Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold293
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: 1704560
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 2 of 12
Found at i:149876 original size:31 final size:30
Alignment explanation
Indices: 149810--150017 Score: 256
Period size: 30 Copynumber: 6.8 Consensus size: 30
149800 AGGTGCCATA
149810 GAGTCGTGGACTTTG-GAAAGAGATGCCACT
1 GAGTCGTGGACTTTGAG-AAGAGATGCCACT
*
149840 AAGTCGTGGACTTTGAGAAGAGATTGCCACT
1 GAGTCGTGGACTTTGAGAAGAGA-TGCCACT
*
149871 GAGTCGTGGACTTTGAAGAAAAGATGCCACT
1 GAGTCGTGGACTTTG-AGAAGAGATGCCACT
* *
149902 GAGTCGCGGACTTTGGGAAGAGATGCCACT
1 GAGTCGTGGACTTTGAGAAGAGATGCCACT
* *
149932 GAGTCGCGGACTTTGGGAAGAGATGCCACT
1 GAGTCGTGGACTTTGAGAAGAGATGCCACT
* * *
149962 AAGTCGTGGACTTTAAAGAAAAAAGATGCCACT
1 GAGTCGTGGACTTT---GAGAAGAGATGCCACT
* *
149995 GAGTTGTGGACTTTGAAAAGAGA
1 GAGTCGTGGACTTTGAGAAGAGA
150018 GATTTAAAGA
Statistics
Matches: 158, Mismatches: 14, Indels: 12
0.86 0.08 0.07
Matches are distributed among these distances:
30 83 0.53
31 43 0.27
32 7 0.04
33 25 0.16
ACGTcount: A:0.30, C:0.16, G:0.31, T:0.23
Consensus pattern (30 bp):
GAGTCGTGGACTTTGAGAAGAGATGCCACT
Found at i:149906 original size:92 final size:92
Alignment explanation
Indices: 149783--150017 Score: 321
Period size: 92 Copynumber: 2.5 Consensus size: 92
149773 CCACGGAGTT
* * * *
149783 GTGGGCTTTAAAAAAAAAGGTGCCA-TAGAGTCGTGGACTTTGGAAAGAGATGCCACTAAGTCGT
1 GTGGACTTTAAAGAAAAAGATGCCACT-GAGTCGTGGACTTTGGAAAGAGATGCCACTAAGTCGC
*
149847 GGACTTTGAGAAGAGATTGCCACTGAGTC
65 GGACTTTGAGAAGAGA-TGCCACTAAGTC
* * * *
149876 GTGGACTTTGAAG-AAAAGATGCCACTGAGTCGCGGACTTTGGGAAGAGATGCCACTGAGTCGCG
1 GTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGGAAAGAGATGCCACTAAGTCGCG
*
149940 GACTTTGGGAAGAGATGCCACTAAGTC
66 GACTTTGAGAAGAGATGCCACTAAGTC
* *
149967 GTGGACTTTAAAGAAAAAAGATGCCACTGAGTTGTGGACTTTGAAAAGAGA
1 GTGGACTTTAAAG-AAAAAGATGCCACTGAGTCGTGGACTTTGGAAAGAGA
150018 GATTTAAAGA
Statistics
Matches: 124, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
91 23 0.19
92 58 0.47
93 43 0.35
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (92 bp):
GTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGGAAAGAGATGCCACTAAGTCGCG
GACTTTGAGAAGAGATGCCACTAAGTC
Found at i:151308 original size:13 final size:13
Alignment explanation
Indices: 151290--151320 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
151280 CTTTGCACTC
151290 TTTTTTTTGTGTG
1 TTTTTTTTGTGTG
*
151303 TTTTTTTTTTGTG
1 TTTTTTTTGTGTG
151316 TTTTT
1 TTTTT
151321 ACTGTTGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (13 bp):
TTTTTTTTGTGTG
Found at i:151310 original size:15 final size:14
Alignment explanation
Indices: 151290--151320 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
151280 CTTTGCACTC
151290 TTTTTTTTGTGTGTT
1 TTTTTTTTGTGT-TT
151305 TTTTTTTTGTGTTT
1 TTTTTTTTGTGTTT
151319 TT
1 TT
151321 ACTGTTGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (14 bp):
TTTTTTTTGTGTTT
Found at i:157680 original size:12 final size:12
Alignment explanation
Indices: 157663--157691 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
157653 CCTAAAGCCA
157663 CCACATCCAAGG
1 CCACATCCAAGG
157675 CCACATCCAAGG
1 CCACATCCAAGG
157687 CCACA
1 CCACA
157692 AATGACCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.45, G:0.14, T:0.07
Consensus pattern (12 bp):
CCACATCCAAGG
Found at i:160385 original size:22 final size:21
Alignment explanation
Indices: 160360--160404 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
160350 TATTTTATAT
* *
160360 AAATAAATTTAATTTTTTTAAA
1 AAAT-AATTTAATATATTTAAA
*
160382 AAATATTTTAATATATTTAAA
1 AAATAATTTAATATATTTAAA
160403 AA
1 AA
160405 TTTTATTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATAATTTAATATATTTAAA
Found at i:171062 original size:19 final size:19
Alignment explanation
Indices: 171020--171067 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 19
171010 GACTTGCATG
*
171020 CAGGGTTGG-AAAAAACAA
1 CAGGATTGGAAAAAAACAA
*
171038 CA--ATTGGAAAAAAAGAA
1 CAGGATTGGAAAAAAACAA
171055 CAGGATTGGAAAA
1 CAGGATTGGAAAA
171068 TCTTTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 4 0.16
17 10 0.40
18 2 0.08
19 9 0.36
ACGTcount: A:0.54, C:0.08, G:0.25, T:0.12
Consensus pattern (19 bp):
CAGGATTGGAAAAAAACAA
Found at i:171700 original size:17 final size:19
Alignment explanation
Indices: 171686--171723 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
171676 GTTAAAATTA
171686 ATATTGAATATAAATATAT
1 ATATTGAATATAAATATAT
**
171705 ATATTTTATATAAATATAT
1 ATATTGAATATAAATATAT
171724 TTAATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
ATATTGAATATAAATATAT
Found at i:171732 original size:21 final size:21
Alignment explanation
Indices: 171693--171748 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
171683 TTAATATTGA
*
171693 ATATAAATATATAT-A-TTTT
1 ATATAAATATATTTAATTTTT
171712 ATATAAATATATTTAATTTTT
1 ATATAAATATATTTAATTTTT
* *
171733 AAAAAAATAT-TTTAAT
1 ATATAAATATATTTAAT
171749 ATATTTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.41
20 7 0.22
21 12 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATAAATATATTTAATTTTT
Found at i:171742 original size:19 final size:19
Alignment explanation
Indices: 171697--171759 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 19
171687 TATTGAATAT
* *
171697 AAATATATATATTTTATATAA
1 AAATATTTA-ATTTT-TAAAA
*
171718 ATATATTTAATTTTTAAAA
1 AAATATTTAATTTTTAAAA
171737 AAATATTTTAATATATTTAAAA
1 AAATA-TTTAAT-T-TTTAAAA
171759 A
1 A
171760 TTTATATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 8 0.23
20 11 0.31
21 8 0.23
22 8 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AAATATTTAATTTTTAAAA
Found at i:171813 original size:16 final size:16
Alignment explanation
Indices: 171794--171837 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
171784 AATATAAATA
*
171794 TAAAAAATAAATATTT
1 TAAAAAATAAAAATTT
171810 T-AAAAATAAAAATTT
1 TAAAAAATAAAAATTT
*
171825 AAAAAACATAAAA
1 TAAAAA-ATAAAA
171838 TAAAACTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 13 0.54
16 5 0.21
17 6 0.25
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAAAATAAAAATTT
Found at i:171825 original size:14 final size:15
Alignment explanation
Indices: 171796--171829 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
171786 TATAAATATA
*
171796 AAAAATAAATATTTT
1 AAAAATAAATAATTT
171811 AAAAATAAA-AATTT
1 AAAAATAAATAATTT
171825 AAAAA
1 AAAAA
171830 ACATAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAATAAATAATTT
Found at i:171830 original size:15 final size:15
Alignment explanation
Indices: 171784--171830 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
171774 TATATGTGGT
* *
171784 AATATAAATATAAAA
1 AATAAAAATTTAAAA
* *
171799 AATAAATATTTTAAA
1 AATAAAAATTTAAAA
171814 AATAAAAATTTAAAA
1 AATAAAAATTTAAAA
171829 AA
1 AA
171831 CATAAAATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AATAAAAATTTAAAA
Found at i:172515 original size:16 final size:16
Alignment explanation
Indices: 172471--172592 Score: 86
Period size: 16 Copynumber: 7.3 Consensus size: 16
172461 TTAGTTTGGG
*
172471 TTATATTAAA-TTAGAA
1 TTATTTTAAATTTA-AA
* * * *
172487 TTATTATATATTTTAT
1 TTATTTTAAATTTAAA
172503 TTATTTTAAATTTAAA
1 TTATTTTAAATTTAAA
* *
172519 TGATGTTAAATTTAAA
1 TTATTTTAAATTTAAA
*
172535 TAATTTTAATTTTATATTAAAA
1 TTATTTTAA----AT-TT-AAA
172557 TTA-TTTAAATTTAAA
1 TTATTTTAAATTTAAA
*
172572 TTATTTTAAATTTAAT
1 TTATTTTAAATTTAAA
172588 TTATT
1 TTATT
172593 AATTTTAAAA
Statistics
Matches: 83, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
15 6 0.07
16 59 0.71
17 4 0.05
20 2 0.02
21 7 0.08
22 5 0.06
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
TTATTTTAAATTTAAA
Found at i:172563 original size:15 final size:15
Alignment explanation
Indices: 172545--172616 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
172535 TAATTTTAAT
*
172545 TTTATATTAAAATTA
1 TTTAAATTAAAATTA
*
172560 TTTAAATTTAAATTA
1 TTTAAATTAAAATTA
* *
172575 TTTTAAATTTAATTTA
1 -TTTAAATTAAAATTA
*
172591 -TTAATTTTAAAATTA
1 TTTAA-ATTAAAATTA
* *
172606 TATAGATTAAA
1 TTTAAATTAAA
172617 TTTAAATATT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
14 4 0.09
15 25 0.56
16 16 0.36
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (15 bp):
TTTAAATTAAAATTA
Found at i:172565 original size:37 final size:38
Alignment explanation
Indices: 172505--172586 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 38
172495 TATTTTATTT
*
172505 ATTTTAAATTTAAATGATGTTAAATTTAAATAATTTTA
1 ATTTTAAATTAAAATGATGTTAAATTTAAATAATTTTA
* * *
172543 ATTTTATATTAAAATTAT-TTAAATTTAAATTATTTTA
1 ATTTTAAATTAAAATGATGTTAAATTTAAATAATTTTA
*
172580 AATTTAA
1 ATTTTAA
172587 TTTATTAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
37 23 0.61
38 15 0.39
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (38 bp):
ATTTTAAATTAAAATGATGTTAAATTTAAATAATTTTA
Found at i:172578 original size:31 final size:31
Alignment explanation
Indices: 172471--172606 Score: 78
Period size: 31 Copynumber: 4.1 Consensus size: 31
172461 TTAGTTTGGG
* * * *
172471 TTATATTAAATTAGAATTATTATATATTT-TAT
1 TTATTTTAAATTAAAATTATTA-A-ATTTAAAA
* *
172503 TTATTTTAAATTTAAATGATGTTAAATTTAAATAA
1 TTATTTTAAATTAAAAT--TATTAAATTT-AA-AA
*
172538 TTTTAATTTTATATTAAAATTATTTAAATTT-AAA
1 --TT-ATTTTAAATTAAAATTA-TTAAATTTAAAA
* * *
172572 TTATTTTAAATTTAATTTATTAATTTTAAAA
1 TTATTTTAAATTAAAATTATTAAATTTAAAA
172603 TTAT
1 TTAT
172607 ATAGATTAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 21
0.70 0.11 0.18
Matches are distributed among these distances:
30 7 0.09
31 21 0.26
32 20 0.25
33 1 0.01
34 6 0.07
35 2 0.02
36 1 0.01
37 10 0.12
38 13 0.16
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (31 bp):
TTATTTTAAATTAAAATTATTAAATTTAAAA
Found at i:172604 original size:37 final size:37
Alignment explanation
Indices: 172526--172604 Score: 90
Period size: 37 Copynumber: 2.1 Consensus size: 37
172516 AAATGATGTT
* *
172526 AAATTTAAATAATTTTAATTTTATATTAAAATTATTT
1 AAATTTAAATAATTTTAATTTAATATTAAAATTATTA
* *
172563 AAATTTAAATTATTTTAAATTTAAT-TTATTAATT-TTA
1 AAATTTAAATAATTTT-AATTTAATATTA-AAATTATTA
172600 AAATT
1 AAATT
172605 ATATAGATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 25 0.69
38 11 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (37 bp):
AAATTTAAATAATTTTAATTTAATATTAAAATTATTA
Found at i:173482 original size:2 final size:2
Alignment explanation
Indices: 173475--173520 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
173465 GTCCGAATGC
* * * *
173475 AT AT AT AT AA AT AA AT AT AT AT AT AT AT AT AC AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
173517 AT AT
1 AT AT
173521 TCACGCGATA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:173520 original size:18 final size:18
Alignment explanation
Indices: 173475--173520 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
173465 GTCCGAATGC
*
173475 ATATATATAAATAAATAT
1 ATATATATATATAAATAT
*
173493 ATATATATATATACATAT
1 ATATATATATATAAATAT
*
173511 TTATATATAT
1 ATATATATAT
173521 TCACGCGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATATATATATAAATAT
Found at i:175026 original size:30 final size:30
Alignment explanation
Indices: 174990--175049 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
174980 CATATTGGTG
*
174990 TATTGCATCATCATATTATTCTAATTTTAA
1 TATTGCATCATCATATTAGTCTAATTTTAA
** *
175020 TATTGCATGGTCATATTGGTCTAATTTTAA
1 TATTGCATCATCATATTAGTCTAATTTTAA
175050 AAAGCATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.48
Consensus pattern (30 bp):
TATTGCATCATCATATTAGTCTAATTTTAA
Found at i:177278 original size:2 final size:2
Alignment explanation
Indices: 177271--177304 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
177261 TTAATAAGGA
177271 AT AT AT AT AT AT AT AT AT AT GAT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT A
177305 ATAGTAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:180938 original size:13 final size:13
Alignment explanation
Indices: 180920--180945 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
180910 TACACCAAGT
180920 ATGTATCGATACA
1 ATGTATCGATACA
180933 ATGTATCGATACA
1 ATGTATCGATACA
180946 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:180943 original size:32 final size:33
Alignment explanation
Indices: 180902--180965 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
180892 TAGCCAAACT
* **
180902 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
180934 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
180966 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:183203 original size:21 final size:21
Alignment explanation
Indices: 183170--183214 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
183160 TTGCAAGTTG
*
183170 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
183192 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
183212 AAA
1 AAA
183215 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:185038 original size:15 final size:15
Alignment explanation
Indices: 185018--185048 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
185008 TAAAAATGTC
*
185018 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
185033 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
185048 C
1 C
185049 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:187137 original size:13 final size:13
Alignment explanation
Indices: 187119--187157 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
187109 ACATTTTTCT
187119 TTGTATCGATACA
1 TTGTATCGATACA
187132 TTGTATCGATACA
1 TTGTATCGATACA
*
187145 CTGTATCGATACA
1 TTGTATCGATACA
187158 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:187321 original size:20 final size:19
Alignment explanation
Indices: 187280--187322 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
187270 ATCTTTTACA
187280 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
187300 AAATCACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
187320 AAA
1 AAA
187323 ACCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:189718 original size:13 final size:13
Alignment explanation
Indices: 189700--189725 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
189690 TACACCAAGT
189700 ATGTATCGATACA
1 ATGTATCGATACA
189713 ATGTATCGATACA
1 ATGTATCGATACA
189726 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:189723 original size:32 final size:33
Alignment explanation
Indices: 189682--189745 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
189672 TAGCCAAACT
* **
189682 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
189714 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
189746 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:191861 original size:20 final size:20
Alignment explanation
Indices: 191838--191878 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
191828 AGAAAATTTT
*
191838 TTGTTCAAAAAGAAGAATGA
1 TTGTTCAAAAAGAAAAATGA
191858 TTGTTCAAAAAGAAAAATGA
1 TTGTTCAAAAAGAAAAATGA
191878 T
1 T
191879 GTAAGTTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27
Consensus pattern (20 bp):
TTGTTCAAAAAGAAAAATGA
Found at i:193338 original size:28 final size:28
Alignment explanation
Indices: 193293--195052 Score: 978
Period size: 28 Copynumber: 61.4 Consensus size: 28
193283 TCTTTTTCTA
*
193293 TGGGCTTT-AAAGAGATGCCACTGACTCG
1 TGGGCTTTGAAAG-GATGCCACTGACTTG
* *
193321 TTGGCTTTGAAAGAATGCCACTGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
*
193349 TGGGCTTTGGAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* *
193377 TGGGCTTTGGAAGGATGCCACTGACTCG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * * *
193405 TGGGCTTTGAAAAGTTACCACTGACTCG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* *
193433 TGGGCTTTGAAAAGTTGCCACTGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* *
193461 TGGGCTTGGAAAAGATGCCACTGACTTATG
1 TGGGCTTTGAAAGGATGCCACTGAC-T-TG
* * **
193491 TGGGCTTTGAAATGGGTTACCACCAACTTGTG
1 TGGGCTTTGAAA--GGATGCCACTGAC-T-TG
*
193523 TGGGCTTTGAAATGAGTTGCCA-TCGACTTGTG
1 TGGGCTTTGAAA-G-GATGCCACT-GAC-T-TG
* * **
193555 TGGGCTTTCAAATGGGTTGCCACCAACTTGTG
1 TGGGCTTTGAAA--GGATGCCACTGAC-T-TG
* *
193587 TGGGCTTTGAAATAGGTTGCCAC-CAGCTTGTG
1 TGGGCTTTG-AA-AGGATGCCACTGA-C-T-TG
* * **
193619 TGGGCTTTGAAATGGGTTACCACCAACTTGTG
1 TGGGCTTTGAAA--GGATGCCACTGAC-T-TG
* * *
193651 TGGGCTTTCAAATGAGTTGCCACCGACTTGTG
1 TGGGCTTTGAAA-G-GATGCCACTGAC-T-TG
* *
193683 TGGGCTTTGAAAGGGTGCCACCGACTTGTG
1 TGGGCTTTGAAAGGATGCCACTGAC-T-TG
* * *
193713 TGGGCTTTGAAAAGATACCACCGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * *
193741 TGGGCTTTAAAATGGGCTGCCACCGACTTGTG
1 TGGGCTTTGAAA--GGATGCCACTGAC-T-TG
*
193773 TGGGCTTTG-AAGTGATGCCACTAACTTG
1 TGGGCTTTGAAAG-GATGCCACTGACTTG
193801 TGGGCTTTGAAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
193829 TGGGCTTTGAAATGG-TGCCACTGACTTG
1 TGGGCTTTGAAA-GGATGCCACTGACTTG
* *
193857 TGGGCTTTGAAATGGGCTGCCACCGACTTGTG
1 TGGGCTTTGAAA--GGATGCCACTGAC-T-TG
*
193889 TGGGCTTTG-AAGTGATGCCACTAACTTG
1 TGGGCTTTGAAAG-GATGCCACTGACTTG
193917 TGGGCTTTGGAAA-GATGCCACTGACTTG
1 TGGGCTTT-GAAAGGATGCCACTGACTTG
193945 TGGGCTTTGAAATGG-TGCCACTGACTTG
1 TGGGCTTTGAAA-GGATGCCACTGACTTG
*
193973 TGGGCTTTGAAAGGATACCACTGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
194001 TGGGCTTTGAAATGG-TGCCACTGACTTG
1 TGGGCTTTGAAA-GGATGCCACTGACTTG
*
194029 TGGGCTTTGAAAGGATGCCACTAACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* *
194057 TGGGCTTTGAAATGGGCTGCCACCGACTTGTG
1 TGGGCTTTGAAA--GGATGCCACTGAC-T-TG
*
194089 TGGGCTTTG-AAGTGATGCCACTAACTTG
1 TGGGCTTTGAAAG-GATGCCACTGACTTG
194117 TGGGCTTTGAAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
194145 TGGGCTTTGAAATGG-TGCCACTGACTTG
1 TGGGCTTTGAAA-GGATGCCACTGACTTG
*
194173 TGGGCTTTGAAAGGATACCACTGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* *
194201 TGGGCTTTGAAAAGATGCCACTGACTTA
1 TGGGCTTTGAAAGGATGCCACTGACTTG
*
194229 TGGGCTTTTAGAAGGATGCCACTGACTTG
1 TGGGCTTTGA-AAGGATGCCACTGACTTG
* *
194258 TGGGCTTTGAAAGG-TGCCACAGATTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * *
194285 TGGAC-TT-ACAAGGATGCCACGGAGTTG
1 TGGGCTTTGA-AAGGATGCCACTGACTTG
* * * * * *
194312 TGGAC-TTAAAAGGGTGCCACAGAGTTA
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* ** * * *
194339 TGGACTTAAAAATG-TGCCACGGAGTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * * * *
194366 TGGAC-GTAAAAGGGTGCCA-TAGAGTTG
1 TGGGCTTTGAAAGGATGCCACT-GACTTG
* * * *
194393 TGGAC-TTAAAAGGGTGCCA-TAGAGTTG
1 TGGGCTTTGAAAGGATGCCACT-GACTTG
* * * * * * *
194420 TCGAC-TTAAAAGGGTGTCACGGAGTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * * *
194447 TGGACTTTAAAAGGGTGCCA-TGGAGTTG
1 TGGGCTTTGAAAGGATGCCACT-GACTTG
* *
194475 TGGACTTTAAAAGGATGCCACGGGTGTCACGGAGTTG
1 TGGGCTTTGAAAGGATGCCAC---TG--AC----TTG
* * * * *
194512 TGGACTTTAAAAGGGTGCCACGGAGTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * * *
194540 TGGACTTTAAAAGGATGCCACAGAGTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * * * *
194568 TGGAC-TTAAAAGGATGTCACGGAGTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * * *
194595 TGGACTTTAAAAGGATGCCACGGAGTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * * ** *
194623 TAGGC-TTAAAAGGATGCCACGGGGTTA
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * * * **
194650 TGGACTTTAAAAAGAAATGCCACTGAATCA
1 TGGGCTTT-GAAAG-GATGCCACTGACTTG
* * *
194680 TGGACTTT-AAAAGAGTGCCAC-GAAGTTG
1 TGGGCTTTGAAAGGA-TGCCACTG-ACTTG
* * * *
194708 TGGAC-TTAAAAGGGTGCCA-TGGAGTTG
1 TGGGCTTTGAAAGGATGCCACT-GACTTG
* * * * *
194735 TGGAC-TTAAAAGGATGCCACGGAGTTA
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * * * **
194762 TGGACTTTAAAAGGGTGCCACGGAGGTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * * * *
194790 TGGACTTTAAAAGGGTGCCACAGAGTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * *
194818 TGGACTTT-AAAGGGTGCCACAAGA-TTG
1 TGGGCTTTGAAAGGATGCCAC-TGACTTG
* * * * *
194845 TGGAC-TTAAAAGGGTGCCACGGAGTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * * * * *
194872 TGGACTCTAAAAGGGTGCCACAGAGTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * * * *
194900 TGGACTTTAAAAGGGTGCCACAGAGTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * * * *
194928 TGGACTTTAAAAGGGTGCCACAGAGTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * * *
194956 TGGACTTTAAAAGGATGCCACGGAGTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * *
194984 TGGAC-TTAAAAGGATGCCA-TAGAGTTG
1 TGGGCTTTGAAAGGATGCCACT-GACTTG
* * * * *
195011 TGGACTTTAAAAGGAAATGCCATTGAGTCG
1 TGGGCTTTGAAAGG--ATGCCACTGACTTG
*
195041 TGGACTTTGAAA
1 TGGGCTTTGAAA
195053 AGGTCACAGT
Statistics
Matches: 1505, Mismatches: 144, Indels: 164
0.83 0.08 0.09
Matches are distributed among these distances:
25 1 0.00
26 15 0.01
27 298 0.20
28 757 0.50
29 58 0.04
30 150 0.10
31 17 0.01
32 179 0.12
33 5 0.00
34 2 0.00
37 23 0.02
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.28
Consensus pattern (28 bp):
TGGGCTTTGAAAGGATGCCACTGACTTG
Found at i:193594 original size:96 final size:93
Alignment explanation
Indices: 193432--194088 Score: 563
Period size: 96 Copynumber: 7.3 Consensus size: 93
193422 CCACTGACTC
* * * ** * * * *
193432 GTGGGCTTTGAAA-AGTTGCCACTGACTTGTGGGCTTGGAAA--AGATGCCACTGACTTATGTGG
1 GTGGGCTTTGAAAGAGATACCACCGACTTGTGGGCTTTCAAATGGGTTGCCACCGACTTGTGTGG
*
193494 GCTTTGAAATGGGTTACCACCAACTTGT
66 GCTTTGAAATGGGTTGCCACCAACTTGT
* * * *
193522 GTGGGCTTTGAAATGAGTTGCCATCGACTTGTGTGGGCTTTCAAATGGGTTGCCACCAACTTGTG
1 GTGGGCTTTGAAA-GAGATACCACCGAC-T-TGTGGGCTTTCAAATGGGTTGCCACCGACTTGTG
* *
193587 TGGGCTTTGAAATAGGTTGCCACCAGCTTGT
63 TGGGCTTTGAAATGGGTTGCCACCAACTTGT
* * * *
193618 GTGGGCTTTGAAATGGGTTACCACCAACTTGTGTGGGCTTTCAAATGAGTTGCCACCGACTTGTG
1 GTGGGCTTTGAAA-GAGATACCACCGAC-T-TGTGGGCTTTCAAATGGGTTGCCACCGACTTGTG
*
193683 TGGGCTTTGAAA-GGG-TGCCACCGACTTGT
63 TGGGCTTTGAAATGGGTTGCCACCAACTTGT
* *
193712 GTGGGCTTTGAAA-AGATACCACCGACTTGTGGGCTTTAAAATGGGCTGCCACCGACTTGTGTGG
1 GTGGGCTTTGAAAGAGATACCACCGACTTGTGGGCTTTCAAATGGGTTGCCACCGACTTGTGTGG
* * *
193776 GCTTTG-AA-GTGATGCCACTAAC-T-T
66 GCTTTGAAATGGGTTGCCACCAACTTGT
* * * *
193800 GTGGGCTTTGAAAG-GATGCCACTGACTTGTGGGCTTTGAAAT-GG-TGCCACTGAC-T-TGTGG
1 GTGGGCTTTGAAAGAGATACCACCGACTTGTGGGCTTTCAAATGGGTTGCCACCGACTTGTGTGG
* *
193860 GCTTTGAAATGGGCTGCCACCGACTTGT
66 GCTTTGAAATGGGTTGCCACCAACTTGT
* * ** * * *
193888 GTGGGCTTTG-AAGTGATGCCACTAACTTGTGGGCTTTGGAAA---GATGCCACTGAC-T-TGTG
1 GTGGGCTTTGAAAGAGATACCACCGACTTGTGGGCTTT-CAAATGGGTTGCCACCGACTTGTGTG
**
193947 GGCTTTGAAAT-GG-TGCCACTGAC-T-T
65 GGCTTTGAAATGGGTTGCCACCAACTTGT
* * *
193972 GTGGGCTTTGAAAG-GATACCACTGACTTGTGGGCTTTGAAAT-GG-TGCCACTGAC-T-TGTGG
1 GTGGGCTTTGAAAGAGATACCACCGACTTGTGGGCTTTCAAATGGGTTGCCACCGACTTGTGTGG
* *
194032 GCTTTGAAA--GGATGCCACTAAC-T-T
66 GCTTTGAAATGGGTTGCCACCAACTTGT
* * *
194056 GTGGGCTTTGAAATGGGCTGCCACCGACTTGTG
1 GTGGGCTTTGAAA-GAGATACCACCGACTTGTG
194089 TGGGCTTTGA
Statistics
Matches: 500, Mismatches: 46, Indels: 46
0.84 0.08 0.08
Matches are distributed among these distances:
83 6 0.01
84 92 0.18
85 9 0.02
86 42 0.08
87 9 0.02
88 98 0.20
89 9 0.02
90 61 0.12
91 1 0.00
92 21 0.04
93 1 0.00
94 37 0.07
95 2 0.00
96 112 0.22
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.30
Consensus pattern (93 bp):
GTGGGCTTTGAAAGAGATACCACCGACTTGTGGGCTTTCAAATGGGTTGCCACCGACTTGTGTGG
GCTTTGAAATGGGTTGCCACCAACTTGT
Found at i:194028 original size:200 final size:201
Alignment explanation
Indices: 193293--194269 Score: 1066
Period size: 200 Copynumber: 4.8 Consensus size: 201
193283 TCTTTTTCTA
* * * *
193293 TGGGCTTTAAAGAGATGCCACTGACTCGTTGGCTTTGAAA-GAATGCCACTGACTTGTGGGCTTT
1 TGGGCTTTGAA-AGATGCCACTGACTTGTGGGCTTTGAAATG-GTGCCACTGACTTGTGGGCTTT
* * * * * *
193357 GGAAGGATGCCACTGACTTGTGGGCTTTGGAAGGATGCCACTGACTCGTGGGCTTTGAAAAGTTA
64 GAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATG
* * * * **
193422 CCACTGACTCGTGGGCTTTGAAA--AGTTGCCACTGAC-T-TGTGGGCTTGGAAAAGATGCCACT
129 CCACTGACTTGTGGGCTTTGAAATGAGCTGCCACCGACTTGTGTGGGCTTTGAAGTGATGCCACT
*
193483 GACTTATG
194 AACTTATG
* * **
193491 TGGGCTTTGAAATGGGTTACCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCA-TCGACTTGTG
1 TGGGCTTTGAAA---GATGCCACTGAC-T-TGTGGGCTTTGAAATG-G-TGCCACT-GAC-T-TG
* * ** * *
193555 TGGGCTTTCAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAATAGGTTGCCAC-CAGCTTGTG
56 TGGGCTTTGAAA--GGATGCCACTGAC-T-TGTGGGCTTTG-AA-AGGATGCCACTGA-C-T-TG
* * ** * *
193619 TGGGCTTTGAAATGGGTTACCACCAACTTGTGTGGGCTTTCAAATGAGTTGCCACCGACTTGTGT
112 TGGGCTTTGAAA--GGATGCCACTGAC-T-TGTGGGCTTTGAAATGAGCTGCCACCGACTTGTGT
* ** *
193684 GGGCTTTGAAAG-GGTGCCACCGACTTGTG
173 GGGCTTTG-AAGTGATGCCACTAACTTATG
* * * *
193713 TGGGCTTTGAAAAGATACCACCGACTTGTGGGCTTTAAAATGGGCTGCCACCGACTTGTGTGGGC
1 TGGGCTTTG-AAAGATGCCACTGACTTGTGGGCTTTGAAAT-GG-TGCCACTGAC-T-TGTGGGC
*
193778 TTTG-AAGTGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAT
61 TTTGAAAG-GATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAA-
*
193842 GG-TGCCACTGACTTGTGGGCTTTGAAATGGGCTGCCACCGACTTGTGTGGGCTTTGAAGTGATG
124 GGATGCCACTGACTTGTGGGCTTTGAAATGAGCTGCCACCGACTTGTGTGGGCTTTGAAGTGATG
193906 CCACTAAC-T-TG
189 CCACTAACTTATG
193917 TGGGCTTTGGAAAGATGCCACTGACTTGTGGGCTTTGAAATGGTGCCACTGACTTGTGGGCTTTG
1 TGGGCTTT-GAAAGATGCCACTGACTTGTGGGCTTTGAAATGGTGCCACTGACTTGTGGGCTTTG
*
193982 AAAGGATACCACTGACTTGTGGGCTTTGAAATGG-TGCCACTGACTTGTGGGCTTTGAAAGGATG
65 AAAGGATGCCACTGACTTGTGGGCTTTGAAA-GGATGCCACTGACTTGTGGGCTTTGAAAGGATG
* *
194046 CCACTAACTTGTGGGCTTTGAAATGGGCTGCCACCGACTTGTGTGGGCTTTGAAGTGATGCCACT
129 CCACTGACTTGTGGGCTTTGAAATGAGCTGCCACCGACTTGTGTGGGCTTTGAAGTGATGCCACT
194111 AAC-T-TG
194 AACTTATG
194117 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATGGTGCCACTGACTTGTGGGCTTTG
1 TGGGCTTTGAAA-GATGCCACTGACTTGTGGGCTTTGAAATGGTGCCACTGACTTGTGGGCTTTG
* * * *
194182 AAAGGATACCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTATGGGCTTTTAGAAGGATG
65 AAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGA-AAGGATG
194247 CCACTGACTTGTGGGCTTTGAAA
129 CCACTGACTTGTGGGCTTTGAAA
194270 GGTGCCACAG
Statistics
Matches: 679, Mismatches: 59, Indels: 79
0.83 0.07 0.10
Matches are distributed among these distances:
197 1 0.00
198 10 0.01
199 7 0.01
200 253 0.37
201 36 0.05
202 21 0.03
203 5 0.01
204 46 0.07
205 6 0.01
206 61 0.09
207 1 0.00
208 17 0.03
209 3 0.00
210 25 0.04
211 3 0.00
212 20 0.03
213 4 0.01
214 24 0.04
215 2 0.00
216 20 0.03
217 3 0.00
218 48 0.07
219 2 0.00
220 22 0.03
221 1 0.00
222 33 0.05
223 5 0.01
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (201 bp):
TGGGCTTTGAAAGATGCCACTGACTTGTGGGCTTTGAAATGGTGCCACTGACTTGTGGGCTTTGA
AAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCC
ACTGACTTGTGGGCTTTGAAATGAGCTGCCACCGACTTGTGTGGGCTTTGAAGTGATGCCACTAA
CTTATG
Found at i:194336 original size:27 final size:27
Alignment explanation
Indices: 194270--195024 Score: 830
Period size: 27 Copynumber: 27.0 Consensus size: 27
194260 GGCTTTGAAA
* * *
194270 GGTGCCACAGATTTGTGGACTTACAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
*
194297 GATGCCACGGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
* * *
194324 GGTGCCACAGAGTTATGGACTTAAAAA
1 GGTGCCACGGAGTTGTGGACTTAAAAG
* *
194351 TGTGCCACGGAGTTGTGGACGTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
**
194378 GGTGCCATAGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
** *
194405 GGTGCCATAGAGTTGTCGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
*
194432 GGTGTCACGGAGTTGTGGACTTTAAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAG
*
194460 GGTGCCATGGAGTTGTGGACTTTAAAAGGATGCCACG
1 GGTGCCACGGAGTTGTGGAC-TT--AA--A----A-G
*
194497 GGTGTCACGGAGTTGTGGACTTTAAAAG
1 GGTGCCACGGAGTTGTGGACT-TAAAAG
194525 GGTGCCACGGAGTTGTGGACTTTAAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAG
* *
194553 GATGCCACAGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
* *
194580 GATGTCACGGAGTTGTGGACTTTAAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAG
*
194608 GATGCCACGGAGTTGTAGG-CTTAAAAG
1 GGTGCCACGGAGTTGT-GGACTTAAAAG
* * *
194635 GATGCCACGGGGTTATGGACTTTAAAAAG
1 GGTGCCACGGAGTTGTGGAC-TT-AAAAG
** * * **
194664 AAATGCCACTGAATCATGGACTTTAAAAG
1 -GGTGCCACGGAGTTGTGGAC-TTAAAAG
* *
194693 AGTGCCACGAAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
*
194720 GGTGCCATGGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
* *
194747 GATGCCACGGAGTTATGGACTTTAAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAG
*
194775 GGTGCCACGGAGGTGTGGACTTTAAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAG
* *
194803 GGTGCCACAGAGTTGTGGACTTTAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
*
194830 GGTGCCAC-AAGATTGTGGACTTAAAAG
1 GGTGCCACGGAG-TTGTGGACTTAAAAG
194857 GGTGCCACGGAGTTGTGGACTCTAAAAG
1 GGTGCCACGGAGTTGTGGACT-TAAAAG
*
194885 GGTGCCACAGAGTTGTGGACTTTAAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAG
*
194913 GGTGCCACAGAGTTGTGGACTTTAAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAG
*
194941 GGTGCCACAGAGTTGTGGACTTTAAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAG
*
194969 GATGCCACGGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
* **
194996 GATGCCATAGAGTTGTGGACTTTAAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAG
195024 G
1 G
195025 AAATGCCATT
Statistics
Matches: 639, Mismatches: 65, Indels: 47
0.85 0.09 0.06
Matches are distributed among these distances:
26 4 0.01
27 298 0.47
28 276 0.43
29 15 0.02
30 20 0.03
32 1 0.00
33 1 0.00
35 2 0.00
36 2 0.00
37 20 0.03
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.25
Consensus pattern (27 bp):
GGTGCCACGGAGTTGTGGACTTAAAAG
Found at i:194481 original size:55 final size:54
Alignment explanation
Indices: 194270--195024 Score: 866
Period size: 55 Copynumber: 13.5 Consensus size: 54
194260 GGCTTTGAAA
* * *
194270 GGTGCCACAGATTTGTGGACTTACAAGGATGCCACGGAGTTGTGGACTTAAAAG
1 GGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
* ** *
194324 GGTGCCACAGAGTTATGGACTTAAAAATGTGCCACGGAGTTGTGGACGTAAAAG
1 GGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
* ** *
194378 GGTGCCATAGAGTTGTGGACTTAAAAGGGTGCCATAGAGTTGTCGACTTAAAAG
1 GGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
* * *
194432 GGTGTCACGGAGTTGTGGACTTTAAAAGGGTGCCATGGAGTTGTGGACTTTAAAAG
1 GGTGCCACAGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAG
*
194488 GATGCCACGGGTGTCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAG
1 GGTGCCA-------CA--GAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAG
* * *
194553 GATGCCACAGAGTTGTGGACTTAAAAGGATGTCACGGAGTTGTGGACTTTAAAAG
1 GGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAG
* * * * *
194608 GATGCCACGGAGTTGTAGG-CTTAAAAGGATGCCACGGGGTTATGGACTTTAAAAAG
1 GGTGCCACAGAGTTGT-GGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TT-AAAAG
** * * ** * *
194664 AAATGCCACTGAATCATGGACTTTAAAAGAGTGCCACGAAGTTGTGGACTTAAAAG
1 -GGTGCCACAGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
** * *
194720 GGTGCCATGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTATGGACTTTAAAAG
1 GGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAG
* * * *
194775 GGTGCCACGGAGGTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAG
1 GGTGCCACAGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
194830 GGTGCCACA-AGATTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTCTAAAAG
1 GGTGCCACAGAG-TTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACT-TAAAAG
*
194885 GGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAG
1 GGTGCCACAGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAG
*
194941 GGTGCCACAGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAG
1 GGTGCCACAGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
* *
194996 GATGCCATAGAGTTGTGGACTTTAAAAGG
1 GGTGCCACAGAGTTGTGGAC-TTAAAAGG
195025 AAATGCCATT
Statistics
Matches: 612, Mismatches: 66, Indels: 45
0.85 0.09 0.06
Matches are distributed among these distances:
54 162 0.26
55 216 0.35
56 141 0.23
57 15 0.02
58 24 0.04
63 1 0.00
65 53 0.09
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.25
Consensus pattern (54 bp):
GGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
Found at i:194509 original size:37 final size:37
Alignment explanation
Indices: 194459--194534 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
194449 GACTTTAAAA
*
194459 GGGTGCCATGGAGTTGTGGACTTTAAAAGGATGCCAC
1 GGGTGCCACGGAGTTGTGGACTTTAAAAGGATGCCAC
* *
194496 GGGTGTCACGGAGTTGTGGACTTTAAAAGGGTGCCAC
1 GGGTGCCACGGAGTTGTGGACTTTAAAAGGATGCCAC
194533 GG
1 GG
194535 AGTTGTGGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.22, C:0.16, G:0.38, T:0.24
Consensus pattern (37 bp):
GGGTGCCACGGAGTTGTGGACTTTAAAAGGATGCCAC
Found at i:196093 original size:12 final size:11
Alignment explanation
Indices: 196066--196095 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
196056 GGGTGAAAAG
196066 GTTTTTTTTTT
1 GTTTTTTTTTT
196077 GTTTTTTTTTT
1 GTTTTTTTTTT
*
196088 CTTTTTTT
1 GTTTTTTT
196096 AGGATTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (11 bp):
GTTTTTTTTTT
Found at i:196402 original size:23 final size:24
Alignment explanation
Indices: 196376--196421 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
196366 TACTTTTGCA
*
196376 CTTTTTCTATTCA-TTTTTTTGTG
1 CTTTTGCTATTCACTTTTTTTGTG
* *
196399 CTTTTGCTTTTGACTTTTTTTGT
1 CTTTTGCTATTCACTTTTTTTGT
196422 CATTTTAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.07, C:0.13, G:0.11, T:0.70
Consensus pattern (24 bp):
CTTTTGCTATTCACTTTTTTTGTG
Found at i:203598 original size:23 final size:23
Alignment explanation
Indices: 203572--203626 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
203562 TTATTCACAA
*
203572 AATATATTCGATTATAT-TTTATG
1 AATATATTCGATTA-ATGTTTACG
* *
203595 AATATGTTCGTTTAATGTTTACG
1 AATATATTCGATTAATGTTTACG
*
203618 AATAAATTC
1 AATATATTC
203627 ATTTAATTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.47
Consensus pattern (23 bp):
AATATATTCGATTAATGTTTACG
Found at i:205889 original size:23 final size:24
Alignment explanation
Indices: 205843--205889 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
205833 AGTAATTAAA
* *
205843 AAATTAAATAGTTATTAATCATTT
1 AAATTAAATAGTGATTAAACATTT
*
205867 AAATTAAATA-TGATTAAAGATTT
1 AAATTAAATAGTGATTAAACATTT
205890 TTGAAAAGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (24 bp):
AAATTAAATAGTGATTAAACATTT
Found at i:210411 original size:21 final size:21
Alignment explanation
Indices: 210393--210430 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 21
210383 ACAATAATTG
210393 TAATTAAT-T-ATTGTTTAAT
1 TAATTAATATAATTGTTTAAT
210412 TAATTAATATAATTGTTTA
1 TAATTAATATAATTGTTTA
210431 TTACTGTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.47
20 1 0.06
21 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (21 bp):
TAATTAATATAATTGTTTAAT
Found at i:210584 original size:26 final size:25
Alignment explanation
Indices: 210541--210600 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 25
210531 TTATTATAAT
* *
210541 TAATTGTTTCCTAATGTATGTGTATA
1 TAATTGTTTCCTAATGTATATAT-TA
** *
210567 TAATTGTTTGTTAGTGTATATATTA
1 TAATTGTTTCCTAATGTATATATTA
210592 TAATTGTTT
1 TAATTGTTT
210601 TTTAATTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 11 0.38
26 18 0.62
ACGTcount: A:0.27, C:0.03, G:0.15, T:0.55
Consensus pattern (25 bp):
TAATTGTTTCCTAATGTATATATTA
Found at i:210718 original size:31 final size:31
Alignment explanation
Indices: 210631--210744 Score: 88
Period size: 31 Copynumber: 3.6 Consensus size: 31
210621 AATTAATAAA
210631 TTTTT-ATAAATGGT-ATTATAAAATAATTTT
1 TTTTTCATAAAT-GTAATTATAAAATAATTTT
* ** ** *
210661 TTATTGGTGTACGTACATATATAAAATAATTTT
1 TTTTTCATAAATGTA-AT-TATAAAATAATTTT
* **
210694 TTTTTCATAAATGTAATTATAAAATTATTAA
1 TTTTTCATAAATGTAATTATAAAATAATTTT
* *
210725 ATTTTCATAAATTTAATTAT
1 TTTTTCATAAATGTAATTAT
210745 GATTTAGTTT
Statistics
Matches: 64, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
30 6 0.09
31 31 0.48
32 4 0.06
33 23 0.36
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (31 bp):
TTTTTCATAAATGTAATTATAAAATAATTTT
Found at i:213605 original size:24 final size:24
Alignment explanation
Indices: 213549--213620 Score: 81
Period size: 24 Copynumber: 2.9 Consensus size: 24
213539 CCACTCTCTA
* *
213549 TATTTGTCAAAAATAGTGGTTCTTTTT
1 TATTTGTCAAAAATGGTGG--C-TTGT
213576 TATTTGTCAAAAATGGTGGCTTGT
1 TATTTGTCAAAAATGGTGGCTTGT
* *
213600 TGTTTGTCAAAATTGGTGGCT
1 TATTTGTCAAAAATGGTGGCT
213621 AATTTTTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
24 22 0.54
25 1 0.02
27 18 0.44
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (24 bp):
TATTTGTCAAAAATGGTGGCTTGT
Found at i:218093 original size:27 final size:27
Alignment explanation
Indices: 218058--218151 Score: 131
Period size: 27 Copynumber: 3.6 Consensus size: 27
218048 AAAGCCACCC
218058 TTTGTGTTTGTCAAAAATAGTGGTTCT
1 TTTGTGTTTGTCAAAAATAGTGGTTCT
* *
218085 TTTGTGTTTGTCAAAAATAGTAGTTCC
1 TTTGTGTTTGTCAAAAATAGTGGTTCT
*
218112 TTTGTGTTTGTCAAAAATGGTGG--CT
1 TTTGTGTTTGTCAAAAATAGTGGTTCT
*
218137 TGT-TGTTTGTCAAAA
1 TTTGTGTTTGTCAAAA
218152 TTGGTGGCTA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.20
25 3 0.05
27 46 0.75
ACGTcount: A:0.23, C:0.09, G:0.22, T:0.46
Consensus pattern (27 bp):
TTTGTGTTTGTCAAAAATAGTGGTTCT
Found at i:222870 original size:22 final size:22
Alignment explanation
Indices: 222844--222899 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
222834 TATACTAATT
222844 TTAATCTCACCATTTAAAATAA
1 TTAATCTCACCATTTAAAATAA
* *
222866 TTAATCTCACC-GTTATAATAA
1 TTAATCTCACCATTTAAAATAA
*
222887 CTAATCTCACCAT
1 TTAATCTCACCAT
222900 CATCATTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.39, C:0.23, G:0.02, T:0.36
Consensus pattern (22 bp):
TTAATCTCACCATTTAAAATAA
Found at i:228284 original size:3 final size:3
Alignment explanation
Indices: 228276--228307 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
228266 AACTTATGAT
228276 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
228308 GGCACTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:229361 original size:15 final size:15
Alignment explanation
Indices: 229341--229375 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
229331 TATTTAAATT
229341 ATATTTTTATATATC
1 ATATTTTTATATATC
*
229356 ATATTTTTATTTATC
1 ATATTTTTATATATC
229371 A-ATTT
1 ATATTT
229376 ATGAGGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (15 bp):
ATATTTTTATATATC
Found at i:229525 original size:25 final size:25
Alignment explanation
Indices: 229497--229546 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
229487 ATTTGGTATC
229497 AACACTAACACTAAAAGCCCATAAA
1 AACACTAACACTAAAAGCCCATAAA
* * *
229522 AACATTAACACTAGAAGCTCATAAA
1 AACACTAACACTAAAAGCCCATAAA
229547 TCTTAGTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.24, G:0.06, T:0.16
Consensus pattern (25 bp):
AACACTAACACTAAAAGCCCATAAA
Found at i:230398 original size:2 final size:2
Alignment explanation
Indices: 230391--230477 Score: 99
Period size: 2 Copynumber: 44.0 Consensus size: 2
230381 TTATAATGGA
230391 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
** * *
230433 -T CCC AC A- AT AGC A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT -AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
230474 AT AT
1 AT AT
230478 TGTCTTTCAA
Statistics
Matches: 77, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
1 3 0.04
2 73 0.95
3 1 0.01
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (2 bp):
AT
Found at i:233722 original size:11 final size:11
Alignment explanation
Indices: 233706--233730 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
233696 GATCTAAAAA
233706 ATAATATAAAT
1 ATAATATAAAT
233717 ATAATATAAAT
1 ATAATATAAAT
233728 ATA
1 ATA
233731 TGAATGCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:233885 original size:22 final size:23
Alignment explanation
Indices: 233855--233902 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
233845 AATATTTTGT
233855 TAATAATATACAAATA-AAAGAAA
1 TAATAATATA-AAATATAAAGAAA
*
233878 TAAT-ATATAAAATATAAATAAA
1 TAATAATATAAAATATAAAGAAA
233900 TAA
1 TAA
233903 AATGACATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 5 0.22
22 14 0.61
23 4 0.17
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (23 bp):
TAATAATATAAAATATAAAGAAA
Found at i:235215 original size:50 final size:50
Alignment explanation
Indices: 235156--235361 Score: 328
Period size: 50 Copynumber: 4.1 Consensus size: 50
235146 ACTTAGAGTT
235156 AACAATTATGGCCACCTCCCTT-TATTGTCAAAGGTTGGTGAAGAATTGTC
1 AACAATTATGGCCACCT-CCTTCTATTGTCAAAGGTTGGTGAAGAATTGTC
*
235206 AACAATTATGACCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATTGTC
1 AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATTGTC
* *
235256 AACAATTATGGCCACCTCTTTCTATTGTCAAAGGTTGGTGAAGAATCGTC
1 AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATTGTC
*
235306 AACAATTATGGCCACCT-CTCTCTATTGTCAAAGGTTGGTGAATG-ATAGTC
1 AACAATTATGGCCACCTCCT-TCTATTGTCAAAGGTTGGTGAA-GAATTGTC
235356 AACAAT
1 AACAAT
235362 GATAACAACT
Statistics
Matches: 147, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
49 5 0.03
50 141 0.96
51 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Consensus pattern (50 bp):
AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATTGTC
Found at i:240447 original size:36 final size:36
Alignment explanation
Indices: 240404--240497 Score: 179
Period size: 36 Copynumber: 2.6 Consensus size: 36
240394 GAAGGTTGCA
*
240404 GAGCTGCTGCCGGTGTTCGTGGGTTGGAAGCTGATG
1 GAGCTGCTGCCAGTGTTCGTGGGTTGGAAGCTGATG
240440 GAGCTGCTGCCAGTGTTCGTGGGTTGGAAGCTGATG
1 GAGCTGCTGCCAGTGTTCGTGGGTTGGAAGCTGATG
240476 GAGCTGCTGCCAGTGTTCGTGG
1 GAGCTGCTGCCAGTGTTCGTGG
240498 CTAGAAGTTG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.12, C:0.18, G:0.43, T:0.28
Consensus pattern (36 bp):
GAGCTGCTGCCAGTGTTCGTGGGTTGGAAGCTGATG
Found at i:240712 original size:20 final size:19
Alignment explanation
Indices: 240675--240713 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
240665 GAGCAGACGC
*
240675 TGGAAGCTGCTGCTATGGA
1 TGGAAGCTGCTGCAATGGA
*
240694 TGGAAGGCTGCTGGAATGGA
1 TGGAA-GCTGCTGCAATGGA
240714 AGTTGGAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.23, C:0.13, G:0.41, T:0.23
Consensus pattern (19 bp):
TGGAAGCTGCTGCAATGGA
Found at i:241141 original size:15 final size:15
Alignment explanation
Indices: 241046--241141 Score: 126
Period size: 15 Copynumber: 6.5 Consensus size: 15
241036 CGGCCGTTTC
241046 ATGC-ATGAAA-GCA
1 ATGCAATGAAATGCA
*
241059 ATGTAATGAAATGCA
1 ATGCAATGAAATGCA
*
241074 ATGCAATGAAATGAA
1 ATGCAATGAAATGCA
*
241089 ATGAAATGAAATGCA
1 ATGCAATGAAATGCA
241104 ATGCAATGAAATGCA
1 ATGCAATGAAATGCA
*
241119 ATGAAATGAAATG-A
1 ATGCAATGAAATGCA
241133 AGTGCAATG
1 A-TGCAATG
241142 CAATAAAATG
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
13 3 0.04
14 8 0.11
15 61 0.85
ACGTcount: A:0.49, C:0.08, G:0.22, T:0.21
Consensus pattern (15 bp):
ATGCAATGAAATGCA
Found at i:241145 original size:5 final size:5
Alignment explanation
Indices: 241058--241133 Score: 98
Period size: 5 Copynumber: 15.2 Consensus size: 5
241048 GCATGAAAGC
* * * * *
241058 AATGT AATGA AATGC AATGC AATGA AATGA AATGA AATGA AATGC AATGC
1 AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA
*
241108 AATGA AATGC AATGA AATGA AATGA A
1 AATGA AATGA AATGA AATGA AATGA A
241134 GTGCAATGCA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 64 1.00
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.21
Consensus pattern (5 bp):
AATGA
Found at i:241151 original size:10 final size:10
Alignment explanation
Indices: 241046--241141 Score: 106
Period size: 10 Copynumber: 9.8 Consensus size: 10
241036 CGGCCGTTTC
241046 ATGC-ATGAA
1 ATGCAATGAA
*
241055 A-GCAATGTA
1 ATGCAATGAA
* *
241064 ATGAAATGCA
1 ATGCAATGAA
241074 ATGCAATGAA
1 ATGCAATGAA
*
241084 ATGAAATGAA
1 ATGCAATGAA
* *
241094 ATGAAATGCA
1 ATGCAATGAA
241104 ATGCAATGAA
1 ATGCAATGAA
241114 ATGCAATGAA
1 ATGCAATGAA
*
241124 ATGAAATGAA
1 ATGCAATGAA
*
241134 GTGCAATG
1 ATGCAATG
241142 CAATAAAATG
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
8 2 0.03
9 6 0.08
10 65 0.89
ACGTcount: A:0.49, C:0.08, G:0.22, T:0.21
Consensus pattern (10 bp):
ATGCAATGAA
Found at i:241186 original size:22 final size:22
Alignment explanation
Indices: 241160--241236 Score: 81
Period size: 22 Copynumber: 3.5 Consensus size: 22
241150 TGTTTTTGAA
241160 ATGCATGAAATGAAAATTATGC
1 ATGCATGAAATGAAAATTATGC
*
241182 ATGCATGAAATG----TTACGTGAA
1 ATGCATGAAATGAAAATTA--TG-C
*
241203 AAGCATGAAATGAAAATTATGC
1 ATGCATGAAATGAAAATTATGC
241225 ATGCATGAAATG
1 ATGCATGAAATG
241237 TTACGTGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
18 3 0.07
20 2 0.05
21 11 0.25
22 23 0.52
23 2 0.05
25 3 0.07
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (22 bp):
ATGCATGAAATGAAAATTATGC
Found at i:241209 original size:43 final size:43
Alignment explanation
Indices: 241163--241300 Score: 214
Period size: 43 Copynumber: 3.3 Consensus size: 43
241153 TTTTGAAATG
*
241163 CATGAAATGAAAATTATGCATGCATGAAATGTTACGTGAAAAG
1 CATGAAATGAAAATTATGCATGCATGAAATGTTACGTGAAAAA
241206 CATGAAATGAAAATTATGCATGCATGAAATGTTACGTGAAAAA
1 CATGAAATGAAAATTATGCATGCATGAAATGTTACGTGAAAAA
* *
241249 CATAAAATG-AAA--ATGCATGCA--ATATGTTACGTGAAAAA
1 CATGAAATGAAAATTATGCATGCATGAAATGTTACGTGAAAAA
241287 CATGAAATGAAAAT
1 CATGAAATGAAAAT
241301 GCATGCAATG
Statistics
Matches: 89, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
38 24 0.27
39 3 0.03
40 9 0.10
42 3 0.03
43 50 0.56
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.25
Consensus pattern (43 bp):
CATGAAATGAAAATTATGCATGCATGAAATGTTACGTGAAAAA
Found at i:241280 original size:38 final size:38
Alignment explanation
Indices: 241225--241309 Score: 147
Period size: 38 Copynumber: 2.3 Consensus size: 38
241215 AAAATTATGC
241225 ATGCATG-AA-ATGTTACGTGAAAAACATAAAATGAAA
1 ATGCATGCAATATGTTACGTGAAAAACATAAAATGAAA
*
241261 ATGCATGCAATATGTTACGTGAAAAACATGAAATGAAA
1 ATGCATGCAATATGTTACGTGAAAAACATAAAATGAAA
241299 ATGCATGCAAT
1 ATGCATGCAAT
241310 GAAAAAAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
36 7 0.15
37 2 0.04
38 37 0.80
ACGTcount: A:0.48, C:0.11, G:0.18, T:0.24
Consensus pattern (38 bp):
ATGCATGCAATATGTTACGTGAAAAACATAAAATGAAA
Found at i:242590 original size:50 final size:50
Alignment explanation
Indices: 242531--242786 Score: 406
Period size: 50 Copynumber: 5.1 Consensus size: 50
242521 ACTTAGAGTT
* *
242531 AACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTGTA
1 AACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATCGTC
* * *
242581 AACAATTATGACCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTT
1 AACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATCGTC
* *
242631 AACAATTATGGCCACCTCCCTCTATTGTCAAAGATTGGTGAAGAATTGTC
1 AACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATCGTC
*
242681 AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTC
1 AACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATCGTC
* *
242731 AACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAATG-ATAGTC
1 AACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAA-GAATCGTC
242781 AACAAT
1 AACAAT
242787 GACAACAACT
Statistics
Matches: 190, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
50 189 0.99
51 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (50 bp):
AACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATCGTC
Found at i:242701 original size:100 final size:100
Alignment explanation
Indices: 242528--242786 Score: 448
Period size: 100 Copynumber: 2.6 Consensus size: 100
242518 TATACTTAGA
*
242528 GTTAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTGTAAACAATTATGAC
1 GTTAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTGTCAACAATTATGAC
242593 CACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
66 CACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
* *
242628 GTTAACAATTATGGCCACCTCCCTCTATTGTCAAAGATTGGTGAAGAATTGTCAACAATTATGGC
1 GTTAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTGTCAACAATTATGAC
242693 CACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
66 CACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
242728 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAATG-ATAGTCAACAAT
1 GTTAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAA-GAATTGTCAACAAT
242787 GACAACAACT
Statistics
Matches: 151, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
100 150 0.99
101 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (100 bp):
GTTAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTGTCAACAATTATGAC
CACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:251331 original size:17 final size:17
Alignment explanation
Indices: 251309--251343 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
251299 AGAACCAACT
251309 CTGAAACACAAAATGAA
1 CTGAAACACAAAATGAA
251326 CTGAAACACAAAATGAA
1 CTGAAACACAAAATGAA
251343 C
1 C
251344 CTAATATCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.20, G:0.11, T:0.11
Consensus pattern (17 bp):
CTGAAACACAAAATGAA
Found at i:251688 original size:30 final size:30
Alignment explanation
Indices: 251628--251688 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
251618 TTTATGCTTT
* * *
251628 TTAAAATTAGATCAATATGACCATGTAATA
1 TTAAAATTAAAACAATATGACCATGCAATA
**
251658 TTAAAATTAAAACAATATGATGATGCAATA
1 TTAAAATTAAAACAATATGACCATGCAATA
251688 T
1 T
251689 ACCAATATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (30 bp):
TTAAAATTAAAACAATATGACCATGCAATA
Found at i:251748 original size:16 final size:16
Alignment explanation
Indices: 251710--251749 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
251700 TAAATTTTTT
* * *
251710 TAAAATGATTTGAATT
1 TAAAATTATTTAAATA
251726 TAAAATTATTTAAATA
1 TAAAATTATTTAAATA
251742 TAAAATTA
1 TAAAATTA
251750 ACTTAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (16 bp):
TAAAATTATTTAAATA
Found at i:252719 original size:17 final size:17
Alignment explanation
Indices: 252692--252747 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
252682 TTTATTCATT
252692 ATAAA-TTATTTAATA-
1 ATAAATTTATTTAATAG
252707 ATTAAATTTATTTAATAG
1 A-TAAATTTATTTAATAG
252725 ATAAATATT-TTTAATAG
1 ATAAAT-TTATTTAATAG
*
252742 AAAAAT
1 ATAAAT
252748 AATCTTAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
15 1 0.03
16 4 0.11
17 28 0.78
18 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (17 bp):
ATAAATTTATTTAATAG
Found at i:252755 original size:17 final size:17
Alignment explanation
Indices: 252718--252757 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
252708 TTAAATTTAT
* * *
252718 TTAATAGATAAATATTT
1 TTAATAGAAAAATAATC
252735 TTAATAGAAAAATAATC
1 TTAATAGAAAAATAATC
252752 TTAATA
1 TTAATA
252758 AATCAATTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (17 bp):
TTAATAGAAAAATAATC
Found at i:253193 original size:14 final size:14
Alignment explanation
Indices: 253157--253195 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
253147 CGCTTGAATA
*
253157 TATATATAAATATG
1 TATATATATATATG
* *
253171 TATATATATTTATT
1 TATATATATATATG
253185 TATATATATAT
1 TATATATATAT
253196 GCATGCGGAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (14 bp):
TATATATATATATG
Found at i:254052 original size:15 final size:15
Alignment explanation
Indices: 254034--254089 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
254024 TTTAATCTAT
*
254034 ATAATTTTAAAATTA
1 ATAATTTTAAATTTA
*
254049 ATAA-ATTAAATTTA
1 ATAATTTTAAATTTA
254063 A-AATAATTTAAATTTAA
1 ATAAT--TTTAAATTT-A
254080 ATAATTTTAA
1 ATAATTTTAA
254090 TATAAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
13 2 0.06
14 9 0.27
15 4 0.12
16 13 0.39
17 2 0.06
18 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTTTAAATTTA
Found at i:254067 original size:16 final size:16
Alignment explanation
Indices: 254048--254144 Score: 61
Period size: 16 Copynumber: 5.8 Consensus size: 16
254038 TTTTAAAATT
254048 AATAAATTAAATTTAA
1 AATAAATTAAATTTAA
*
254064 AATAATTTAAATTTAAA
1 AATAAATTAAATTT-AA
* *
254081 TAATTTTAATATAAAATTAA
1 -AA--TAAAT-TAAATTTAA
*
254101 AAT-TATCTAAATTTAA
1 AATAAAT-TAAATTTAA
* * *
254117 TATTATTTAAATTTAA
1 AATAAATTAAATTTAA
*
254133 AATAAATAAAAT
1 AATAAATTAAAT
254145 ATATAATAAT
Statistics
Matches: 61, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
16 42 0.69
17 4 0.07
18 2 0.03
19 2 0.03
20 5 0.08
21 6 0.10
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAAATTAAATTTAA
Found at i:254083 original size:31 final size:31
Alignment explanation
Indices: 254034--254097 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
254024 TTTAATCTAT
*
254034 ATAATTTTAAAATTAATAAATTAAATTTAAA
1 ATAATTTTAAAATTAATAAATTAAATATAAA
* * *
254065 ATAA-TTTAAATTTAAATAATTTTAATATAAA
1 ATAATTTTAAAATT-AATAAATTAAATATAAA
254096 AT
1 AT
254098 TAAAATTATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 8 0.29
31 20 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
ATAATTTTAAAATTAATAAATTAAATATAAA
Found at i:254095 original size:15 final size:15
Alignment explanation
Indices: 254024--254095 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
254014 AATATTTAAA
* *
254024 TTTAATCTATATAAT
1 TTTAATATAAATAAT
* * *
254039 TTTAAAATTAATAAA
1 TTTAATATAAATAAT
* *
254054 TTAAATTTAAAATAAT
1 TTTAATAT-AAATAAT
* *
254070 TTAAATTTAAATAAT
1 TTTAATATAAATAAT
254085 TTTAATATAAA
1 TTTAATATAAA
254096 ATTAAAATTA
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
15 31 0.70
16 13 0.30
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (15 bp):
TTTAATATAAATAAT
Found at i:254606 original size:23 final size:23
Alignment explanation
Indices: 254562--254606 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
254552 TTATAAAATA
* *
254562 ATATAAATATTTTTTATTATATC
1 ATATAAATATTTTTCATCATATC
254585 ATATATAA-ATTTTTCATCATAT
1 ATATA-AATATTTTTCATCATAT
254607 TATCAAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATAAATATTTTTCATCATATC
Found at i:256401 original size:27 final size:27
Alignment explanation
Indices: 256299--256403 Score: 112
Period size: 27 Copynumber: 4.0 Consensus size: 27
256289 CAATAAAAAT
*
256299 TAACCACCAATTTTGACAAACA-ACAAG
1 TAACCACCATTTTTGACAAACACA-AAG
* * *
256326 T---CACAATTTTTGATAAACAAAAAAG
1 TAACCACCATTTTTGACAAAC-ACAAAG
*
256351 -AACCACCATTTTTGACAAATACAAAG
1 TAACCACCATTTTTGACAAACACAAAG
256377 TAACCACCATTTTTGACAAACACAAAG
1 TAACCACCATTTTTGACAAACACAAAG
256404 GGTGGCTTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
24 14 0.22
25 4 0.06
26 6 0.09
27 40 0.62
ACGTcount: A:0.48, C:0.22, G:0.08, T:0.23
Consensus pattern (27 bp):
TAACCACCATTTTTGACAAACACAAAG
Found at i:257832 original size:19 final size:18
Alignment explanation
Indices: 257807--257903 Score: 97
Period size: 19 Copynumber: 5.8 Consensus size: 18
257797 ATTTCAGCGA
257807 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
257825 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
257841 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
257857 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
257873 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
257889 TTTTGTATCGATACA
1 -TTTGTATCGATACA
257904 ATGTATTGCT
Statistics
Matches: 66, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
18 1 0.02
19 35 0.53
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:257845 original size:32 final size:32
Alignment explanation
Indices: 257809--257909 Score: 193
Period size: 32 Copynumber: 3.2 Consensus size: 32
257799 TTCAGCGATT
257809 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
257841 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
257873 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
257905 TGTAT
1 TGTAT
257910 TGCTAGGAAG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 68 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:257846 original size:13 final size:13
Alignment explanation
Indices: 257828--257884 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
257818 ACATAAGTGT
257828 TGTATCGATACAA
1 TGTATCGATACAA
257841 TGTATCGATACATAA
1 TGTATCGATAC--AA
257856 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
257873 TGTATCGATACA
1 TGTATCGATACA
257885 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:257999 original size:34 final size:33
Alignment explanation
Indices: 257935--258001 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
257925 GCCAAGGAAA
* *
257935 TGTATCGATACATTTTTCTGTGTATTGATACAT
1 TGTATCGATACATTATTCTGTGTATCGATACAT
*
257968 TGTATCGATACATCTATTCTTTGTATCGATACAT
1 TGTATCGATACAT-TATTCTGTGTATCGATACAT
258002 CTAGGAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 13 0.43
34 17 0.57
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.46
Consensus pattern (33 bp):
TGTATCGATACATTATTCTGTGTATCGATACAT
Found at i:260404 original size:51 final size:51
Alignment explanation
Indices: 260348--260446 Score: 157
Period size: 51 Copynumber: 1.9 Consensus size: 51
260338 CAATTCTCCG
*
260348 TAATCGGGGATA-TCCCAACTCCGATTTTATTT-TCAAAACATTAATTTTCTA
1 TAATCGGGGATACT-CCAACTCCGATTTTATTTCT-AAAACATCAATTTTCTA
260399 TAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAATTTT
1 TAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAATTTT
260447 TCATCGAGGA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
51 43 0.96
52 2 0.04
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.38
Consensus pattern (51 bp):
TAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAATTTTCTA
Found at i:260519 original size:28 final size:27
Alignment explanation
Indices: 260447--260523 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 27
260437 CATCAATTTT
*
260447 TCATCGAGGATACTCCAACCCCGTTAA
1 TCATCGGGGATACTCCAACCCCGTTAA
260474 TCATCGGGGATACTCCAACCCCGTT-A
1 TCATCGGGGATACTCCAACCCCGTTAA
**
260500 TTTTCGAGGGGATACTCCAACCCC
1 TCATC--GGGGATACTCCAACCCC
260524 CGGCTTTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 4 0.09
27 24 0.53
28 17 0.38
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (27 bp):
TCATCGGGGATACTCCAACCCCGTTAA
Found at i:260652 original size:79 final size:80
Alignment explanation
Indices: 260476--260655 Score: 258
Period size: 80 Copynumber: 2.3 Consensus size: 80
260466 CCCGTTAATC
* *
260476 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAA
* *
260541 TATTAATTTCTCATA
66 TATGAATTTCTCACA
* *
260556 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAA-CCCCGGTTTTATTTC-CAAA
1 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAA
*
260619 TCATCGATTTTC-CACA
66 T-AT-GAATTTCTCACA
260635 ATCGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
260656 GCTTTATTTT
Statistics
Matches: 91, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
78 4 0.04
79 40 0.44
80 47 0.52
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (80 bp):
ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAA
TATGAATTTCTCACA
Found at i:260714 original size:52 final size:51
Alignment explanation
Indices: 260587--260756 Score: 214
Period size: 52 Copynumber: 3.3 Consensus size: 51
260577 TTATCTCCGA
* * *
260587 GGGGATACTCCAACCCCGGTTTTATTTCCAAATCATCGATTTTCCACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACAATC
* * **
260638 GGGGATACTCCAACCCCGGCTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCC-ACAATC
* * * *
260690 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATT
1 GGGGATACTCCAACCCCGGTTTTATTTCC-AAAACACCAATTTTCCACAATC
*
260742 GAGGATACTCCAACC
1 GGGGATACTCCAACC
260757 TCATTATTTC
Statistics
Matches: 100, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
51 40 0.40
52 45 0.45
53 15 0.15
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACAATC
Found at i:260879 original size:291 final size:285
Alignment explanation
Indices: 260349--260946 Score: 840
Period size: 291 Copynumber: 2.1 Consensus size: 285
260339 AATTCTCCGT
* * **
260349 AATCGGGGATA-TCCCAACTCCGATTTTATTTTCAAAACATTAATTTTCTATAATCGGGGATACT
1 AATCGGGGATACT-CCAACCCCGACTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACT
* * *
260413 CCAACTCCGATTTTATTTCTAAAACATCAATTTTTCATCGAGGATACTCCAACCCCGTTAATCAT
65 CCAACTCCGATTTTATTTCAAAAACACCAATTTTTCATCGAGGATACTCCAACCCCATTAATCAT
** * *
260478 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAATA
130 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCCGGCTTTATTCCTAAAATA
*
260543 TTAATTTCTCATAATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCGGTT
195 TTAATTTCTCATAATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCGATT
260608 TTATTTCCAAATCATCGATTTTCCAC
260 TTATTTCCAAATCATCGATTTTCCAC
* *
260634 AATCGGGGATACTCCAACCCCGGCTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
1 AATCGGGGATACTCCAACCCCGACTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGATACT
* *
260699 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATTGAGGATACTCCAACCTCATTAT
65 CCAACTCCGATTTTATTT-CAAAAACACCAATTTTT--C-ATCGAGGATACTCCAACCCCATTA-
* *
260764 TTCATCGGGGGATACTCCAATCCCGTTACCTCCGAGGGGATACTCCAA-CCCCGGCTTTATTCCT
125 ATCATC-GGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCCGGCTTTATTCCT
* * * * * *
260828 AAAATATTGATTTCTCATTATTGGGGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCAATC
189 AAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACC
* * * *
260893 CCGATTTTTTTTTCTAATCATCGATTTTTCAC
254 CCGATTTTATTTCCAAATCATCGATTTTCCAC
* *
260925 AACCGGGGATACTCCAGCCCCG
1 AATCGGGGATACTCCAACCCCG
260947 TTATTTTCAA
Statistics
Matches: 275, Mismatches: 30, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
285 40 0.15
286 35 0.13
287 15 0.05
289 1 0.00
290 21 0.08
291 126 0.46
292 37 0.13
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (285 bp):
AATCGGGGATACTCCAACCCCGACTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
CAACTCCGATTTTATTTCAAAAACACCAATTTTTCATCGAGGATACTCCAACCCCATTAATCATC
GGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCCGGCTTTATTCCTAAAATAT
TAATTTCTCATAATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCGATTT
TATTTCCAAATCATCGATTTTCCAC
Found at i:260919 original size:79 final size:77
Alignment explanation
Indices: 260771--260974 Score: 185
Period size: 79 Copynumber: 2.6 Consensus size: 77
260761 TATTTCATCG
** *
260771 GGGGATACTCCAATCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAATATT
1 GGGGATACTCCAA-CCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCT-AAATATC
** **
260836 GATTTCTCATTATT
64 GATTTCTCACAACC
* ** * *
260850 GGGGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCAATCCCGATTTTTTTTTCT-AATCAT
1 GGGGATACTCCAACC-CGTTATTTCCGAGGGGATACTCCAACCCCG-GCTTTATTCCTAAAT-AT
*
260914 CGATTTTTCACAACC
63 CGATTTCTCACAACC
* * * * *
260929 GGGGATACTCCAGCCCCGTTATTTTCAAGGGGACAGTCCAACCCCG
1 GGGGATACTCCA-ACCCGTTATTTCCGAGGGGATACTCCAACCCCG
260975 TTATTATCTC
Statistics
Matches: 102, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
78 5 0.05
79 88 0.86
80 9 0.09
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.30
Consensus pattern (77 bp):
GGGGATACTCCAACCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAATATCGA
TTTCTCACAACC
Found at i:262038 original size:20 final size:20
Alignment explanation
Indices: 262009--262085 Score: 82
Period size: 20 Copynumber: 3.7 Consensus size: 20
261999 TTTTACCTAG
* *
262009 ATGTACCGATATATTTCTCA
1 ATGTATCGATACATTTCTCA
*
262029 ATGTATCGATACATTCTATCCA
1 ATGTATCGATACATT-TCT-CA
* *
262051 GATGTATCAATACATTGCTCA
1 -ATGTATCGATACATTTCTCA
262072 ATGTATCGATACAT
1 ATGTATCGATACAT
262086 CTAGTTAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
20 26 0.55
21 4 0.09
22 3 0.06
23 14 0.30
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTTCTCA
Found at i:275369 original size:10 final size:10
Alignment explanation
Indices: 275354--275413 Score: 59
Period size: 12 Copynumber: 5.7 Consensus size: 10
275344 CTTTACACCC
*
275354 AAAAATAACA
1 AAAAATAAAA
275364 AAAAATAAAA
1 AAAAATAAAA
*
275374 AAACA-AAAA
1 AAAAATAAAA
275383 AAAAATCAAGAA
1 AAAAAT-AA-AA
275395 AAAAATAGCAAA
1 AAAAATA--AAA
275407 AAAAATA
1 AAAAATA
275414 GAAATGGGTC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
9 8 0.19
10 13 0.31
11 3 0.07
12 17 0.40
13 1 0.02
ACGTcount: A:0.82, C:0.07, G:0.03, T:0.08
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:275384 original size:11 final size:12
Alignment explanation
Indices: 275370--275411 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
275360 AACAAAAAAT
275370 AAAAAAA-CAAA
1 AAAAAAAGCAAA
*
275381 AAAAAAATCAAGA
1 AAAAAAAGCAA-A
275394 AAAAAATAGCAAA
1 AAAAAA-AGCAAA
275407 AAAAA
1 AAAAA
275412 TAGAAATGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 7 0.26
12 3 0.11
13 13 0.48
14 4 0.15
ACGTcount: A:0.83, C:0.07, G:0.05, T:0.05
Consensus pattern (12 bp):
AAAAAAAGCAAA
Found at i:276704 original size:29 final size:29
Alignment explanation
Indices: 276631--277644 Score: 1206
Period size: 29 Copynumber: 34.6 Consensus size: 29
276621 GAACGTTCAA
276631 CCCTTTCAAAGCCCACAAGTCAGTGGCA-
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
*
276659 CCCTTTCAAAGCTCACAAGTCAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
*
276688 CCCTTTCAAAGCCCACAAGTCAGTGGTA-
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
276716 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
*
276745 CCCTTTCAAAGCCTACGCAAGTCAGTGGCA-
1 CCCTTTCAAAGCC--CACAAGTCAGTGGCAC
* * *
276775 ACCTTTTAAAGCTCACAAGTCAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
276804 TCTTTTCAAAGCCCATAAGAT-AGTGGCAC
1 CCCTTTCAAAGCCCACAAG-TCAGTGGCAC
276833 CCCTTTCAAAGCCCACAAGTCAGTGGCA-
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
276861 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
276890 TCTTTTCCAAGCCCACAAGTCAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
* *
276919 TCTTTTCAAAGCCCACATGAGTCAGTGGCAAC
1 CCCTTTCAAAGCCCACA--AGTCAGTGGC-AC
* *
276951 TCTTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
* *
276980 CTCTTTCAAAGCCCACAAGTCAGTGGC-T
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
277008 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
277037 CCCTTTCAAAGCCCACGCAAGTCAGTGGCA-
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCAC
* *
277067 CCCTTTTAAAGCCCACAAGTCAATGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
277096 TCTTTTCAAAGCCCACAAGACAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
*
277125 CCCTTTCAAAGCCCACAAGTTAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
277154 TCTTTTCAAAGCCCACAAGTTAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
277183 TCTTTTCAAAGCCCACACGAGTCGGTGGCAAC
1 CCCTTTCAAAGCCCACA--AGTCAGTGGC-AC
* *
277215 TCTTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
* *
277244 TCCTTTCAAAGCCCACGAGTCAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
277273 CCCTTTCAAAGCCCACGCAAGTCAGTGGCA-
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCAC
*
277303 CCCTTTTAAAGCCCACAAGTCAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
277332 TCTTTTCAAAGCCCACAAGACAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
277361 CCCTTTCAAAGCCCACAAGTCAGTGGCA-
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
**
277389 CCCTTTCAAAGCCCACAAGTCAGTAACAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
277418 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
277447 TCTTTTCAAAGCTCACAAGTCAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
277476 TCTTTTCAAAGCCCACACAAGTCGGTAGCAAC
1 CCCTTTCAAAG-CC-CACAAGTCAGTGGC-AC
* * * *
277508 TCTTTTCAAAGCCCACACAAATCAGTTGCA-
1 CCCTTTCAAAG-CC-CACAAGTCAGTGGCAC
277538 CCCTTTCAAAGCCCACAAGTCAGTGGCA-
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC
* *
277566 CCCTTTTAAAGCCCACAAG-CTAGTGGTAAC
1 CCCTTTCAAAGCCCACAAGTC-AGTGG-CAC
* * * *
277596 TCTTTTCAAAGCCTACACGAGTCGGTGGCAAC
1 CCCTTTCAAAGCC--CACAAGTCAGTGGC-AC
* *
277628 TCTTTTCAAAGCCCACA
1 CCCTTTCAAAGCCCACA
277645 TAAGTTAGTG
Statistics
Matches: 873, Mismatches: 81, Indels: 62
0.86 0.08 0.06
Matches are distributed among these distances:
27 1 0.00
28 210 0.24
29 420 0.48
30 81 0.09
31 70 0.08
32 90 0.10
33 1 0.00
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.21
Consensus pattern (29 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:276719 original size:57 final size:57
Alignment explanation
Indices: 276631--277644 Score: 1219
Period size: 57 Copynumber: 17.3 Consensus size: 57
276621 GAACGTTCAA
*
276631 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCTCACAAGTCAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
*
276688 CCCTTTCAAAGCCCACAAGTCAGTGGTACCCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
276745 CCCTTTCAAAGCCTACGCAAGTCAGTGGCAACCTTTTAAAGCTCACAAGTCAGTGGCAC
1 CCCTTTCAAAGCC--CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
276804 TCTTTTCAAAGCCCATAAGAT-AGTGGCACCCCTTTCAAAGCCCACAAGTCAGTGGCA-
1 CCCTTTCAAAGCCCACAAG-TCAGTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCAC
* *
276861 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCCAAGCCCACAAGTCAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
276919 TCTTTTCAAAGCCCACATGAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCCTTTCAAAGCCCACA--AGTCAGTGGC-AC-CCTTTCAAAGCCCACAAGTCAGTGGCAC
* *
276980 CTCTTTCAAAGCCCACAAGTCAGTGGCTCCCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* *
277037 CCCTTTCAAAGCCCACGCAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAATGGCAC
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
277096 TCTTTTCAAAGCCCACAAGACAGTGGCACCCCTTTCAAAGCCCACAAGTTAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * * *
277154 TCTTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACACGAGTCGGTGGCAAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACA--AGTCAGTGGC-AC
* * *
277215 TCTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACGAGTCAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
277273 CCCTTTCAAAGCCCACGCAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCAC
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
277332 TCTTTTCAAAGCCCACAAGACAGTGGCACCCCTTTCAAAGCCCACAAGTCAGTGGCA-
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCAC
**
277389 CCCTTTCAAAGCCCACAAGTCAGTAACACCCCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * * * *
277447 TCTTTTCAAAGCTCACAAGTCAGTGGCACTCTTTTCAAAGCCCACACAAGTCGGTAGCAAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAG-CC-CACAAGTCAGTGGC-AC
* * * *
277508 TCTTTTCAAAGCCCACACAAATCAGTTGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-
1 CCCTTTCAAAG-CC-CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * * *
277566 CCCTTTTAAAGCCCACAAG-CTAGTGGTAACTCTTTTCAAAGCCTACACGAGTCGGTGGCAAC
1 CCCTTTCAAAGCCCACAAGTC-AGTGG-CAC-CCTTTCAAAGCC--CACAAGTCAGTGGC-AC
* *
277628 TCTTTTCAAAGCCCACA
1 CCCTTTCAAAGCCCACA
277645 TAAGTTAGTG
Statistics
Matches: 838, Mismatches: 85, Indels: 63
0.85 0.09 0.06
Matches are distributed among these distances:
55 1 0.00
56 11 0.01
57 250 0.30
58 202 0.24
59 163 0.19
60 68 0.08
61 105 0.13
62 24 0.03
63 14 0.02
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.21
Consensus pattern (57 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:277160 original size:264 final size:259
Alignment explanation
Indices: 276634--277644 Score: 1399
Period size: 264 Copynumber: 3.8 Consensus size: 259
276624 CGTTCAACCC
* * * *
276634 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCTCACAAGTCAGTGGCACCCCTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* *
276698 GCCCACAAGTCAGTGGTACC-CTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCAAAGCCTACG
66 GCCCACAAGTCAGTGGCACCTCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCAAAGCC--CA
* * *
276762 CAAGTCAGTGGCAACCTTTTAAAGCTCACAAGTCAGTGGCACTCTTTTCAAAGCCCATAAGAT-A
129 CAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAG-TCA
276826 GTGGCACCCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
193 GTGGCACCCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
276891 CT
258 CT
*
276893 TTTCCAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACATGAGTCAGTGGCAACTCTTTTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACA--AGTCAGTGGC-ACTCTTTTC
*
276958 AAAGCCCACAAGTCAGTGGCACCTCTTTCAAAGCCCACAAGTCAGTGGC-TCCCTTTCAAAGCCC
63 AAAGCCCACAAGTCAGTGGCACCTCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCAAAGCCC
* *
277022 ACAAGTCAGTGGCACCCCTTTCAAAGCCCACGCAAGTCAGTGGCACCCTTTT-AAAGCCCACAAG
128 ACAAGTCAGTGGCA-CCCTTTTAAAGCCCA--CAAGTCAGTGGCACTCTTTTCAAAGCCCACAAG
* * * * *
277086 TCAATGGCACTCTTTTCAAAGCCCACAAGACAGTGGCACCCCTTTCAAAGCCCACAAGTTAGTGG
190 TCAGTGGCACCCCTTTCAAAGCCCACAAGTCAGTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGG
277151 CACTCT
254 CACTCT
* *
277157 TTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACACGAGTCGGTGGCAACTCTTTTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACA--AGTCAGTGGC-ACTCTTTTC
*
277222 AAAGCCCACAAGTCAGTGGCA-CTCCTTTCAAAGCCCACGAGTCAGTGGCACCCCTTTCAAAGCC
63 AAAGCCCACAAGTCAGTGGCACCT-CTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCAAAGCC
277286 CACGCAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAG
127 CA--CAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAG
* **
277351 ACAGTGGCACCCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTAAC
190 TCAGTGGCACCCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC
* *
277416 ACCCC
255 ACTCT
*
277421 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCTCACAAGTCAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* * * * *
277486 GCCCACACAAGTCGGTAGCAACTCTTTTCAAAGCCCACACAAATCAGTTGCA-CCCTTTCAAAGC
66 G-CC-CACAAGTCAGTGGCACCTC-TTTCAAAG-CC-CACAAGTCAGTGGCACCCCTTTCAAAGC
*
277550 CCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAG-CTAGTGGTAACTCTTTTCAAAGCCTACAC
126 CCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTC-AGTGG-CACTCTTTTCAAAGCC--CAC
* * * *
277614 GAGTCGGTGGCAACTCTTTTCAAAGCCCACA
187 AAGTCAGTGGC-ACCCCTTTCAAAGCCCACA
277645 TAAGTTAGTG
Statistics
Matches: 676, Mismatches: 50, Indels: 44
0.88 0.06 0.06
Matches are distributed among these distances:
259 25 0.04
260 14 0.02
261 27 0.04
262 35 0.05
263 138 0.20
264 293 0.43
265 77 0.11
266 37 0.05
267 30 0.04
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (259 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
GCCCACAAGTCAGTGGCACCTCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCAAAGCCCACA
AGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTG
GCACCCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCT
Found at i:278250 original size:20 final size:20
Alignment explanation
Indices: 278225--278341 Score: 137
Period size: 20 Copynumber: 5.7 Consensus size: 20
278215 TTTTACCTAG
*
278225 ATGTACCGATACATTTCTCA
1 ATGTATCGATACATTTCTCA
*
278245 ATGTACCGATACATTTCTCA
1 ATGTATCGATACATTTCTCA
278265 ATGTATCGATACA-TTCTTCA
1 ATGTATCGATACATTTC-TCA
* *
278285 ATATATCGATACATTCTATCTA
1 ATGTATCGATACATT-TCTC-A
* *
278307 GATGTATCAATACATTGCTCA
1 -ATGTATCGATACATTTCTCA
278328 ATGTATCGATACAT
1 ATGTATCGATACAT
278342 CTAGTTAAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
19 3 0.04
20 60 0.71
21 4 0.05
22 4 0.05
23 13 0.15
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTTCTCA
Found at i:281446 original size:15 final size:15
Alignment explanation
Indices: 281428--281483 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
281418 TTTAATCTAT
*
281428 ATAATTTTAAAATTA
1 ATAATTTTAAATTTA
*
281443 ATAA-ATTAAATTTA
1 ATAATTTTAAATTTA
281457 A-AATAATTTAAATTTAA
1 ATAAT--TTTAAATTT-A
281474 ATAATTTTAA
1 ATAATTTTAA
281484 TATAAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
13 2 0.06
14 9 0.27
15 4 0.12
16 13 0.39
17 2 0.06
18 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTTTAAATTTA
Found at i:281461 original size:16 final size:16
Alignment explanation
Indices: 281442--281538 Score: 61
Period size: 16 Copynumber: 5.8 Consensus size: 16
281432 TTTTAAAATT
281442 AATAAATTAAATTTAA
1 AATAAATTAAATTTAA
*
281458 AATAATTTAAATTTAAA
1 AATAAATTAAATTT-AA
* *
281475 TAATTTTAATATAAAATTAA
1 -AA--TAAAT-TAAATTTAA
*
281495 AAT-TATCTAAATTTAA
1 AATAAAT-TAAATTTAA
* * *
281511 TATTATTTAAATTTAA
1 AATAAATTAAATTTAA
*
281527 AATAAATAAAAT
1 AATAAATTAAAT
281539 ATATAATAAT
Statistics
Matches: 61, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
16 42 0.69
17 4 0.07
18 2 0.03
19 2 0.03
20 5 0.08
21 6 0.10
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAAATTAAATTTAA
Found at i:281477 original size:31 final size:31
Alignment explanation
Indices: 281428--281491 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
281418 TTTAATCTAT
*
281428 ATAATTTTAAAATTAATAAATTAAATTTAAA
1 ATAATTTTAAAATTAATAAATTAAATATAAA
* * *
281459 ATAA-TTTAAATTTAAATAATTTTAATATAAA
1 ATAATTTTAAAATT-AATAAATTAAATATAAA
281490 AT
1 AT
281492 TAAAATTATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 8 0.29
31 20 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
ATAATTTTAAAATTAATAAATTAAATATAAA
Found at i:281489 original size:15 final size:15
Alignment explanation
Indices: 281418--281489 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
281408 AATATTTAAA
* *
281418 TTTAATCTATATAAT
1 TTTAATATAAATAAT
* * *
281433 TTTAAAATTAATAAA
1 TTTAATATAAATAAT
* *
281448 TTAAATTTAAAATAAT
1 TTTAATAT-AAATAAT
* *
281464 TTAAATTTAAATAAT
1 TTTAATATAAATAAT
281479 TTTAATATAAA
1 TTTAATATAAA
281490 ATTAAAATTA
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
15 31 0.70
16 13 0.30
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (15 bp):
TTTAATATAAATAAT
Found at i:281908 original size:2 final size:2
Alignment explanation
Indices: 281895--281928 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
281885 CAAAATTTTA
* *
281895 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
281929 TTATTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:281969 original size:23 final size:23
Alignment explanation
Indices: 281943--282029 Score: 63
Period size: 23 Copynumber: 3.8 Consensus size: 23
281933 TTTTAATTAA
281943 TTATAAAATAATATA-AATATTTT
1 TTATAAAATAATATATAA-ATTTT
* * *
281966 TTATTATATCATATATAAATTTT
1 TTATAAAATAATATATAAATTTT
* * * * *
281989 TCATAAAATTATCAAATCAATTTA
1 TTATAAAATAAT-ATATAAATTTT
282013 TTATAAAA-AATA-ATAAA
1 TTATAAAATAATATATAAA
282030 AATTAATCAT
Statistics
Matches: 49, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
21 4 0.08
22 1 0.02
23 27 0.55
24 17 0.35
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (23 bp):
TTATAAAATAATATATAAATTTT
Found at i:285719 original size:14 final size:14
Alignment explanation
Indices: 285700--285749 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
285690 TAAGCTTAAT
285700 TAAAAATTTACATG
1 TAAAAATTTACATG
285714 TAAAAAGTTTA-AT-
1 TAAAAA-TTTACATG
*
285727 TAAACATTTTACATG
1 TAAA-AATTTACATG
285742 TAAAAATT
1 TAAAAATT
285750 CAATAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 8 0.27
14 14 0.47
15 8 0.27
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (14 bp):
TAAAAATTTACATG
Found at i:285735 original size:27 final size:28
Alignment explanation
Indices: 285695--285747 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
285685 ATTGATAAGC
285695 TTAATTAAAAA-TTTACATGTAAAAAGT
1 TTAATTAAAAATTTTACATGTAAAAAGT
*
285722 TTAATTAAACATTTTACATGTAAAAA
1 TTAATTAAAAATTTTACATGTAAAAA
285748 TTCAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.38
Consensus pattern (28 bp):
TTAATTAAAAATTTTACATGTAAAAAGT
Found at i:285880 original size:14 final size:14
Alignment explanation
Indices: 285822--285880 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
285812 ATGTACATGC
285822 AAAAGTTTAATTAA
1 AAAAGTTTAATTAA
* *
285836 AAATGTTAAATT-A
1 AAAAGTTTAATTAA
*
285849 AAAA-TTCT-ATGTAT
1 AAAAGTT-TAAT-TAA
285863 AAAAGTTTAATTAA
1 AAAAGTTTAATTAA
285877 AAAA
1 AAAA
285881 TATATACATA
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
12 4 0.12
13 5 0.15
14 21 0.62
15 4 0.12
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (14 bp):
AAAAGTTTAATTAA
Found at i:286144 original size:21 final size:22
Alignment explanation
Indices: 286099--286145 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
286089 GGTTTTTAAC
* * *
286099 TAAAGTATTGATACTTGTGCCA
1 TAAAATATAGATACTTGTACCA
286121 TAAAATATAGATACTT-TACCA
1 TAAAATATAGATACTTGTACCA
286142 TAAA
1 TAAA
286146 GTATCAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.34
Consensus pattern (22 bp):
TAAAATATAGATACTTGTACCA
Found at i:286155 original size:21 final size:21
Alignment explanation
Indices: 286099--286155 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 21
286089 GGTTTTTAAC
* *
286099 TAAAGTATTGATACTTGTGCCA
1 TAAAGTA-TAATACTTGTACCA
*
286121 TAAAATATAGATACTT-TACCA
1 TAAAGTATA-ATACTTGTACCA
286142 TAAAGTATCAATAC
1 TAAAGTAT-AATAC
286156 CCTAGTATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (21 bp):
TAAAGTATAATACTTGTACCA
Found at i:287522 original size:22 final size:20
Alignment explanation
Indices: 287494--287533 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
287484 ATGAACACGT
287494 TTAAACTTAAATAACTTTAATA
1 TTAAACTT-AATAA-TTTAATA
287516 TTAAACTTAATAATTTAA
1 TTAAACTTAATAATTTAA
287534 ACTTAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAAACTTAATAATTTAATA
Found at i:287535 original size:14 final size:15
Alignment explanation
Indices: 287511--287550 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
287501 TAAATAACTT
287511 TAATATTAAACTT-AA
1 TAAT-TTAAACTTAAA
287526 TAATTTAAACTTAAAA
1 TAATTTAAACTT-AAA
287542 TAATTTAAA
1 TAATTTAAA
287551 TAAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.35
15 4 0.17
16 11 0.48
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATTTAAACTTAAA
Found at i:287557 original size:16 final size:16
Alignment explanation
Indices: 287524--287556 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
287514 TATTAAACTT
*
287524 AATAATTTAAACTTAA
1 AATAATTTAAACTAAA
287540 AATAATTTAAA-TAAA
1 AATAATTTAAACTAAA
287555 AA
1 AA
287557 AATAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAATTTAAACTAAA
Found at i:287565 original size:37 final size:36
Alignment explanation
Indices: 287493--287568 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 36
287483 CATGAACACG
** * *
287493 TTTAAACTTAAATAACTTTAATATTAAACTTAATAA
1 TTTAAACTTAAATAACTTTAATAAAAAAATAAATAA
287529 TTTAAACTTAAAATAA-TTTAAATAAAAAAATAAATAA
1 TTTAAACTT-AAATAACTTT-AATAAAAAAATAAATAA
287566 TTT
1 TTT
287569 TAAAATACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 12 0.35
37 22 0.65
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (36 bp):
TTTAAACTTAAATAACTTTAATAAAAAAATAAATAA
Found at i:288044 original size:13 final size:13
Alignment explanation
Indices: 288016--288049 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
288006 TTTTATTTAA
*
288016 ATTTTAATTTATTT
1 ATTTT-ATTAATTT
288030 ATTTTATTAATTT
1 ATTTTATTAATTT
288043 ATTTTAT
1 ATTTTAT
288050 GACATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
ATTTTATTAATTT
Found at i:290531 original size:12 final size:12
Alignment explanation
Indices: 290514--290545 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
290504 CTCATCCTTT
290514 AGCCCAAGTCTA
1 AGCCCAAGTCTA
290526 AGCCCAAGTCTA
1 AGCCCAAGTCTA
290538 AGCCCAAG
1 AGCCCAAG
290546 CTCAACTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.19, T:0.12
Consensus pattern (12 bp):
AGCCCAAGTCTA
Found at i:293833 original size:3 final size:3
Alignment explanation
Indices: 293825--293869 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
293815 AACCCCTGAT
293825 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
293870 AGGTTTTGCG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:296240 original size:19 final size:20
Alignment explanation
Indices: 296218--296256 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
296208 AAATTTATAG
*
296218 TATTTTAAATATAAA-AAAA
1 TATTATAAATATAAACAAAA
*
296237 TATTATGAATATAAACAAAA
1 TATTATAAATATAAACAAAA
296257 CACAAACACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (20 bp):
TATTATAAATATAAACAAAA
Found at i:296963 original size:73 final size:73
Alignment explanation
Indices: 296840--296976 Score: 186
Period size: 73 Copynumber: 1.9 Consensus size: 73
296830 AGTTAAATAC
* * * * **
296840 TCAAAGGTTAATAAAAATTGATTATTGAATATGTCAAGAGGCAATGATAATAAATAGTAAAAACG
1 TCAAAGATCAATAAAAATTGATTATTGAATATGCCAAAAGGCAACAATAATAAATAGTAAAAACG
296905 TCAATCAT
66 TCAATCAT
* *
296913 TCAAAGATCAATAAAAATTGATTATTGAATATGCCAAAAGAG-AACAATAATATATGGTAAAAAC
1 TCAAAGATCAATAAAAATTGATTATTGAATATGCCAAAAG-GCAACAATAATAAATAGTAAAAAC
296977 ATTAATCACA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
73 54 0.98
74 1 0.02
ACGTcount: A:0.50, C:0.09, G:0.14, T:0.27
Consensus pattern (73 bp):
TCAAAGATCAATAAAAATTGATTATTGAATATGCCAAAAGGCAACAATAATAAATAGTAAAAACG
TCAATCAT
Found at i:297157 original size:2 final size:2
Alignment explanation
Indices: 297146--297179 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
297136 TTCGAAATGT
297146 TA TA -A 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 TA TA TA T
297180 CTTTCCATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:302010 original size:18 final size:17
Alignment explanation
Indices: 301987--302043 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 17
301977 TAAAAGTATT
301987 ATATATTATTAAATTTTA
1 ATATATTA-TAAATTTTA
302005 ATATATTA-ATAA-TTT-
1 ATATATTATA-AATTTTA
*
302020 ATATTTTATAAATTTTA
1 ATATATTATAAATTTTA
302037 ATATATT
1 ATATATT
302044 TATATTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
15 9 0.27
16 8 0.24
17 8 0.24
18 8 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATATTATAAATTTTA
Found at i:302013 original size:15 final size:15
Alignment explanation
Indices: 301993--302043 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
301983 TATTATATAT
301993 TATTAAATTTTAATA
1 TATTAAATTTTAATA
*
302008 TATTAATAATTT-ATA
1 TATTAA-ATTTTAATA
*
302023 TTTTATAAATTTTAATA
1 -TAT-TAAATTTTAATA
302040 TATT
1 TATT
302044 TATATTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
15 10 0.36
16 12 0.43
17 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTAAATTTTAATA
Found at i:302034 original size:32 final size:30
Alignment explanation
Indices: 301983--302091 Score: 103
Period size: 32 Copynumber: 3.4 Consensus size: 30
301973 TATTTAAAAG
*
301983 TATTATATATTATTAAATTTTAATATATTAA
1 TATTATATTTTA-TAAATTTTAATATATTAA
*
302014 TAATTTATATTTTATAAATTTTAATATATTTA
1 T-A-TTATATTTTATAAATTTTAATATATTAA
* * *
302046 TATTATA-TTTATAATTTTTTATTTTATATTTTA
1 TATTATATTTTATAA-ATTTTA--ATATA-TTAA
302079 TATTATATTTTAT
1 TATTATATTTTAT
302092 TTATTTTTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
29 7 0.10
30 10 0.15
31 2 0.03
32 23 0.34
33 20 0.30
34 5 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TATTATATTTTATAAATTTTAATATATTAA
Found at i:306481 original size:79 final size:79
Alignment explanation
Indices: 306398--306660 Score: 249
Period size: 79 Copynumber: 3.3 Consensus size: 79
306388 CTAATTTTTT
* *
306398 ACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACTCCGGTTTTATTTTTAA
1 ACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTTTAA
* **
306463 AATATTGATTTCTC
66 AACACCGATTTCTC
* * ** * ** ** *
306477 ACAATCGGAGATATTCCAACCCTATTATTTTCGCGGGGATACTCTGACCCCGGCCTTATTTCTAA
1 ACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTTTAA
* *
306542 AGCACCGATTTTTC
66 AACACCGATTTCTC
* * * ** * *
306556 ACAATCGAGAATACTCCAACTCCGTTATTTTCGAGGGGATACTCCAACCCCAATTTTATTTTCAG
1 ACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTTTAA
* *
306621 AACATCAATTT-TCC
66 AACACCGATTTCT-C
* * *
306635 ATAATCGGAGATACTCCAGCCCCGTT
1 ACAATCGGGGATACTCCAACCCCGTT
306661 GTTATCCCCA
Statistics
Matches: 140, Mismatches: 43, Indels: 2
0.76 0.23 0.01
Matches are distributed among these distances:
78 1 0.01
79 139 0.99
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.32
Consensus pattern (79 bp):
ACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTTTAA
AACACCGATTTCTC
Found at i:314406 original size:2 final size:2
Alignment explanation
Indices: 314401--314438 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
314391 GAAAAAAAAA
314401 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
314439 CTAAGATGTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:320964 original size:13 final size:15
Alignment explanation
Indices: 320948--320980 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
320938 ATATTTAAGG
320948 AAAAATT-AA-ATAT
1 AAAAATTAAACATAT
320961 AAAAATTAAACATAT
1 AAAAATTAAACATAT
320976 AAAAA
1 AAAAA
320981 AATACAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 2 0.11
15 9 0.50
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATTAAACATAT
Done.