATGG
1 AAAGCGCCGCTAAAGATAAGGTTCTTTAGCGGAGTTTGTGAAAAAAGCGCCCCTAAAGATCATAG
43894164 TCTTTC-GCGGCGTTTGTGGGG
66 TC-TTCAGCGGCGTTTGTGGGG
* **** * * * *
43894185 AAAGCGCCGCTAAAGATTAGGTTCTTTA-CTGGAGTTTGTGGTCGAAGTGCCGCTATAGATCTTA
1 AAAGCGCCGCTAAAGATAAGGTTCTTTAGC-GGAGTTTGTGAAAAAAGCGCCCCTAAAGATCATA
43894249 GTCTTCAGCGGCGTTTGTG
65 GTCTTCAGCGGCGTTTGTG
43894268 CTAGAAGCGC
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
85 4 0.06
86 65 0.94
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.29
Consensus pattern (86 bp):
AAAGCGCCGCTAAAGATAAGGTTCTTTAGCGGAGTTTGTGAAAAAAGCGCCCCTAAAGATCATAG
TCTTCAGCGGCGTTTGTGGGG
Found at i:43894401 original size:43 final size:43
Alignment explanation
Indices: 43894326--43894457 Score: 149
Period size: 43 Copynumber: 3.1 Consensus size: 43
43894316 GGCTTCTGTT
* * * *
43894326 AAGACCCTGATCTATAGCGACGCTTCGACCACAAACGCCACTA
1 AAGAACCTAATCTATAGCGGCGCTTCAACCACAAACGCCACTA
* * * *
43894369 AAGAACCTAATCTTTAGCGGCGCTTTC-CCCACAAACGCCGCAA
1 AAGAACCTAATCTATAGCGGCGC-TTCAACCACAAACGCCACTA
* * *
43894412 AAGACCCTGATCTATAGCGGCGCTTCAACCATAAACGCCACTA
1 AAGAACCTAATCTATAGCGGCGCTTCAACCACAAACGCCACTA
43894455 AAG
1 AAG
43894458 GTCTTAGTCT
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
42 3 0.04
43 67 0.92
44 3 0.04
ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17
Consensus pattern (43 bp):
AAGAACCTAATCTATAGCGGCGCTTCAACCACAAACGCCACTA
Found at i:43897370 original size:34 final size:35
Alignment explanation
Indices: 43897326--43897393 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
43897316 AAATTTCTTT
* *
43897326 ATATATATTTTAGAA-TTTCTAT-AATTTTTTAAAA
1 ATATAAATTTT-GAACTTTCTATAAATATTTTAAAA
*
43897360 ATATAAATTTTGAACTTTTTATAAATATTTTAAA
1 ATATAAATTTTGAACTTTCTATAAATATTTTAAA
43897394 TTTTTGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 3 0.10
34 16 0.55
35 10 0.34
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (35 bp):
ATATAAATTTTGAACTTTCTATAAATATTTTAAAA
Found at i:43919303 original size:45 final size:46
Alignment explanation
Indices: 43919230--43919342 Score: 180
Period size: 46 Copynumber: 2.5 Consensus size: 46
43919220 TACGTATGAT
*
43919230 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACCTGATCAGATAAGTGTAGCTAAAGCTAC
*
43919273 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACCTGATCAGATAAGTGTAGCTAAAGCTAC
43919319 CACTTATCACTTTGTCACCT-ATCA
1 CACTTATCACTTTGTCACCTGATCA
43919343 CTTATCACTT
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
43 10 0.16
44 5 0.08
45 24 0.38
46 25 0.39
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTGTCACCTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:43919358 original size:15 final size:14
Alignment explanation
Indices: 43919319--43919366 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
43919309 CTAAAGCTAC
43919319 CACTTATCACTTTGT
1 CACTTATCAC-TTGT
* *
43919334 CACCTATCACTTAT
1 CACTTATCACTTGT
*
43919348 CACTTTGTCACTTGT
1 CAC-TTATCACTTGT
43919363 CACT
1 CACT
43919367 GATTAGAAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 7 0.26
15 20 0.74
ACGTcount: A:0.21, C:0.31, G:0.06, T:0.42
Consensus pattern (14 bp):
CACTTATCACTTGT
Found at i:43929343 original size:124 final size:124
Alignment explanation
Indices: 43929199--43929478 Score: 404
Period size: 124 Copynumber: 2.3 Consensus size: 124
43929189 TTTTTTCGAG
* ** ** *
43929199 TTGACGTATCTG-GTCAAATAGTGGGAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTGTAAAATCGCTAATACCAGGATGCTATATGAGAAGAAATTGT
* *
43929263 GAAATCATGGCCTTGTGGACACGATTTCGCTACAG-TGGTCATGTA-AGAAATAATTTTTT
65 GAAATCATGCCCTCGTGGACACGATTTCGCTACAGTTGGTCATGTAGA-AAATAATTTTTT
*
43929322 TTGACGTTTTCTGAGCAAATAGTATAAAATCGCTAATACCAGGATGCTATATGAGAAGAAATTGT
1 TTGACG-TTTCTGAGCAAATAGTGTAAAATCGCTAATACCAGGATGCTATATGAGAAGAAATTGT
* *
43929387 GAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGAAAATAATTTTTT
65 GAAATCATGCCCTCGTGGACACGATTTCGCTACAGTTGGTCATGTAGAAAATAATTTTTT
*
43929447 TTGACGTTTCTGAGCAAATAGTGTCAAATCGC
1 TTGACGTTTCTGAGCAAATAGTGTAAAATCGC
43929479 GCCCTCGTGG
Statistics
Matches: 140, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
123 6 0.04
124 104 0.74
125 29 0.21
126 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTGTAAAATCGCTAATACCAGGATGCTATATGAGAAGAAATTGTG
AAATCATGCCCTCGTGGACACGATTTCGCTACAGTTGGTCATGTAGAAAATAATTTTTT
Found at i:43932791 original size:29 final size:29
Alignment explanation
Indices: 43932696--43933068 Score: 226
Period size: 29 Copynumber: 12.7 Consensus size: 29
43932686 GGTTTTTACA
*
43932696 TTAATTAAATTAGGTTAGGGTTAGGGATTT
1 TTAATTAAATTAAGTTAGGGTTAGGG-TTT
** * * * * *
43932726 CAAATAAAATGATAAATCAGGGTAAGAGTTT
1 TTAATTAAAT--TAAGTTAGGGTTAGGGTTT
* * *
43932757 TCAATTAAATTAGGTTAGGGTTAGGGATT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
* *
43932786 TTAATTAAAATAGGTTAGGGTTAGGG-TT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
* * *
43932814 TTCATGTAAAATAGGTTAGGGTTAGGGTAGGTT
1 TTAAT-TAAATTAAGTTAGGGTTAGGGT---TT
* ** *
43932847 AGGGTT-TTTAATTAAATTAAAATAGGGTAAGGGTTT
1 ----TTAATT-A--AA-TTAAGTTAGGGTTAGGGTTT
** *
43932883 TTAATTAAATTAAAATAGGGTAAGGG-TT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
** *
43932911 TTAATTAAATTAAAATAGGGTAAGGGTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
** *
43932940 TTAATTAAATTAAAATAGGGTAAGGGTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
*
43932969 TTAATTAAATTAAATTA-GGTTAGGG--T
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
*
43932995 TT--TT-AATTAAGTTA-AGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
* *
43933020 TTAATTAAAATAGGTTAGGGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
* *
43933049 TTAACTAAATTAGGTTAGGG
1 TTAATTAAATTAAGTTAGGG
43933069 ATTTTAATTA
Statistics
Matches: 284, Mismatches: 36, Indels: 47
0.77 0.10 0.13
Matches are distributed among these distances:
23 16 0.06
24 2 0.01
25 3 0.01
26 3 0.01
27 2 0.01
28 49 0.17
29 150 0.53
30 9 0.03
31 10 0.04
32 14 0.05
33 4 0.01
35 1 0.00
36 4 0.01
37 2 0.01
38 2 0.01
39 13 0.05
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (29 bp):
TTAATTAAATTAAGTTAGGGTTAGGGTTT
Found at i:43932834 original size:58 final size:59
Alignment explanation
Indices: 43932698--43932840 Score: 175
Period size: 61 Copynumber: 2.4 Consensus size: 59
43932688 TTTTTACATT
43932698 AATTAAATTAGGTTAGGGTTAGGGATTTCAAATAAAATGATAAATCAGGGTAAGAGTTTTC
1 AATTAAATTAGGTTAGGGTTAGGGATTTCAAATAAAATGAT--ATCAGGGTAAGAGTTTTC
* * * * *
43932759 AATTAAATTAGGTTAGGGTTAGGGATTTTAATTAAAATAGGT-T-AGGGTTAGGGTTTTC
1 AATTAAATTAGGTTAGGGTTAGGGATTTCAAATAAAAT-GATATCAGGGTAAGAGTTTTC
*
43932817 -ATGTAAAATAGGTTAGGGTTAGGG
1 AAT-TAAATTAGGTTAGGGTTAGGG
43932841 TAGGTTAGGG
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
57 2 0.03
58 33 0.45
59 1 0.01
61 36 0.49
62 2 0.03
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (59 bp):
AATTAAATTAGGTTAGGGTTAGGGATTTCAAATAAAATGATATCAGGGTAAGAGTTTTC
Found at i:43933014 original size:28 final size:29
Alignment explanation
Indices: 43932843--43933060 Score: 281
Period size: 29 Copynumber: 7.8 Consensus size: 29
43932833 GGTTAGGGTA
43932843 GGTTAGGGTTTTTAATTAAATTAAAATAG
1 GGTTAGGGTTTTTAATTAAATTAAAATAG
*
43932872 GGTAAGGGTTTTTAATTAAATTAAAATAG
1 GGTTAGGGTTTTTAATTAAATTAAAATAG
*
43932901 GGTAAGGG-TTTTAATTAAATTAAAATAG
1 GGTTAGGGTTTTTAATTAAATTAAAATAG
*
43932929 GGTAAGGGTTTTTAATTAAATTAAAATAG
1 GGTTAGGGTTTTTAATTAAATTAAAATAG
* *
43932958 GGTAAGGGTTTTTAATTAAATTAAATTA-
1 GGTTAGGGTTTTTAATTAAATTAAAATAG
*
43932986 GGTTAGGGTTTTTAATTAAGTT---A-A-
1 GGTTAGGGTTTTTAATTAAATTAAAATAG
* ***
43933010 -GTTAGGGTTTTTAATTAAAATAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAAAATAG
*
43933038 GGTTAGGGTTTTTAACTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
43933061 GGTTAGGGAT
Statistics
Matches: 172, Mismatches: 10, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
23 19 0.11
24 1 0.01
27 1 0.01
28 48 0.28
29 103 0.60
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAAAATAG
Found at i:43933017 original size:57 final size:58
Alignment explanation
Indices: 43932847--43933009 Score: 285
Period size: 57 Copynumber: 2.8 Consensus size: 58
43932837 AGGGTAGGTT
43932847 AGGGTTTTTAATTAAATTAAAATAGGGTAAGGGTTTTTAATTAAATTAAAATAGGGTA
1 AGGGTTTTTAATTAAATTAAAATAGGGTAAGGGTTTTTAATTAAATTAAAATAGGGTA
43932905 AGGG-TTTTAATTAAATTAAAATAGGGTAAGGGTTTTTAATTAAATTAAAATAGGGTA
1 AGGGTTTTTAATTAAATTAAAATAGGGTAAGGGTTTTTAATTAAATTAAAATAGGGTA
* * *
43932962 AGGGTTTTTAATTAAATTAAATTA-GGTTAGGGTTTTTAATTAAGTTAA
1 AGGGTTTTTAATTAAATTAAAATAGGGTAAGGGTTTTTAATTAAATTAA
43933010 GTTAGGGTTT
Statistics
Matches: 101, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
57 79 0.78
58 22 0.22
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (58 bp):
AGGGTTTTTAATTAAATTAAAATAGGGTAAGGGTTTTTAATTAAATTAAAATAGGGTA
Found at i:43933017 original size:86 final size:86
Alignment explanation
Indices: 43932847--43933009 Score: 283
Period size: 86 Copynumber: 1.9 Consensus size: 86
43932837 AGGGTAGGTT
43932847 AGGGTTTTTAATTAAATTAAAATAGGGTAAGGGTTTTTAATTAAATTAAAATAGGGTAAGGGTTT
1 AGGGTTTTTAATTAAATTAAAATAGGGTAAGGGTTTTTAATTAAATTAAAATAGGGTAAGGGTTT
43932912 TAATTAAATTAAAATAGGGTA
66 TAATTAAATTAAAATAGGGTA
* *
43932933 AGGGTTTTTAATTAAATTAAAATAGGGTAAGGGTTTTTAATTAAATTAAATTA-GGTTAGGGTTT
1 AGGGTTTTTAATTAAATTAAAATAGGGTAAGGGTTTTTAATTAAATTAAAATAGGGTAAGGG-TT
*
43932997 TTAATTAAGTTAA
65 TTAATTAAATTAA
43933010 GTTAGGGTTT
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
85 7 0.10
86 66 0.90
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (86 bp):
AGGGTTTTTAATTAAATTAAAATAGGGTAAGGGTTTTTAATTAAATTAAAATAGGGTAAGGGTTT
TAATTAAATTAAAATAGGGTA
Found at i:43933036 original size:23 final size:23
Alignment explanation
Indices: 43932947--43933091 Score: 110
Period size: 23 Copynumber: 5.8 Consensus size: 23
43932937 TTTTTAATTA
*
43932947 AATTAAAATAGGGTAAGGGTTTTT
1 AATTAAAATA-GGTTAGGGTTTTT
43932971 AATTAAATTAAATTAGGTTAGGGTTTTT
1 AATT--A--AAA-TAGGTTAGGGTTTTT
** *
43932999 AATTAAGTTAAGTTAGGGTTTTT
1 AATTAAAATAGGTTAGGGTTTTT
43933022 AATTAAAATAGGTTAGGGTTAGGGTTTTT
1 AATT-AAA-A---TA-GGTTAGGGTTTTT
* * *
43933051 AACTAAATTAGGTTAGGGATTTT
1 AATTAAAATAGGTTAGGGTTTTT
*
43933074 AATTAAATTAGGTTAGGG
1 AATTAAAATAGGTTAGGG
43933092 ATTACATCGT
Statistics
Matches: 99, Mismatches: 11, Indels: 23
0.74 0.08 0.17
Matches are distributed among these distances:
23 47 0.47
24 9 0.09
26 2 0.02
28 24 0.24
29 17 0.17
ACGTcount: A:0.34, C:0.01, G:0.23, T:0.41
Consensus pattern (23 bp):
AATTAAAATAGGTTAGGGTTTTT
Found at i:43933094 original size:23 final size:23
Alignment explanation
Indices: 43932976--43933091 Score: 142
Period size: 23 Copynumber: 4.8 Consensus size: 23
43932966 TTTTTAATTA
43932976 AATTAAATTAGGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTT
* *
43932999 AATTAAGTTAAGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTT
43933022 AATTAAAATAGGTTAGGGTTAGGGTTTTT
1 AATT--AA-A--TTA-GGTTAGGGTTTTT
* *
43933051 AACTAAATTAGGTTAGGGATTTT
1 AATTAAATTAGGTTAGGGTTTTT
43933074 AATTAAATTAGGTTAGGG
1 AATTAAATTAGGTTAGGG
43933092 ATTACATCGT
Statistics
Matches: 80, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
23 54 0.68
24 3 0.04
25 2 0.03
26 1 0.01
27 2 0.03
28 3 0.04
29 15 0.19
ACGTcount: A:0.33, C:0.01, G:0.24, T:0.42
Consensus pattern (23 bp):
AATTAAATTAGGTTAGGGTTTTT
Found at i:43933251 original size:21 final size:21
Alignment explanation
Indices: 43933227--43933275 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
43933217 CTTCTTTTAG
43933227 CTTCCGGCGGTGATTGTTCTT
1 CTTCCGGCGGTGATTGTTCTT
* * *
43933248 CTTCAGGTGGTGATTGTTGTT
1 CTTCCGGCGGTGATTGTTCTT
43933269 CTTCCGG
1 CTTCCGG
43933276 TTCGGCATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.06, C:0.20, G:0.31, T:0.43
Consensus pattern (21 bp):
CTTCCGGCGGTGATTGTTCTT
Found at i:43935508 original size:41 final size:41
Alignment explanation
Indices: 43935451--43935677 Score: 402
Period size: 41 Copynumber: 5.5 Consensus size: 41
43935441 TTTAACATAT
*
43935451 TCACCGGCACTTAGCCTGCTAGGTTTA-AAGCCTGATTCAGA
1 TCACCGGCACGTAGCCTGCTAGGTTTATAA-CCTGATTCAGA
*
43935492 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAAA
1 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
43935533 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAAA
1 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
43935574 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
43935615 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
43935656 TCACCGGCATGTAGCCTGCTAG
1 TCACCGGCACGTAGCCTGCTAG
43935678 ACTTAAAGTC
Statistics
Matches: 181, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
41 179 0.99
42 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (41 bp):
TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
Found at i:43935720 original size:123 final size:123
Alignment explanation
Indices: 43935449--43935731 Score: 394
Period size: 123 Copynumber: 2.3 Consensus size: 123
43935439 AATTTAACAT
*
43935449 ATTCACCGGCACTTAGCCTGCTAGGTTTA-AAGCCTGATTCAGATCACCGGCACGTAGCCTGCTA
1 ATTCACCGGCACATAGCCTGCTAGGTTTATAA-CCTGATTCAGATCACCGGCACGTAGCCTGCTA
**
43935513 GGTTTATAACCTGATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCA
65 GGTTTATAACCTGATTCAAATCACCGGCACGTAGCCTGCTAGACTTATAACCTGATTCA
* *
43935572 AATCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACGTAGCCTGCTAG
1 ATTCACCGGCACATAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACGTAGCCTGCTAG
* * *
43935637 GTTTATAACCTGATTCAGATCACCGGCATGTAGCCTGCTAGACTTA-AAGTCTGAATT-A
66 GTTTATAACCTGATTCAAATCACCGGCACGTAGCCTGCTAGACTTATAA-CCTG-ATTCA
* * * *
43935695 TTTCACCGGCACAAAGCCGGTTAGGTTT-TAAACCTGA
1 ATTCACCGGCACATAGCCTGCTAGGTTTAT-AACCTGA
43935732 AGATTTCAGT
Statistics
Matches: 143, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
122 3 0.02
123 135 0.94
124 5 0.03
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (123 bp):
ATTCACCGGCACATAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACGTAGCCTGCTAG
GTTTATAACCTGATTCAAATCACCGGCACGTAGCCTGCTAGACTTATAACCTGATTCA
Found at i:43942884 original size:41 final size:41
Alignment explanation
Indices: 43942827--43943053 Score: 402
Period size: 41 Copynumber: 5.5 Consensus size: 41
43942817 TTTAACATAT
*
43942827 TCACCGGCACTTAGCCTGCTAGGTTTA-AAGCCTGATTCAGA
1 TCACCGGCACGTAGCCTGCTAGGTTTATAA-CCTGATTCAGA
*
43942868 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAAA
1 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
43942909 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAAA
1 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
43942950 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
43942991 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
43943032 TCACCGGCATGTAGCCTGCTAG
1 TCACCGGCACGTAGCCTGCTAG
43943054 ACTTAAAGTC
Statistics
Matches: 181, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
41 179 0.99
42 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (41 bp):
TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
Found at i:43943096 original size:123 final size:123
Alignment explanation
Indices: 43942825--43943107 Score: 394
Period size: 123 Copynumber: 2.3 Consensus size: 123
43942815 AATTTAACAT
*
43942825 ATTCACCGGCACTTAGCCTGCTAGGTTTA-AAGCCTGATTCAGATCACCGGCACGTAGCCTGCTA
1 ATTCACCGGCACATAGCCTGCTAGGTTTATAA-CCTGATTCAGATCACCGGCACGTAGCCTGCTA
**
43942889 GGTTTATAACCTGATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCA
65 GGTTTATAACCTGATTCAAATCACCGGCACGTAGCCTGCTAGACTTATAACCTGATTCA
* *
43942948 AATCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACGTAGCCTGCTAG
1 ATTCACCGGCACATAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACGTAGCCTGCTAG
* * *
43943013 GTTTATAACCTGATTCAGATCACCGGCATGTAGCCTGCTAGACTTA-AAGTCTGAATT-A
66 GTTTATAACCTGATTCAAATCACCGGCACGTAGCCTGCTAGACTTATAA-CCTG-ATTCA
* * * *
43943071 TTTCACCGGCACAAAGCCGGTTAGGTTT-TAAACCTGA
1 ATTCACCGGCACATAGCCTGCTAGGTTTAT-AACCTGA
43943108 AGATTTCAGT
Statistics
Matches: 143, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
122 3 0.02
123 135 0.94
124 5 0.03
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (123 bp):
ATTCACCGGCACATAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACGTAGCCTGCTAG
GTTTATAACCTGATTCAAATCACCGGCACGTAGCCTGCTAGACTTATAACCTGATTCA
Found at i:43945423 original size:14 final size:15
Alignment explanation
Indices: 43945406--43945439 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
43945396 AATAAATATC
43945406 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
43945420 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
43945435 TAAAA
1 TAAAA
43945440 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:43945706 original size:22 final size:22
Alignment explanation
Indices: 43945678--43945747 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
43945668 ATTTGAGAGT
43945678 TTGAGAGAA-TTTTGGAAGGAA
1 TTGAGAGAACTTTTGGAAGGAA
*
43945699 TTTTAGAGAACTTTT-GAACGGAA
1 -TTGAGAGAACTTTTGGAA-GGAA
*
43945722 TTGAGAGAATTTTTGG-AGGAAA
1 TTGAGAGAACTTTTGGAAGG-AA
43945744 TTGA
1 TTGA
43945748 TATTGAATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
21 2 0.05
22 30 0.73
23 9 0.22
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.33
Consensus pattern (22 bp):
TTGAGAGAACTTTTGGAAGGAA
Found at i:43951696 original size:19 final size:21
Alignment explanation
Indices: 43951672--43951719 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
43951662 TTGTTTCACA
43951672 GAAAATAG-CTT-GGTCAACG
1 GAAAATAGACTTAGGTCAACG
43951691 GAAAAT-GACTTACAGGTCAACG
1 GAAAATAGACTT--AGGTCAACG
43951713 GAAAATA
1 GAAAATA
43951720 AGCCTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 1 0.04
19 9 0.38
22 14 0.58
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.19
Consensus pattern (21 bp):
GAAAATAGACTTAGGTCAACG
Found at i:43953947 original size:41 final size:41
Alignment explanation
Indices: 43953891--43954247 Score: 467
Period size: 41 Copynumber: 8.8 Consensus size: 41
43953881 TTTTGAGGCA
* * * *
43953891 TTTAGCGGTGCTTTTGAGAAAGAGCCGCTAATGCTCGAGGC
1 TTTAGCGGCGTTTTTGAGAAAGAGCCGCTAATGCTCGTGCC
* * * **
43953932 TTTAGCTGCGTTTTTGGGAAAGCGCCGCTAATGCTCG-GGA
1 TTTAGCGGCGTTTTTGAGAAAGAGCCGCTAATGCTCGTGCC
43953972 TTTAGCGGCGTTTTTGAGAAAGCA-CCGCTAATGCTCGTGCC
1 TTTAGCGGCGTTTTTGAGAAAG-AGCCGCTAATGCTCGTGCC
*
43954013 TTTAGCGGCATTTTTGAGAAAGCA-CCGCTAATGCTCGTGCC
1 TTTAGCGGCGTTTTTGAGAAAG-AGCCGCTAATGCTCGTGCC
43954054 TTTAGCGGCGTTTTTGAGAAAGCA-CCGCTAATGCTCGTGCC
1 TTTAGCGGCGTTTTTGAGAAAG-AGCCGCTAATGCTCGTGCC
* * *
43954095 TTTAGCGGCGTTTTTGAGAAAGCGCTGCTAATGCTTGTGCC
1 TTTAGCGGCGTTTTTGAGAAAGAGCCGCTAATGCTCGTGCC
* * *
43954136 ATTAGCGGCGTTTTTGATAAAGTGCCGCTAATGCTCGTGCC
1 TTTAGCGGCGTTTTTGAGAAAGAGCCGCTAATGCTCGTGCC
*
43954177 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCT-G-GCC
1 TTTAGCGGCGTTTTTGAGAAAGAGCCGCTAATGCTCGTGCC
*
43954216 TTTAGCGGCGTTTTTGA-AAAAACGCCGCTAAT
1 TTTAGCGGCGTTTTTGAGAAAGA-GCCGCTAAT
43954248 AATAAAATCT
Statistics
Matches: 286, Mismatches: 26, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
38 3 0.01
39 29 0.10
40 36 0.13
41 218 0.76
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAGAAAGAGCCGCTAATGCTCGTGCC
Found at i:43954164 original size:123 final size:122
Alignment explanation
Indices: 43953892--43954247 Score: 518
Period size: 123 Copynumber: 2.9 Consensus size: 122
43953882 TTTGAGGCAT
* * * * * *
43953892 TTAGCGGTGCTTTTGAGAAAGAGCCGCTAATGCTCGAGGCTTTAGCTGCGTTTTTGGGAAAGCGC
1 TTAGCGGCGTTTTTGAGAAAGAGCCGCTAATGCTCGTGCCTTTAGCGGCGTTTTTGAGAAAGCGC
** * *
43953957 CGCTAATGCTCGGGATTTAGCGGCGTTTTTGAGAAAGCACCGCTAATGCTCGTGCCT
66 CGCTAATGCTCGGCCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGTGCCA
* *
43954014 TTAGCGGCATTTTTGAGAAAGCA-CCGCTAATGCTCGTGCCTTTAGCGGCGTTTTTGAGAAAGCA
1 TTAGCGGCGTTTTTGAGAAAG-AGCCGCTAATGCTCGTGCCTTTAGCGGCGTTTTTGAGAAAGCG
* *
43954078 CCGCTAATGCTCGTGCCTTTAGCGGCGTTTTTGAGAAAGCGCTGCTAATGCTTGTGCCA
65 CCGCTAATGCTCG-GCCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGTGCCA
* *
43954137 TTAGCGGCGTTTTTGATAAAGTGCCGCTAATGCTCGTGCCTTTAGCGGCGTTTTTGAGAAAGCGC
1 TTAGCGGCGTTTTTGAGAAAGAGCCGCTAATGCTCGTGCCTTTAGCGGCGTTTTTGAGAAAGCGC
* *
43954202 CGCTAATGCT-GGCCTTTAGCGGCGTTTTTGAAAAAACGCCGCTAAT
66 CGCTAATGCTCGGCCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAAT
43954248 AATAAAATCT
Statistics
Matches: 210, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
121 32 0.15
122 68 0.32
123 110 0.52
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (122 bp):
TTAGCGGCGTTTTTGAGAAAGAGCCGCTAATGCTCGTGCCTTTAGCGGCGTTTTTGAGAAAGCGC
CGCTAATGCTCGGCCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGTGCCA
Found at i:43960517 original size:42 final size:42
Alignment explanation
Indices: 43960438--43960526 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
43960428 TAAATTTTTT
* * *
43960438 TAAAGGTTATGTTTTTAGTGGCGTTTCTGTGAGAAGCGTCGC
1 TAAAGGTTATGTTTTTAGCGGCGTTTCTGTGAAAAGCGCCGC
*
43960480 TAAAGGTT-TGTTCTTTAGCGGCGTTTGTAG-GAAAAGCGCCGC
1 TAAAGGTTATGTT-TTTAGCGGCGTTTCT-GTGAAAAGCGCCGC
43960522 TAAAG
1 TAAAG
43960527 ATAATATTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 4 0.10
42 36 0.88
43 1 0.02
ACGTcount: A:0.22, C:0.13, G:0.30, T:0.34
Consensus pattern (42 bp):
TAAAGGTTATGTTTTTAGCGGCGTTTCTGTGAAAAGCGCCGC
Found at i:43960544 original size:116 final size:117
Alignment explanation
Indices: 43960415--43960643 Score: 388
Period size: 116 Copynumber: 2.0 Consensus size: 117
43960405 AAATAAATAT
* * *
43960415 TATTTGATTAAAATAAATTTTTTTAAAGGTTATGTTTTTAGTGGCGTTTCTGTGAGAAGCGTCGC
1 TATTTGATTAAAATAAATTTTTTTAAAGGTTATGTTTTTAGCGGCGTTTCTGCGAGAAGCGCCGC
* *
43960480 TAAAGGT-TTGTTCTTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGATAA
66 TAAAGGTCGTGATCTTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGATAA
*
43960531 TATTTGATTAAAATAAATTTTTTTAAAGGTTATGTTTTTAGCGGCGTTTTTGCGAGAAGCGCCGC
1 TATTTGATTAAAATAAATTTTTTTAAAGGTTATGTTTTTAGCGGCGTTTCTGCGAGAAGCGCCGC
*
43960596 TAAAGGTCGTGATCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
66 TAAAGGTCGTGATCTTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAG
43960644 GTCGCGGTCT
Statistics
Matches: 105, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
116 68 0.65
117 37 0.35
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (117 bp):
TATTTGATTAAAATAAATTTTTTTAAAGGTTATGTTTTTAGCGGCGTTTCTGCGAGAAGCGCCGC
TAAAGGTCGTGATCTTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGATAA
Found at i:43960616 original size:43 final size:42
Alignment explanation
Indices: 43960567--43960879 Score: 358
Period size: 43 Copynumber: 7.3 Consensus size: 42
43960557 AGGTTATGTT
* * *
43960567 TTTAGCGGCGTTTTTGCGAGAAGCGCCGCTAAAGGTCGTGATC
1 TTTAGCGGCGTTTGTG-GAAAAGCGCCGCTAAAGGTCGTGGTC
*
43960610 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGCGGTC
1 TTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCGTGGTC
* * *
43960653 TATACCGGCGTTTGTGGGGAAAA-CGCCGCTAAAGGTCGCGGTC
1 TTTAGCGGCGTTTGT--GGAAAAGCGCCGCTAAAGGTCGTGGTC
* * * *
43960696 TATAGCGGCGTTTCTGGGAAAAGCGCCTCTAAAGGTCGTAGTC
1 TTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCGTGGTC
* * *
43960739 TATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAATGTCTTGGTC
1 TTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCGTGGTC
* *
43960782 TTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGCCTTGGTC
1 TTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCGTGGTC
*** * *
43960825 TTTAGCAATGTTTGTAGGAAAAGCGTCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCGTGGTC
43960868 TTTAGCGGCGTT
1 TTTAGCGGCGTT
43960880 CTAAATTTTT
Statistics
Matches: 239, Mismatches: 28, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
42 7 0.03
43 224 0.94
44 8 0.03
ACGTcount: A:0.21, C:0.20, G:0.33, T:0.27
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGGTCGTGGTC
Done.