Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold43
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: 2559314
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 13088 characters in sequence are not A, C, G, or T
File 8 of 19
Found at i:957010 original size:21 final size:21
Alignment explanation
Indices: 956986--957029 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
956976 ATTAAAAATT
956986 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
957007 TATTTTATAATTAAATTTATA
1 TATTTTATAATTAAATTTATA
957028 TA
1 TA
957030 AAATATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:957036 original size:21 final size:20
Alignment explanation
Indices: 956991--957058 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
956981 AAATTTATTT
***
956991 TATATTAATATTTATATATTT
1 TATATTAA-ATTTATATAAAA
957012 TATAATTAAATTTATATAAAA
1 TAT-ATTAAATTTATATAAAA
*
957033 TATATT-ATTTTAATATAAAA
1 TATATTAAATTT-ATATAAAA
957053 -ATATTA
1 TATATTA
957059 TATCAAGTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 9 0.22
20 11 0.28
21 15 0.38
22 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATATTAAATTTATATAAAA
Found at i:957255 original size:21 final size:21
Alignment explanation
Indices: 957218--957261 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
957208 TTCAGTTGAG
*
957218 TTTAAATTTAATATATTTTAA
1 TTTAAATTTAATATATTTAAA
*
957239 TTTAAA-TTAATTTTATTTAAA
1 TTTAAATTTAA-TATATTTAAA
957260 TT
1 TT
957262 ATTTTTATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTAAATTTAATATATTTAAA
Found at i:957256 original size:15 final size:15
Alignment explanation
Indices: 957232--957301 Score: 59
Period size: 15 Copynumber: 4.2 Consensus size: 15
957222 AATTTAATAT
957232 ATTTTAATTTAAATTA
1 ATTTT-ATTTAAATTA
957248 ATTTTATTTAAATTA
1 ATTTTATTTAAATTA
*
957263 TTTTTATCTAATAAAATAATA
1 ATTTTAT-T--T-AAAT--TA
*
957284 ATTTTATTTAATTTA
1 ATTTTATTTAAATTA
957299 ATT
1 ATT
957302 ATAAATATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
15 21 0.47
16 6 0.13
17 3 0.07
18 2 0.04
19 4 0.09
20 1 0.02
21 8 0.18
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTATTTAAATTA
Found at i:957305 original size:21 final size:21
Alignment explanation
Indices: 957234--957305 Score: 51
Period size: 21 Copynumber: 3.5 Consensus size: 21
957224 TTTAATATAT
* * *
957234 TTTAATT-TAAATTAATTTTA
1 TTTAATTATAATTTTATTTAA
*
957254 TTTAAATTAT--TTTTATCTAA
1 TTT-AATTATAATTTTATTTAA
** *
957274 TAAAATAATAATTTTATTTAA
1 TTTAATTATAATTTTATTTAA
957295 TTTAATTATAA
1 TTTAATTATAA
957306 ATATATAAAT
Statistics
Matches: 37, Mismatches: 11, Indels: 7
0.67 0.20 0.13
Matches are distributed among these distances:
19 5 0.14
20 10 0.27
21 21 0.57
22 1 0.03
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTAATTATAATTTTATTTAA
Found at i:957727 original size:23 final size:23
Alignment explanation
Indices: 957692--957744 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
957682 TAAGAAAATT
957692 TTTTAAATATATTAAA-ATTTATA
1 TTTTAAATATATTAAATA-TTATA
* *
957715 TTTTATATTTATTAAATATTATA
1 TTTTAAATATATTAAATATTATA
957738 TTTTAAA
1 TTTTAAA
957745 AATAATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTAAATATATTAAATATTATA
Found at i:957905 original size:18 final size:19
Alignment explanation
Indices: 957882--957919 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
957872 AGTCTATCTT
957882 TTTATAATAT-TTTATATA
1 TTTATAATATATTTATATA
*
957900 TTTATAATATATTTTTATA
1 TTTATAATATATTTATATA
957919 T
1 T
957920 ACATAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTATAATATATTTATATA
Found at i:958088 original size:17 final size:17
Alignment explanation
Indices: 958066--958100 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
958056 TAAAATAGAT
958066 AGGAAAAATAATTCATG
1 AGGAAAAATAATTCATG
958083 AGGAAAAATAATTCATG
1 AGGAAAAATAATTCATG
958100 A
1 A
958101 AATATGGTTG
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:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (17 bp):
AGGAAAAATAATTCATG
Found at i:963307 original size:20 final size:21
Alignment explanation
Indices: 963284--963329 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
963274 ATACCTACTG
*
963284 ATATAAATTAAAACATAT-TA
1 ATATAAATTAAAACAAATATA
*
963304 ATAT-AATTAATACAAATATA
1 ATATAAATTAAAACAAATATA
963324 ATATAA
1 ATATAA
963330 TTTTAAGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 11 0.50
20 10 0.45
21 1 0.05
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (21 bp):
ATATAAATTAAAACAAATATA
Found at i:963330 original size:20 final size:19
Alignment explanation
Indices: 963284--963331 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
963274 ATACCTACTG
*
963284 ATATAAATTAAAACATATTA
1 ATAT-AATTAAAACAAATTA
*
963304 ATATAATTAATACAAATATA
1 ATATAATTAAAACAAAT-TA
963324 ATATAATT
1 ATATAATT
963332 TTAAGAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
ATATAATTAAAACAAATTA
Found at i:963843 original size:18 final size:17
Alignment explanation
Indices: 963805--963843 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
963795 AAAATTATTA
963805 TTTTTTATTTTAATTAAT
1 TTTTTTATTTTAA-TAAT
963823 TTTTTTATCTTTAA-AAT
1 TTTTTTAT-TTTAATAAT
963840 TTTT
1 TTTT
963844 AAAATAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 8 0.40
19 5 0.25
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTTATTTTAATAAT
Found at i:964683 original size:32 final size:30
Alignment explanation
Indices: 964629--964691 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 30
964619 ATTTAACTTA
964629 AATTAAAAAATTATTTATTATATTATAACTAT
1 AATTAAAAAATTATTTATTATATT-TAA-TAT
* *
964661 AATTAAAATATTTTATTA-TATATTTAATAT
1 AATTAAAAAATTAT-TTATTATATTTAATAT
964691 A
1 A
964692 TTTTTATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 4 0.14
31 3 0.11
32 18 0.64
33 3 0.11
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAAAAAATTATTTATTATATTTAATAT
Found at i:964713 original size:21 final size:21
Alignment explanation
Indices: 964651--964713 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
964641 ATTTATTATA
* *
964651 TTATAACTATAATTAAAATATT
1 TTATAA-TATATTTAATATATT
*
964673 TTATTATATATTTAATATATTT
1 TTATAATATATTTAATATA-TT
964695 TTATAATTATATTTAATAT
1 TTATAA-TATATTTAATAT
964714 CACGTAAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.31
22 12 0.34
23 12 0.34
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATAATATATTTAATATATT
Found at i:965298 original size:20 final size:19
Alignment explanation
Indices: 965249--965298 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
965239 TTAATACAAT
965249 TTTTATAAATTTAAATTTTA
1 TTTTAT-AATTTAAATTTTA
*
965269 TTTAATTAATTTAAATTATTA
1 TTTTA-TAATTTAAATT-TTA
965290 TTTTATAAT
1 TTTTATAAT
965299 AAAAATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTATAATTTAAATTTTA
Found at i:965323 original size:22 final size:21
Alignment explanation
Indices: 965261--965325 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
965251 TTATAAATTT
* * *
965261 AAATTTTATTTAATTAATTTA
1 AAATATTATTTAAATAATTAA
* *
965282 AATTATTATTT-TATAA-TAA
1 AAATATTATTTAAATAATTAA
965301 AAATATTATTATAAATAATTAA
1 AAATATTATT-TAAATAATTAA
965323 AAA
1 AAA
965326 AAGCATTAGA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
19 11 0.32
20 4 0.12
21 13 0.38
22 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AAATATTATTTAAATAATTAA
Found at i:965510 original size:20 final size:20
Alignment explanation
Indices: 965460--965521 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
965450 TTATATTATT
965460 TTTATAATTTAATATAAAAA
1 TTTATAATTTAATATAAAAA
* * *
965480 ATTATATTTTAATATTTAAAA
1 TTTATAATTTAATA-TAAAAA
* *
965501 TTTA-AATTTATTATATAAA
1 TTTATAATTTAATATAAAAA
965520 TT
1 TT
965522 AATTAATATA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
19 6 0.18
20 19 0.58
21 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTATAATTTAATATAAAAA
Found at i:965511 original size:27 final size:28
Alignment explanation
Indices: 965444--965511 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
965434 TATCGATTTT
* *
965444 TTTAAATTATATTATTTTTATAATTTAATA
1 TTTAAATT-TA-TATTTTAATAATTTAAAA
** *
965474 TAAAAAATTATATTTTAAT-ATTTAAAA
1 TTTAAATTTATATTTTAATAATTTAAAA
965501 TTTAAATTTAT
1 TTTAAATTTAT
965512 TATATAAATT
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
27 15 0.50
28 8 0.27
29 2 0.07
30 5 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TTTAAATTTATATTTTAATAATTTAAAA
Found at i:965717 original size:30 final size:29
Alignment explanation
Indices: 965666--965725 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
965656 AATAAAAAAT
* *
965666 TTAATATACTAATATTATTAAATCTTAAA
1 TTAATATACTAATATAATTAAATATTAAA
965695 TTAATATA-TAATATAAATTTAAATATTAAA
1 TTAATATACTAATAT-AA-TTAAATATTAAA
965725 T
1 T
965726 ATTATAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 6 0.22
29 9 0.33
30 12 0.44
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (29 bp):
TTAATATACTAATATAATTAAATATTAAA
Found at i:967381 original size:21 final size:21
Alignment explanation
Indices: 967356--967397 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
967346 AAATAATTTT
967356 ATATAAAT-TTAATTATAAAAA
1 ATATAAATATTAA-TATAAAAA
967377 ATATAAATATTAATATAAAAA
1 ATATAAATATTAATATAAAAA
967398 TATTATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATATAAATATTAATATAAAAA
Found at i:967386 original size:27 final size:28
Alignment explanation
Indices: 967334--967386 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
967324 TTAAATTATT
**
967334 ATTTAATTAATAAAATAATTTTATATAA
1 ATTTAATTAATAAAATAATTAAATATAA
967362 ATTTAATT-ATAAAA-AATATAAATAT
1 ATTTAATTAATAAAATAAT-TAAATAT
967387 TAATATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 3 0.14
27 11 0.50
28 8 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
ATTTAATTAATAAAATAATTAAATATAA
Found at i:967408 original size:19 final size:21
Alignment explanation
Indices: 967356--967411 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
967346 AAATAATTTT
967356 ATATAAA-TTTAATTATAAAAA
1 ATATAAATTTTAA-TATAAAAA
*
967377 ATATAAATATTAATAT-AAAA
1 ATATAAATTTTAATATAAAAA
*
967397 ATAT-TATTTTAATAT
1 ATATAAATTTTAATAT
967412 TTTAAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 9 0.29
20 8 0.26
21 10 0.32
22 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATAAATTTTAATATAAAAA
Found at i:967420 original size:21 final size:22
Alignment explanation
Indices: 967394--967439 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
967384 TATTAATATA
*
967394 AAAAT-ATTATTTTAATATT-TT
1 AAAATAATAATTTTAAT-TTATT
967415 AAAATAATAATTTTAATTTATT
1 AAAATAATAATTTTAATTTATT
967437 AAA
1 AAA
967440 CCCAAGTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AAAATAATAATTTTAATTTATT
Found at i:976724 original size:2 final size:2
Alignment explanation
Indices: 976704--976751 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
976694 AAAATCAAAG
* *
976704 AT AT TT AT AT -T AA 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
976745 AT AT AT A
1 AT AT AT A
976752 AACTTTCGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:977300 original size:15 final size:15
Alignment explanation
Indices: 977275--977308 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
977265 CACGGATATT
977275 AAAAAAA-AAAAGAA
1 AAAAAAAGAAAAGAA
*
977289 AAGAAAAGAAAAGAA
1 AAAAAAAGAAAAGAA
977304 AAAAA
1 AAAAA
977309 GACCTACCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAGAA
Found at i:978340 original size:30 final size:30
Alignment explanation
Indices: 978300--978361 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
978290 AGTTAAAATG
* * *
978300 ATTAAGCCTAAGAAAGCTTTAGAACGCTAA
1 ATTAACCCTAAGAAAGCTTTAAAACACTAA
978330 ATTAACCCTAAGAAAGCTTTAAAACACTAA
1 ATTAACCCTAAGAAAGCTTTAAAACACTAA
978360 AT
1 AT
978362 AAGATGTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (30 bp):
ATTAACCCTAAGAAAGCTTTAAAACACTAA
Found at i:983305 original size:27 final size:27
Alignment explanation
Indices: 983275--983330 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
983265 ACTGTCGTGC
* *
983275 CTCCTCGACCTGCTACTGCTTCTCTCT
1 CTCCTCGACCTACTACTGCTTCGCTCT
*
983302 CTCCTCGACCTACTGCTGCTTCGCTCT
1 CTCCTCGACCTACTACTGCTTCGCTCT
983329 CT
1 CT
983331 TCTCTCCCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.07, C:0.45, G:0.12, T:0.36
Consensus pattern (27 bp):
CTCCTCGACCTACTACTGCTTCGCTCT
Found at i:983387 original size:24 final size:24
Alignment explanation
Indices: 983360--983406 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
983350 TTTTCTCTCC
*
983360 TCTCCCTCTCCCTCTCCCTATCTT
1 TCTCCCTCTCCCTATCCCTATCTT
** *
983384 TCTCTTTCTCCTTATCCCTATCT
1 TCTCCCTCTCCCTATCCCTATCT
983407 CTCCTCTCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.06, C:0.47, G:0.00, T:0.47
Consensus pattern (24 bp):
TCTCCCTCTCCCTATCCCTATCTT
Found at i:984125 original size:28 final size:28
Alignment explanation
Indices: 984092--984147 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
984082 TTAAAATTTT
*
984092 TTAAAATTATATTTATATTAAATATTAA
1 TTAAAATTATATTTATATTAAAAATTAA
984120 TTAAAATTATATTTATATTAAAAATTAA
1 TTAAAATTATATTTATATTAAAAATTAA
984148 GAATATAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TTAAAATTATATTTATATTAAAAATTAA
Found at i:984159 original size:28 final size:28
Alignment explanation
Indices: 984094--984155 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
984084 AAAATTTTTT
* * *
984094 AAAATTATATTTATATTAAATATTAATT
1 AAAATAATATTTATATTAAAAATTAATG
*
984122 AAAATTATATTTATATTAAAAATTAA-G
1 AAAATAATATTTATATTAAAAATTAATG
*
984149 AATATAA
1 AAAATAA
984156 ATATAAAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 5 0.17
28 25 0.83
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
AAAATAATATTTATATTAAAAATTAATG
Found at i:984290 original size:1 final size:1
Alignment explanation
Indices: 984284--984309 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
984274 TCGTCCTGCC
984284 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
984310 CAATTTTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:990553 original size:15 final size:16
Alignment explanation
Indices: 990523--990556 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
990513 TTATTTCAAC
990523 ATTGGAAAATGCACAA
1 ATTGGAAAATGCACAA
*
990539 ATTGGATAA-GCACAA
1 ATTGGAAAATGCACAA
990554 ATT
1 ATT
990557 TTACCTTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.24
Consensus pattern (16 bp):
ATTGGAAAATGCACAA
Found at i:991435 original size:11 final size:11
Alignment explanation
Indices: 991403--991437 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
991393 ATTTTATACC
991403 TATTATATTTT
1 TATTATATTTT
*
991414 AATTA-ATTTT
1 TATTATATTTT
991424 TATTATATTTT
1 TATTATATTTT
991435 TAT
1 TAT
991438 ATTTATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TATTATATTTT
Found at i:991631 original size:14 final size:14
Alignment explanation
Indices: 991614--991640 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
991604 TATAATAAAA
991614 AATTATTAATTTTT
1 AATTATTAATTTTT
991628 AATTATTAATTTT
1 AATTATTAATTTT
991641 ATTCTAACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AATTATTAATTTTT
Found at i:991849 original size:13 final size:13
Alignment explanation
Indices: 991831--991948 Score: 52
Period size: 13 Copynumber: 9.5 Consensus size: 13
991821 TTAAAAATAA
991831 ATATTTAATATAT
1 ATATTTAATATAT
* *
991844 ATATTTAAGATAA
1 ATATTTAATATAT
* * * *
991857 ATATATATTTTTT
1 ATATTTAATATAT
*
991870 A-ATTT--TTTAT
1 ATATTTAATATAT
*
991880 ATATTTAA-AAATT
1 ATATTTAATATA-T
* *
991893 ATATTTTATATTT
1 ATATTTAATATAT
991906 ATATTTAA-ATAT
1 ATATTTAATATAT
* *
991918 AT-TTGAATATAA
1 ATATTTAATATAT
*
991930 ATA-TTATATATAC
1 ATATTTA-ATATAT
991943 ATATTT
1 ATATTT
991949 TAAAAAAATA
Statistics
Matches: 75, Mismatches: 21, Indels: 17
0.66 0.19 0.15
Matches are distributed among these distances:
10 5 0.07
11 8 0.11
12 16 0.21
13 43 0.57
14 3 0.04
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (13 bp):
ATATTTAATATAT
Found at i:992365 original size:24 final size:25
Alignment explanation
Indices: 992321--992367 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
992311 AAATACAATA
*
992321 TATATATTAAATATATCAAATTAAT
1 TATATATTAAACATATCAAATTAAT
992346 TATAT-TTAAACATA-CTAAATTA
1 TATATATTAAACATATC-AAATTA
992368 TATTTATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 14 0.70
25 5 0.25
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (25 bp):
TATATATTAAACATATCAAATTAAT
Found at i:992638 original size:2 final size:2
Alignment explanation
Indices: 992631--992667 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
992621 TTCCCATTAG
*
992631 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
992668 AAAATAATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:993553 original size:2 final size:2
Alignment explanation
Indices: 993548--993572 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
993538 AACCATGGGC
993548 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
993573 GAATAAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:995270 original size:16 final size:16
Alignment explanation
Indices: 995249--995279 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
995239 CATAAAATAA
995249 TTATTTTATTATAATT
1 TTATTTTATTATAATT
*
995265 TTATTTTATTTTAAT
1 TTATTTTATTATAAT
995280 AAACTAAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTTTATTATAATT
Found at i:995928 original size:31 final size:30
Alignment explanation
Indices: 995863--995943 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 30
995853 CGCTACAATT
*
995863 TATTATTTATATATATTAAA-AGATATAAAA
1 TATTATTTTTATA-ATTAAATAGATATAAAA
**
995893 -ATTATTTTTATAATTAAATTTATATAATAA
1 TATTATTTTTATAATTAAATAGATATAA-AA
* *
995923 TATTATTTTAATATTTAAATA
1 TATTATTTTTATAATTAAATA
995944 ATAATTCAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
28 6 0.14
29 17 0.40
30 2 0.05
31 17 0.40
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
TATTATTTTTATAATTAAATAGATATAAAA
Found at i:996329 original size:20 final size:20
Alignment explanation
Indices: 996301--996342 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
996291 TTAAATTTGA
996301 TTAAATTTTTTAATTAAATT
1 TTAAATTTTTTAATTAAATT
* * *
996321 TTAATTTTTTTATTTGAATT
1 TTAAATTTTTTAATTAAATT
996341 TT
1 TT
996343 GCAGCTAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTAAATTTTTTAATTAAATT
Found at i:999888 original size:29 final size:30
Alignment explanation
Indices: 999855--999922 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
999845 CTCAATATTT
* *
999855 AATTTTGTTATTTTAGTTTT-A-TTTGATTG
1 AATTTTGTTA-TTAAATTTTGATTTTGATTG
*
999884 AATTTTATTATTAAATTTTGATTTTTGATTG
1 AATTTTGTTATTAAATTTTGA-TTTTGATTG
999915 AATTTTGT
1 AATTTTGT
999923 CACTTCATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 7 0.22
29 10 0.31
31 15 0.47
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.63
Consensus pattern (30 bp):
AATTTTGTTATTAAATTTTGATTTTGATTG
Found at i:999933 original size:31 final size:31
Alignment explanation
Indices: 999876--999938 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
999866 TTTAGTTTTA
* *
999876 TTTGATTGAATTTTATTATTAAATTTTGATT
1 TTTGATTGAATTTTATCATTAAATTTTAATT
* *
999907 TTTGATTGAATTTTGTCACTT-CATTTTAATT
1 TTTGATTGAATTTTATCA-TTAAATTTTAATT
999938 T
1 T
999939 AAATAGTTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.25, C:0.05, G:0.10, T:0.60
Consensus pattern (31 bp):
TTTGATTGAATTTTATCATTAAATTTTAATT
Found at i:1005333 original size:17 final size:18
Alignment explanation
Indices: 1005313--1005346 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1005303 TATCATAATT
*
1005313 ATATTAT-TTTTTATATC
1 ATATTATATTTATATATC
1005330 ATATTATATTTATATAT
1 ATATTATATTTATATAT
1005347 AATACTCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATTATATTTATATATC
Found at i:1005342 original size:23 final size:25
Alignment explanation
Indices: 1005288--1005346 Score: 79
Period size: 23 Copynumber: 2.5 Consensus size: 25
1005278 TAATCTTGAC
1005288 ATATTTATATATTCATATCATAATT
1 ATATTTATATATTCATATCATAATT
* *
1005313 ATA-TTAT-TTTTTATATCAT-ATT
1 ATATTTATATATTCATATCATAATT
1005335 ATATTTATATAT
1 ATATTTATATAT
1005347 AATACTCTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 6 0.21
23 14 0.48
24 6 0.21
25 3 0.10
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (25 bp):
ATATTTATATATTCATATCATAATT
Found at i:1005795 original size:14 final size:14
Alignment explanation
Indices: 1005778--1005829 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
1005768 GTTATAATTT
1005778 TTAAAATATAAAAA
1 TTAAAATATAAAAA
* *
1005792 TTAAAATATTAAAT
1 TTAAAATATAAAAA
*
1005806 TTAATAATTTAAAAA
1 TTAA-AATATAAAAA
1005821 TTAAAATAT
1 TTAAAATAT
1005830 TTTTCAGTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TTAAAATATAAAAA
Found at i:1005802 original size:8 final size:8
Alignment explanation
Indices: 1005778--1005830 Score: 55
Period size: 7 Copynumber: 7.2 Consensus size: 8
1005768 GTTATAATTT
1005778 TTAAAATA
1 TTAAAATA
1005786 -TAAAA-A
1 TTAAAATA
1005792 TTAAAATA
1 TTAAAATA
1005800 TT-AAAT-
1 TTAAAATA
1005806 TTAATAAT-
1 TTAA-AATA
1005814 TTAAAA-A
1 TTAAAATA
1005821 TTAAAATA
1 TTAAAATA
1005829 TT
1 TT
1005831 TTTCAGTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
6 3 0.08
7 23 0.59
8 13 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TTAAAATA
Found at i:1006596 original size:49 final size:49
Alignment explanation
Indices: 1006493--1006615 Score: 121
Period size: 48 Copynumber: 2.5 Consensus size: 49
1006483 TTGGTAATAG
* *
1006493 TAAAAAA-AATATAATTTAAATAAAATATTATATATAATTTAAAGATGA
1 TAAAAAATAATATAATTTAAATAAAATATGATATATAATATAAAGATGA
* * * *
1006541 TAAAAAATAATATTATTTTAAT-AAATATGATATATATATATATATAT-A
1 TAAAAAATAATATAATTTAAATAAAATATGATATATA-ATATAAAGATGA
1006589 TACAAAAATAA-A-AATCTTAAATTAAAA
1 TA-AAAAATAATATAAT-TTAAA-TAAAA
1006616 AAAAGGAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
47 2 0.03
48 28 0.46
49 28 0.46
50 3 0.05
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (49 bp):
TAAAAAATAATATAATTTAAATAAAATATGATATATAATATAAAGATGA
Found at i:1007820 original size:2 final size:2
Alignment explanation
Indices: 1007813--1007856 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1007803 AACGATTGAA
* *
1007813 AT AT AT AT AT AT AC AT AC 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
1007855 AT
1 AT
1007857 CTATTACTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1009180 original size:33 final size:32
Alignment explanation
Indices: 1009112--1009177 Score: 78
Period size: 34 Copynumber: 2.0 Consensus size: 32
1009102 TTAAGTTACT
* * *
1009112 ATTTAATAATAAAATATAAATTTTTAATTTAA
1 ATTTAATAATAAAATATAAAATATTAATATAA
*
1009144 ATTTAATTATAAAAATATATAAATATTAATATAA
1 ATTTAATAAT-AAAATATA-AAATATTAATATAA
1009178 TTTTTTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 9 0.32
33 8 0.29
34 11 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
ATTTAATAATAAAATATAAAATATTAATATAA
Found at i:1010681 original size:19 final size:17
Alignment explanation
Indices: 1010651--1010685 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
1010641 TTAATTTTTT
1010651 ATTTAAAATTAAATTAA
1 ATTTAAAATTAAATTAA
1010668 ATTTAAAAATTTAAATTA
1 ATTT-AAAA-TTAAATTA
1010686 TTATTCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTAAAATTAAATTAA
Found at i:1012943 original size:19 final size:19
Alignment explanation
Indices: 1012916--1012961 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
1012906 AAATATGTAA
*
1012916 AATTGATTTTTATTAATTT
1 AATTGATTTTTATCAATTT
*
1012935 AATTTATTTTTATCAA-TT
1 AATTGATTTTTATCAATTT
*
1012953 AAATGATTT
1 AATTGATTT
1012962 AATTAAATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (19 bp):
AATTGATTTTTATCAATTT
Found at i:1015813 original size:2 final size:2
Alignment explanation
Indices: 1015806--1015848 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1015796 CCTCCCCCTC
1015806 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1015848 C
1 C
1015849 ATGCAACTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1022560 original size:65 final size:65
Alignment explanation
Indices: 1022491--1022625 Score: 270
Period size: 65 Copynumber: 2.1 Consensus size: 65
1022481 ATGGATGTTC
1022491 TGCATGATATACAGCTAGTTACCATCCACACATGCATGCATGCATTCAATACATAAATAAATACA
1 TGCATGATATACAGCTAGTTACCATCCACACATGCATGCATGCATTCAATACATAAATAAATACA
1022556 TGCATGATATACAGCTAGTTACCATCCACACATGCATGCATGCATTCAATACATAAATAAATACA
1 TGCATGATATACAGCTAGTTACCATCCACACATGCATGCATGCATTCAATACATAAATAAATACA
1022621 TGCAT
1 TGCAT
1022626 ACATACATCC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 70 1.00
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (65 bp):
TGCATGATATACAGCTAGTTACCATCCACACATGCATGCATGCATTCAATACATAAATAAATACA
Found at i:1023565 original size:2 final size:2
Alignment explanation
Indices: 1023560--1023589 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1023550 CATATATTTC
1023560 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1023590 GATAAAAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1024292 original size:18 final size:19
Alignment explanation
Indices: 1024269--1024306 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1024259 AGAAGCGAAC
1024269 TTTTA-TTTTTAAAATATT
1 TTTTATTTTTTAAAATATT
1024287 TTTTATTTTTTTAAAATATT
1 TTTTA-TTTTTTAAAATATT
1024307 CATATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
20 13 0.72
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTATTTTTTAAAATATT
Found at i:1024312 original size:19 final size:20
Alignment explanation
Indices: 1024274--1024313 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1024264 CGAACTTTTA
**
1024274 TTTTTAAAATATTTTTTATT
1 TTTTTAAAATATTTCATATT
1024294 TTTTTAAAATA-TTCATATT
1 TTTTTAAAATATTTCATATT
1024313 T
1 T
1024314 AATATTTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTAAAATATTTCATATT
Found at i:1024533 original size:2 final size:2
Alignment explanation
Indices: 1024528--1024565 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1024518 ATATATATAT
1024528 AG AG AG AG AG AG AG -G AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1024566 TGCCCTTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1027777 original size:25 final size:26
Alignment explanation
Indices: 1027722--1027781 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 26
1027712 AAGTACATGT
* *
1027722 GCCAAAGTACCTTACCAAGTGCCTAT
1 GCCAAAGTACCTTACCAAGTGCCAAC
* * *
1027748 ACCAAA-TACCTTGCCAATTGCCAAC
1 GCCAAAGTACCTTACCAAGTGCCAAC
1027773 GCC-AAGTAC
1 GCCAAAGTAC
1027782 ATGTGCCAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
24 2 0.07
25 20 0.74
26 5 0.19
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.20
Consensus pattern (26 bp):
GCCAAAGTACCTTACCAAGTGCCAAC
Found at i:1027789 original size:13 final size:14
Alignment explanation
Indices: 1027776--1027932 Score: 146
Period size: 13 Copynumber: 12.2 Consensus size: 14
1027766 TGCCAACGCC
*
1027776 AAGTACATGTGCCA
1 AAGTACCTGTGCCA
*
1027790 AAGTACCT-TGTC-
1 AAGTACCTGTGCCA
1027802 AAGTACCTGTGCCA
1 AAGTACCTGTGCCA
1027816 AAGTACC--TG---
1 AAGTACCTGTGCCA
*
1027825 AAGTATCCTGTACCA
1 AAGTA-CCTGTGCCA
1027840 AAGTACCTGTGCC-
1 AAGTACCTGTGCCA
*
1027853 AAGTACCT-TGCCG
1 AAGTACCTGTGCCA
1027866 AAGTACCT-TGCC-
1 AAGTACCTGTGCCA
* *
1027878 TAGTACC-GTGCCG
1 AAGTACCTGTGCCA
1027891 AAGTACCT-TGCC-
1 AAGTACCTGTGCCA
1027903 AAGTACCTGTGCCA
1 AAGTACCTGTGCCA
1027917 AAGTACCT-TGCCA
1 AAGTACCTGTGCCA
1027930 AAG
1 AAG
1027933 AGTATTATGG
Statistics
Matches: 122, Mismatches: 7, Indels: 29
0.77 0.04 0.18
Matches are distributed among these distances:
9 5 0.04
10 2 0.02
12 33 0.27
13 48 0.39
14 29 0.24
15 5 0.04
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (14 bp):
AAGTACCTGTGCCA
Found at i:1027804 original size:26 final size:26
Alignment explanation
Indices: 1027773--1027930 Score: 209
Period size: 26 Copynumber: 6.2 Consensus size: 26
1027763 AATTGCCAAC
*
1027773 GCCAAGTACATGTGCCAAAGTACCTT
1 GCCAAGTACCTGTGCCAAAGTACCTT
*
1027799 GTCAAGTACCTGTGCCAAAGTACC-T
1 GCCAAGTACCTGTGCCAAAGTACCTT
*
1027824 G--AAGTATCCTGTACCAAAGTACCTGT
1 GCCAAGTA-CCTGTGCCAAAGTACCT-T
*
1027850 GCCAAGTACCT-TGCCGAAGTACCTT
1 GCCAAGTACCTGTGCCAAAGTACCTT
* *
1027875 GCCTAGTACC-GTGCCGAAGTACCTT
1 GCCAAGTACCTGTGCCAAAGTACCTT
1027900 GCCAAGTACCTGTGCCAAAGTACCTT
1 GCCAAGTACCTGTGCCAAAGTACCTT
1027926 GCCAA
1 GCCAA
1027931 AGAGTATTAT
Statistics
Matches: 117, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
23 5 0.04
24 15 0.13
25 35 0.30
26 54 0.46
27 3 0.03
28 5 0.04
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.23
Consensus pattern (26 bp):
GCCAAGTACCTGTGCCAAAGTACCTT
Found at i:1027845 original size:38 final size:38
Alignment explanation
Indices: 1027840--1027932 Score: 63
Period size: 38 Copynumber: 2.4 Consensus size: 38
1027830 TCCTGTACCA
*
1027840 AAGTACCTGTGCC-AAGTACCT-TGCCGAAGTACCTTG
1 AAGTACCTGTGCCAAAGTACCTGTGCCAAAGTACCTTG
* *
1027876 CCTAGTACC-GTGCCGAAGTACCT-TGCC-AAGTACCTGTG
1 --AAGTACCTGTGCCAAAGTACCTGTGCCAAAGTACCT-TG
1027914 CCAAAGTACCT-TGCCAAAG
1 ---AAGTACCTGTGCCAAAG
1027933 AGTATTATGG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
37 13 0.28
38 20 0.43
39 14 0.30
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.23
Consensus pattern (38 bp):
AAGTACCTGTGCCAAAGTACCTGTGCCAAAGTACCTTG
Found at i:1027927 original size:64 final size:63
Alignment explanation
Indices: 1027704--1027930 Score: 207
Period size: 64 Copynumber: 3.6 Consensus size: 63
1027694 CTATGCCGAT
* * * * *
1027704 TACCTT-CCAAGTACATGTGCCAAAGTACCTTACCAAGTGCCTATACCAAATACCTTGCC-AAT
1 TACCTTGCCAAGTACATGTGCCAAAGTACCTTGCCAAGTACCTATGCCAAGTACC-TGCCGAAG
* ** * *
1027766 TGCCAACGCCAAGTACATGTGCCAAAGTACCTTGTCAAGTACCTGTGCCAAAGTACCT---GAAG
1 TACC-TTGCCAAGTACATGTGCCAAAGTACCTTGCCAAGTACCTATGCC-AAGTACCTGCCGAAG
* * *
1027828 TATCCTGTACCAAAGTACCTGTGCC-AAGTACCTTGCCGAAGTACCT-TGCCTAGTACCGTGCCG
1 TA-CCT-TGCC-AAGTACATGTGCCAAAGTACCTTGCC-AAGTACCTATGCCAAGTACC-TGCCG
1027891 AAG
61 AAG
*
1027894 TACCTTGCCAAGTACCTGTGCCAAAGTACCTTGCCAA
1 TACCTTGCCAAGTACATGTGCCAAAGTACCTTGCCAA
1027931 AGAGTATTAT
Statistics
Matches: 134, Mismatches: 18, Indels: 25
0.76 0.10 0.14
Matches are distributed among these distances:
62 12 0.09
63 35 0.26
64 72 0.54
65 9 0.07
66 6 0.04
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.24
Consensus pattern (63 bp):
TACCTTGCCAAGTACATGTGCCAAAGTACCTTGCCAAGTACCTATGCCAAGTACCTGCCGAAG
Found at i:1028269 original size:2 final size:2
Alignment explanation
Indices: 1028262--1028292 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1028252 GTGCAAGAAA
*
1028262 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1028293 AGGCTAGCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1028540 original size:64 final size:63
Alignment explanation
Indices: 1028464--1028588 Score: 171
Period size: 64 Copynumber: 2.0 Consensus size: 63
1028454 TAATAGTCGA
* * * *
1028464 CTTCTCATTAAGAGTATTTGTATTGAA-GAGAGTGACAGAAGTGGCGCACAGGACCATAACAAT
1 CTTCTCAGTAAGAATACTTGTATT-AAGGAGAGTGACAGAAGTGGCGCACAGGACCACAACAAT
* *
1028527 CTTCTCTAGTAAGAATACTTGTATTAAGGAGAGTGACGGAAGTGGCGCATAGGACCACAACA
1 CTTCTC-AGTAAGAATACTTGTATTAAGGAGAGTGACAGAAGTGGCGCACAGGACCACAACA
1028589 GTTAACTTCT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
63 8 0.15
64 46 0.85
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (63 bp):
CTTCTCAGTAAGAATACTTGTATTAAGGAGAGTGACAGAAGTGGCGCACAGGACCACAACAAT
Found at i:1028706 original size:135 final size:134
Alignment explanation
Indices: 1028459--1029337 Score: 525
Period size: 134 Copynumber: 6.6 Consensus size: 134
1028449 GACTATAATA
* * * ** * * *
1028459 GTCGACTTCT-CATTAAGAGTATTTGT-ATTGA-AGAGAGTGACAGAAGTGGCGCACAGGACCAT
1 GTCGACTTCTCCATTAA-AGAACTTGTAAATGAGAGA-AGTGATGGAAGTGGCGCATAAGACCAC
* *
1028521 AACAAT---CTTCTCTAGTAAGAATACTTGTATTAA-G-GAGAGTGACG-GAAGTGGCGCAT-AG
64 AACAATCGACTTCTCTATTAAGAGTACTTGTA--AATGAGAGAGTGACGAG-AGTGGCGCATGA-
*
1028579 GACCACAACA
125 GACCACAACG
** * * * * * *
1028589 GTTAACTTCTCCATTTAAAGAACTTGTATATAGGGAGAA-TGATAGAAATGGCACATAAGATCAC
1 GTCGACTTCTCCA-TTAAAGAACTTGTAAAT-GAGAGAAGTGATGGAAGTGGCGCATAAGACCAC
*** * * *
1028653 AATGGTCGACTTCTCTATTAAGTGTACTTGTAAATGAGAGAGTGATGAGAGTGGTGCATGAGACC
64 AACAATCGACTTCTCTATTAAGAGTACTTGTAAATGAGAGAGTGACGAGAGTGGCGCATGAGACC
* *
1028718 ATAATG
129 ACAACG
* * * * * **
1028724 GTCGACTTCTCCATTAAGTGTATTTGTAAATGAGA-AAGTGA-CGAGAGTGGTGCAGGAGACCAC
1 GTCGACTTCTCCATTAA-AGAACTTGTAAATGAGAGAAGTGATGGA-AGTGGCGCATAAGACCAC
* * * * *
1028787 AACAATCGACTTCTCCATTAA-AGCTACTTGCAAATGAGAGTGTGATGAGAGTGACGCATGAGAC
64 AACAATCGACTTCTCTATTAAGAG-TACTTGTAAATGAGAGAGTGACGAGAGTGGCGCATGAGAC
*
1028851 CACAATG
128 CACAACG
* * * *
1028858 ATGGACTTCT-CATT-AAGAATACTTGTAAATGAGAG-AGTGATGGGAGTGGCGCA-AGAGATCA
1 GTCGACTTCTCCATTAAAG-A-ACTTGTAAATGAGAGAAGTGATGGAAGTGGCGCATA-AGACCA
* * * * * *
1028919 CAATAGTCGACTTCTCTATTAAGAATACTTGTAAATGAGAGAGTGACAAGAGTGACGCACGAGAC
63 CAACAATCGACTTCTCTATTAAGAGTACTTGTAAATGAGAGAGTGACGAGAGTGGCGCATGAGAC
1028984 CACAACTG
128 CACAAC-G
* * * *
1028992 GTCGACTTCTCCATT-AAGAATACTTGT-ATTGGGAAAAGTGATGGAAGTGGCGCATAAAACCAC
1 GTCGACTTCTCCATTAAAG-A-ACTTGTAAATGAGAGAAGTGATGGAAGTGGCGCATAAGACCAC
* * * * * *
1029055 AACGATCGACTTCTCTATTAAGAGTACTTGTATAGGAAAAAGTGACGAAAGTGGCGCAT-ATGAC
64 AACAATCGACTTCTCTATTAAGAGTACTTGTAAATGAGAGAGTGACGAGAGTGGCGCATGA-GAC
1029119 CACAACG
128 CACAACG
* ** * * * * * * ** *
1029126 ATTAACTTCTCTATTAAAAGGACTTG-CATTG-GAAAAAGTGACGGAAGTGATGCATATGACCAC
1 GTCGACTTCTCCATT-AAAGAACTTGTAAATGAG-AGAAGTGATGGAAGTGGCGCATAAGACCAC
* * * * * * *
1029189 AACGATCGACTTCTCTATTAAGAGCACTTGT-ATTGGGAAAAGTGACG-GAAGTGACGCAT-ATA
64 AACAATCGACTTCTCTATTAAGAGTACTTGTAAATGAG-AGAGTGACGAG-AGTGGCGCATGA-G
*
1029251 ACCACAATG
126 ACCACAACG
* * * * * * * * * *
1029260 ATCGACTTCTCTATTAAGAGCACTTG-CATTAAGAAAAGTGACGGAAGTGACGCATAAGATCACA
1 GTCGACTTCTCCATTAA-AGAACTTGTAAATGAGAGAAGTGATGGAAGTGGCGCATAAGACCACA
**
1029324 ACGGTCGACTTCTC
65 ACAATCGACTTCTC
1029338 CACAATGTGA
Statistics
Matches: 597, Mismatches: 117, Indels: 66
0.77 0.15 0.08
Matches are distributed among these distances:
130 8 0.01
131 10 0.02
132 27 0.05
133 107 0.18
134 279 0.47
135 160 0.27
136 6 0.01
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.25
Consensus pattern (134 bp):
GTCGACTTCTCCATTAAAGAACTTGTAAATGAGAGAAGTGATGGAAGTGGCGCATAAGACCACAA
CAATCGACTTCTCTATTAAGAGTACTTGTAAATGAGAGAGTGACGAGAGTGGCGCATGAGACCAC
AACG
Found at i:1028948 original size:133 final size:134
Alignment explanation
Indices: 1028650--1029086 Score: 524
Period size: 133 Copynumber: 3.3 Consensus size: 134
1028640 CACATAAGAT
* * **
1028650 CACAATGGTCGACTTCTCTATTAAGTGTACTTGTAAATGAGAGAGTGATGAGAGTGGTGCATGAG
1 CACAATAGTCGACTTCTCTATTAAGAGTACTTGTAAATGAGAGAGTGATGAGAGTGACGCATGAG
* ** * * * * *
1028715 ACCATAATGGTCGACTTCTCCATTAAGTGTATTTGTAAATGAGAAAGTGACGAGAGTGGTGCAGG
66 ACCACAATGGTCGACTTCTCCATTAAGAATACTTGTAAATGAGAAAGTGATGGGAGTGGCGCAAG
1028780 AGAC
131 AGAC
* * * * *
1028784 CACAACAATCGACTTCTCCATTAA-AGCTACTTGCAAATGAGAGTGTGATGAGAGTGACGCATGA
1 CACAATAGTCGACTTCTCTATTAAGAG-TACTTGTAAATGAGAGAGTGATGAGAGTGACGCATGA
* * *
1028848 GACCACAATGATGGACTTCT-CATTAAGAATACTTGTAAATGAGAGAGTGATGGGAGTGGCGCAA
65 GACCACAATGGTCGACTTCTCCATTAAGAATACTTGTAAATGAGAAAGTGATGGGAGTGGCGCAA
*
1028912 GAGAT
130 GAGAC
* ** *
1028917 CACAATAGTCGACTTCTCTATTAAGAATACTTGTAAATGAGAGAGTGACAAGAGTGACGCACGAG
1 CACAATAGTCGACTTCTCTATTAAGAGTACTTGTAAATGAGAGAGTGATGAGAGTGACGCATGAG
* * *
1028982 ACCACAACTGGTCGACTTCTCCATTAAGAATACTTGT-ATTGGGAAAAGTGATGGAAGTGGCGCA
66 ACCACAA-TGGTCGACTTCTCCATTAAGAATACTTGTAAATGAG-AAAGTGATGGGAGTGGCGCA
*
1029046 TA-AAAC
129 -AGAGAC
*
1029052 CACAA-CGATCGACTTCTCTATTAAGAGTACTTGTA
1 CACAATAG-TCGACTTCTCTATTAAGAGTACTTGTA
1029087 TAGGAAAAAG
Statistics
Matches: 256, Mismatches: 40, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
133 102 0.40
134 86 0.34
135 67 0.26
136 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (134 bp):
CACAATAGTCGACTTCTCTATTAAGAGTACTTGTAAATGAGAGAGTGATGAGAGTGACGCATGAG
ACCACAATGGTCGACTTCTCCATTAAGAATACTTGTAAATGAGAAAGTGATGGGAGTGGCGCAAG
AGAC
Found at i:1029124 original size:67 final size:66
Alignment explanation
Indices: 1028460--1029337 Score: 467
Period size: 67 Copynumber: 13.2 Consensus size: 66
1028450 ACTATAATAG
* * * * *
1028460 TCGACTTCTC-ATTAAGAGTATTTGTAT-TGAAGAGAGTGAC-AGAAGTGGCGCACAGGACCATA
1 TCGACTTCTCTATTAAGAGTACTTGTATAGGAA-AAAGTGACGA-AAGTGGCGCATA-GACCACA
*
1028522 ACAA
63 ACGA
* * * *
1028526 T---CTTCTCTAGTAAGAATACTTGTATTAAGG--AGAGTGACGGAAGTGGCGCATAGGACCACA
1 TCGACTTCTCTATTAAGAGTACTTGTA-T-AGGAAAAAGTGACGAAAGTGGCGCATA-GACCACA
1028586 AC-A
63 ACGA
** * * * * * * *
1028589 GTTAACTTCTCCATTTAA-AGAACTTGTATATAGGGAGAA-TGATAGAAA-TGGCACATAAGATC
1 -TCGACTTCTCTA-TTAAGAGTACTTG--TATAGGAAAAAGTGA-CGAAAGTGGCGCAT-AGACC
* *
1028651 ACAATGG
60 ACAACGA
* * * * * * * * * *
1028658 TCGACTTCTCTATTAAGTGTACTTGTAAATGAGAGAGTGATGAGAGTGGTGCATGAGACCATAAT
1 TCGACTTCTCTATTAAGAGTACTTGTATAGGAAAAAGTGACGAAAGTGGCGCAT-AGACCACAAC
*
1028723 GG
65 GA
* * * * * * * * *
1028725 TCGACTTCTCCATTAAGTGTATTTGTAAATGAGAAAGTGACGAGAGTGGTGCAGGAGACCACAAC
1 TCGACTTCTCTATTAAGAGTACTTGTATAGGAAAAAGTGACGAAAGTGGCGCA-TAGACCACAAC
*
1028790 AA
65 GA
* * * * * ** * * *
1028792 TCGACTTCTCCATTAA-AGCTACTTGCAAATGAGAGTGTGATGAGAGTGACGCATGAGACCACAA
1 TCGACTTCTCTATTAAGAG-TACTTGTATAGGAAAAAGTGACGAAAGTGGCGCAT-AGACCACAA
*
1028856 TGA
64 CGA
* * * * * * * ** * *
1028859 TGGACTTCTC-ATTAAGAATACTTGTAAATGAGAGAGTGATGGGAGTGGCGCAAGAGATCACAA-
1 TCGACTTCTCTATTAAGAGTACTTGTATAGGAAAAAGTGACGAAAGTGGCGC-ATAGACCACAAC
*
1028922 TA
65 GA
* * * * * * *
1028924 GTCGACTTCTCTATTAAGAATACTTGTAAATGAGAGAGTGAC-AAGAGTGACGCACGAGACCACA
1 -TCGACTTCTCTATTAAGAGTACTTGTATAGGAAAAAGTGACGAA-AGTGGCGCA-TAGACCACA
*
1028988 ACTGG
63 AC-GA
* * * * * * *
1028993 TCGACTTCTCCATTAAGAATACTTGTATTGGGAAAAGTGATGGAAGTGGCGCATAAAACCACAAC
1 TCGACTTCTCTATTAAGAGTACTTGTATAGGAAAAAGTGACGAAAGTGGCGCAT-AGACCACAAC
1029058 GA
65 GA
1029060 TCGACTTCTCTATTAAGAGTACTTGTATAGGAAAAAGTGACGAAAGTGGCGCATATGACCACAAC
1 TCGACTTCTCTATTAAGAGTACTTGTATAGGAAAAAGTGACGAAAGTGGCGCATA-GACCACAAC
1029125 GA
65 GA
** * * * * * **
1029127 TTAACTTCTCTATTAAAAGGACTTGCATTGGAAAAAGTGACGGAAGTGATGCATATGACCACAAC
1 TCGACTTCTCTATTAAGAGTACTTGTATAGGAAAAAGTGACGAAAGTGGCGCATA-GACCACAAC
1029192 GA
65 GA
* * * * * * *
1029194 TCGACTTCTCTATTAAGAGCACTTGTATTGGGAAAAGTGACGGAAGTGACGCATATAACCACAAT
1 TCGACTTCTCTATTAAGAGTACTTGTATAGGAAAAAGTGACGAAAGTGGCGCATA-GACCACAAC
1029259 GA
65 GA
* * * * * *
1029261 TCGACTTCTCTATTAAGAGCACTTGCATTAAG-AAAAGTGACGGAAGTGACGCATAAGATCACAA
1 TCGACTTCTCTATTAAGAGTACTTGTA-TAGGAAAAAGTGACGAAAGTGGCGCAT-AGACCACAA
*
1029325 CGG
64 CGA
1029328 TCGACTTCTC
1 TCGACTTCTC
1029338 CACAATGTGA
Statistics
Matches: 657, Mismatches: 119, Indels: 71
0.78 0.14 0.08
Matches are distributed among these distances:
63 7 0.01
64 42 0.06
65 2 0.00
66 63 0.10
67 446 0.68
68 89 0.14
69 8 0.01
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.25
Consensus pattern (66 bp):
TCGACTTCTCTATTAAGAGTACTTGTATAGGAAAAAGTGACGAAAGTGGCGCATAGACCACAACG
A
Found at i:1031798 original size:12 final size:12
Alignment explanation
Indices: 1031776--1031854 Score: 52
Period size: 12 Copynumber: 6.2 Consensus size: 12
1031766 AGAAGTATTA
1031776 TTGCTAAAGTATC
1 TTGC-AAAGTATC
1031789 TTGCAAAGTATC
1 TTGCAAAGTATC
*
1031801 TTGTC-AAGTACC
1 TTG-CAAAGTATC
* *
1031813 TGTACCAAAGTACC
1 T-T-GCAAAGTATC
* *
1031827 TTGCCAAGTATT
1 TTGCAAAGTATC
1031839 TGTGTCAAAGTATC
1 T-TG-CAAAGTATC
1031853 TT
1 TT
1031855 ACCAAATACC
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
12 25 0.48
13 11 0.21
14 16 0.31
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (12 bp):
TTGCAAAGTATC
Found at i:1031821 original size:26 final size:26
Alignment explanation
Indices: 1031792--1031865 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
1031782 AAGTATCTTG
*
1031792 CAAAGTATCTTGTCAAGTACCTGTAC
1 CAAAGTATCTTGCCAAGTACCTGTAC
* ** **
1031818 CAAAGTACCTTGCCAAGTATTTGTGT
1 CAAAGTATCTTGCCAAGTACCTGTAC
* *
1031844 CAAAGTATCTTACCAAATACCT
1 CAAAGTATCTTGCCAAGTACCT
1031866 ATGTCAAGTA
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (26 bp):
CAAAGTATCTTGCCAAGTACCTGTAC
Found at i:1031858 original size:39 final size:38
Alignment explanation
Indices: 1031781--1031875 Score: 104
Period size: 38 Copynumber: 2.5 Consensus size: 38
1031771 TATTATTGCT
* *
1031781 AAAGTATCTTGCAAAGTATCTTGTCAAGTACCTGTACC
1 AAAGTACCTTGCCAAGTATCTTGTCAAGTACCTGTACC
* *
1031819 AAAGTACCTTGCCAAGTATTTGTGTCAAAGTATCT-TACC
1 AAAGTACCTTGCCAAGTATCT-TGTC-AAGTACCTGTACC
*
1031858 AAA-TACCTATGTCAAGTA
1 AAAGTACCT-TGCCAAGTA
1031876 CTCGTGCTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
38 23 0.47
39 19 0.39
40 7 0.14
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Consensus pattern (38 bp):
AAAGTACCTTGCCAAGTATCTTGTCAAGTACCTGTACC
Found at i:1031927 original size:27 final size:27
Alignment explanation
Indices: 1031858--1031930 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
1031848 GTATCTTACC
* *
1031858 AAATACCTATGTCAAGTACTCGTGCTA
1 AAATACTTATGTCAAGTATTCGTGCTA
* * *
1031885 AAATATTTGTGTCAAGTATTTGTGCTA
1 AAATACTTATGTCAAGTATTCGTGCTA
*
1031912 AAATACTTATGCCAAGTAT
1 AAATACTTATGTCAAGTAT
1031931 CTTACCAAGC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (27 bp):
AAATACTTATGTCAAGTATTCGTGCTA
Found at i:1032906 original size:21 final size:21
Alignment explanation
Indices: 1032868--1032907 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1032858 GATGTTTAAT
* * *
1032868 TAAATTATAATTTTTAATTTA
1 TAAATTAAAAATTATAATTTA
1032889 TAAATTAAAAATTATAATT
1 TAAATTAAAAATTATAATT
1032908 ATTCAATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATTAAAAATTATAATTTA
Found at i:1033005 original size:18 final size:19
Alignment explanation
Indices: 1032982--1033018 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1032972 TTTTATTTTT
1032982 AAATTAATA-AAAAATATA
1 AAATTAATATAAAAATATA
*
1033000 AAATTATTATAAAAATATA
1 AAATTAATATAAAAATATA
1033019 TTTAACAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATTAATATAAAAATATA
Found at i:1033892 original size:2 final size:2
Alignment explanation
Indices: 1033885--1033915 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1033875 AATCTCAGTT
1033885 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1033916 AGTGTTGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1035137 original size:2 final size:2
Alignment explanation
Indices: 1035130--1035157 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1035120 GTGTATATGC
1035130 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
1035158 GAATGATGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1035933 original size:21 final size:21
Alignment explanation
Indices: 1035909--1035951 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1035899 TTGATTTTTA
1035909 TATTTGAAATT-CAAATTTAAT
1 TATTT-AAATTACAAATTTAAT
* *
1035930 TATTTATATTACAATTTTAAT
1 TATTTAAATTACAAATTTAAT
1035951 T
1 T
1035952 TAAATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (21 bp):
TATTTAAATTACAAATTTAAT
Found at i:1035972 original size:22 final size:24
Alignment explanation
Indices: 1035946--1035991 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
1035936 TATTACAATT
* *
1035946 TTAATTTAAATTA-AAAT-TATTA
1 TTAATTAAAAATACAAATATATTA
1035968 TTAATTAAAAATACAAATATATTA
1 TTAATTAAAAATACAAATATATTA
1035992 AAAAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.55
23 4 0.20
24 5 0.25
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TTAATTAAAAATACAAATATATTA
Found at i:1036157 original size:2 final size:2
Alignment explanation
Indices: 1036150--1036174 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1036140 ATATTTTATT
1036150 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1036175 GTACTCACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1036919 original size:18 final size:18
Alignment explanation
Indices: 1036892--1036938 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
1036882 ATTAAAATTT
*
1036892 AATTTATTTTTAAAT-AA
1 AATTTATTTTTTAATCAA
* *
1036909 ATTTTATTTTTTTATCAA
1 AATTTATTTTTTAATCAA
1036927 AATTTATTTTTT
1 AATTTATTTTTT
1036939 GAGTTTAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
AATTTATTTTTTAATCAA
Found at i:1037108 original size:48 final size:49
Alignment explanation
Indices: 1037014--1037111 Score: 146
Period size: 49 Copynumber: 2.0 Consensus size: 49
1037004 CCGGTCTTTA
* * *
1037014 AACAAGTTAAATTAAAACATATAAAAAAATTTACTTGTTTTGTTTATCT
1 AACAAGTTAAATTAAAAAATATAAAAAAATTTACTTGATTTATTTATCT
1037063 AACAAGTTAAATTAAAAAATAT-AAAAAATTTACCTT-ATTTATTTATCT
1 AACAAGTTAAATTAAAAAATATAAAAAAATTTA-CTTGATTTATTTATCT
1037111 A
1 A
1037112 CTTTTTTATA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
48 21 0.47
49 24 0.53
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (49 bp):
AACAAGTTAAATTAAAAAATATAAAAAAATTTACTTGATTTATTTATCT
Found at i:1038079 original size:25 final size:25
Alignment explanation
Indices: 1038023--1038079 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
1038013 AATATAAAAC
* **
1038023 TTAAATATTAAATTATAAATTTTTA
1 TTAAATATCAAATTATAAATTTAAA
1038048 TTAAATATCAAATTATAAA-TTAAA
1 TTAAATATCAAATTATAAATTTAAA
1038072 TTATAATA
1 TTA-AATA
1038080 AAAAATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 6 0.21
25 22 0.79
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAAATATCAAATTATAAATTTAAA
Found at i:1038469 original size:20 final size:19
Alignment explanation
Indices: 1038424--1038470 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1038414 AAAAAATTAA
1038424 TATTTTAA-AAATAATATT
1 TATTTTAATAAATAATATT
*
1038442 TATATTAATAATATAAT-TT
1 TATTTTAATAA-ATAATATT
1038461 TAATTTTAAT
1 T-ATTTTAAT
1038471 TTATATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 7 0.29
19 5 0.21
20 12 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTTTAATAAATAATATT
Found at i:1038514 original size:16 final size:16
Alignment explanation
Indices: 1038495--1038534 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1038485 TCTCATTAAA
1038495 AATATATATTTTTAT-T
1 AATA-ATATTTTTATAT
*
1038511 AATAATTTTTTTATAT
1 AATAATATTTTTATAT
1038527 AATAATAT
1 AATAATAT
1038535 AATCTACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATAATATTTTTATAT
Found at i:1038553 original size:21 final size:20
Alignment explanation
Indices: 1038522--1038562 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1038512 ATAATTTTTT
*
1038522 TATATAATAATATAATCTAC
1 TATATAATAATATAAACTAC
*
1038542 TATATAACTAATTTAAACTAC
1 TATATAA-TAATATAAACTAC
1038563 ATAAGATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (20 bp):
TATATAATAATATAAACTAC
Found at i:1038637 original size:9 final size:9
Alignment explanation
Indices: 1038623--1038660 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
1038613 TTGAAAAATG
1038623 AAAGAAAAA
1 AAAGAAAAA
1038632 AAAG-AAAA
1 AAAGAAAAA
*
1038640 AAATAAAAA
1 AAAGAAAAA
1038649 AAAGAAAAA
1 AAAGAAAAA
1038658 AAA
1 AAA
1038661 TTTAAGGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.89, C:0.00, G:0.08, T:0.03
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:1038661 original size:18 final size:17
Alignment explanation
Indices: 1038627--1038659 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1038617 AAAATGAAAG
1038627 AAAAAAAAGAAAAAAAT
1 AAAAAAAAGAAAAAAAT
1038644 AAAAAAAAGAAAAAAA
1 AAAAAAAAGAAAAAAA
1038660 ATTTAAGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.91, C:0.00, G:0.06, T:0.03
Consensus pattern (17 bp):
AAAAAAAAGAAAAAAAT
Found at i:1038704 original size:23 final size:23
Alignment explanation
Indices: 1038677--1038744 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 23
1038667 GATTCATATT
1038677 TTTATTATTTTTATATTTAA-AA
1 TTTATTATTTTTATATTTAATAA
1038699 TATTA-TATTTTTATATATTAATAA
1 T-TTATTATTTTTATAT-TTAATAA
1038723 TTTATTTTATTTTATATATTTA
1 TTTA--TTATTTT-TATATTTA
1038745 TATGTATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
22 12 0.31
23 10 0.26
24 3 0.08
26 9 0.23
27 5 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTATTATTTTTATATTTAATAA
Found at i:1038710 original size:22 final size:24
Alignment explanation
Indices: 1038682--1038744 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 24
1038672 ATATTTTTAT
1038682 TATTTTTATATTTAA-AA-TATTA
1 TATTTTTATATTTAATAATTATTA
*
1038704 TATTTTTATATATTAATAATTTATTT
1 TATTTTTATAT-TTAATAA-TTATTA
1038730 TATTTTATATATTTA
1 TATTTT-TATATTTA
1038745 TATGTATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
22 11 0.31
23 4 0.11
24 2 0.06
26 13 0.37
27 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TATTTTTATATTTAATAATTATTA
Found at i:1038765 original size:62 final size:60
Alignment explanation
Indices: 1038699--1038841 Score: 137
Period size: 62 Copynumber: 2.3 Consensus size: 60
1038689 ATATTTAAAA
* *
1038699 TATTATATTTTTATATATTAATAATTTATTTTATT-T-TATATATTTATATGTATATATATTCG
1 TATTATATTTTTAT-TATT-ATAA-TT-TTTTATTATCTATATATTTATATCTATATATATTAG
* * * * *
1038761 TATTATGTGTTATTATTATTATTATTTTTTATTATCTATTTATTTATATCTATATTTATTAT
1 TATTATAT-TT-TTATTATTATAATTTTTTATTATCTATATATTTATATCTATATATATTAG
1038823 TATTATTATTTTTTATTAT
1 TATTA-TA-TTTTTATTAT
1038842 CTATCTATCT
Statistics
Matches: 67, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
60 7 0.10
61 3 0.04
62 43 0.64
63 9 0.13
64 5 0.07
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (60 bp):
TATTATATTTTTATTATTATAATTTTTTATTATCTATATATTTATATCTATATATATTAG
Found at i:1038778 original size:3 final size:3
Alignment explanation
Indices: 1038770--1038841 Score: 57
Period size: 3 Copynumber: 24.3 Consensus size: 3
1038760 GTATTATGTG
1038770 TTA TTA TTA TTA TTA TT- TT- TTA TTA TCTA TTTA TT- TATA TCTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA TTA T-TA T-TA TTA
1038815 TTTA TTA TTA TTA TTA TT- TT- TTA TTA T
1 -TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1038842 CTATCTATCT
Statistics
Matches: 60, Mismatches: 1, Indels: 16
0.78 0.01 0.21
Matches are distributed among these distances:
2 11 0.18
3 39 0.65
4 9 0.15
5 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1038810 original size:14 final size:14
Alignment explanation
Indices: 1038776--1038845 Score: 72
Period size: 14 Copynumber: 4.8 Consensus size: 14
1038766 TGTGTTATTA
1038776 TTATTAT-TATTTT
1 TTATTATCTATTTT
1038789 TTATTATCTATTTAT
1 TTATTATCTATTT-T
1038804 TTA-TATCTATATTT
1 TTATTATCTAT-TTT
*
1038818 ATTATTATTATTATTTT
1 -TTATTA-T-CTATTTT
1038835 TTATTATCTAT
1 TTATTATCTAT
1038846 CTATCTATAC
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
13 7 0.15
14 16 0.33
15 10 0.21
16 8 0.17
17 4 0.08
18 3 0.06
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTATCTATTTT
Found at i:1038826 original size:46 final size:46
Alignment explanation
Indices: 1038770--1038859 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
1038760 GTATTATGTG
* * *
1038770 TTATTATTATTATTATTTTTTATTATCTATTTATTTATATCTATAT
1 TTATTATTATTATTATTTTTTATTATCTATCTATCTATACCTATAT
1038816 TTATTATTATTATTATTTTTTATTATCTATCTATCTATACCTAT
1 TTATTATTATTATTATTTTTTATTATCTATCTATCTATACCTAT
1038860 CTAACATGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (46 bp):
TTATTATTATTATTATTTTTTATTATCTATCTATCTATACCTATAT
Found at i:1039311 original size:2 final size:2
Alignment explanation
Indices: 1039304--1039330 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1039294 CATATAGATT
1039304 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 T
1039331 GCAAAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1039935 original size:23 final size:23
Alignment explanation
Indices: 1039908--1039952 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1039898 AAAATTTACA
**
1039908 TATTTATGTTTTTTATTATTTAT
1 TATTTATAATTTTTATTATTTAT
*
1039931 TATTTATAATTTTTATTGTTTA
1 TATTTATAATTTTTATTATTTA
1039953 AAATATTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (23 bp):
TATTTATAATTTTTATTATTTAT
Found at i:1040014 original size:6 final size:6
Alignment explanation
Indices: 1039994--1040030 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1039984 AAATTATGTT
*
1039994 TTTATA TTTAT- TTTATA TTTATT TTTATA TTT-TA TTT
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTT
1040031 TAATTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 10 0.36
6 18 0.64
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTATA
Found at i:1040019 original size:12 final size:12
Alignment explanation
Indices: 1039992--1040031 Score: 64
Period size: 11 Copynumber: 3.3 Consensus size: 12
1039982 AAAAATTATG
1039992 TTTTTATATTTA
1 TTTTTATATTTA
1040004 -TTTTATATTTA
1 TTTTTATATTTA
1040015 TTTTTATATTTTA
1 TTTTTATA-TTTA
1040028 TTTT
1 TTTT
1040032 AATTAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.42
12 7 0.27
13 8 0.31
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTATATTTA
Found at i:1040020 original size:17 final size:17
Alignment explanation
Indices: 1039994--1040078 Score: 54
Period size: 17 Copynumber: 5.0 Consensus size: 17
1039984 AAATTATGTT
1039994 TTTATATTTAT-TTTATA
1 TTTATATTTATATTT-TA
*
1040011 TTTATTTTTATATTTTA
1 TTTATATTTATATTTTA
*
1040028 TTT-TAATTA-ATTTTAAA
1 TTTATATTTATATTTT--A
* *
1040045 TATTATATATATATGTTA
1 T-TTATATTTATATTTTA
1040063 TTT-T-TTTATATATTTA
1 TTTATATTTATAT-TTTA
1040079 AAATATTAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 15
0.70 0.11 0.20
Matches are distributed among these distances:
15 11 0.21
16 8 0.15
17 19 0.36
18 7 0.13
19 4 0.08
20 4 0.08
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (17 bp):
TTTATATTTATATTTTA
Found at i:1040032 original size:12 final size:11
Alignment explanation
Indices: 1039993--1040066 Score: 69
Period size: 12 Copynumber: 6.4 Consensus size: 11
1039983 AAAATTATGT
1039993 TTTTATATTTA
1 TTTTATATTTA
1040004 TTTTATATTTA
1 TTTTATATTTA
1040015 TTTTTATATTTTA
1 -TTTTATA-TTTA
*
1040028 TTTTA-ATTAA
1 TTTTATATTTA
*
1040038 TTTTAAATATTA
1 TTTTATAT-TTA
*
1040050 TATATATATGTTA
1 T-TTTATAT-TTA
1040063 TTTT
1 TTTT
1040067 TTTATATATT
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
10 8 0.15
11 14 0.27
12 17 0.33
13 13 0.25
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (11 bp):
TTTTATATTTA
Found at i:1040182 original size:38 final size:39
Alignment explanation
Indices: 1040134--1040226 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 39
1040124 TATATATTTT
* * * *
1040134 TTAATATATTTATATATTCATATT-TTTTTATATTATGTT
1 TTAATTTATTT-TATATTCATATTATGTTTATATCATGTC
*
1040173 TTAA-TTATTTT-TATTTATATTATGTTTATATCATGTC
1 TTAATTTATTTTATATTCATATTATGTTTATATCATGTC
1040210 TTAATTTATTTTATATT
1 TTAATTTATTTTATATT
1040227 TTTTTACATA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
36 9 0.20
37 17 0.37
38 12 0.26
39 8 0.17
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (39 bp):
TTAATTTATTTTATATTCATATTATGTTTATATCATGTC
Found at i:1040214 original size:37 final size:37
Alignment explanation
Indices: 1040116--1040227 Score: 111
Period size: 38 Copynumber: 3.0 Consensus size: 37
1040106 ACATATGAAT
* * * *
1040116 TATTTATTTATAT-ATTTTTTAATATATTTATATATTCA
1 TATTTGTTTATATCATGTCTTAAT-TATTT-TATATTTA
* * *
1040154 TATTTTTTTATATTATGTTTTAATTATTTT-TATTTA
1 TATTTGTTTATATCATGTCTTAATTATTTTATATTTA
1040190 TATTATGTTTATATCATGTCTTAATTTATTTTATATTT
1 TATT-TGTTTATATCATGTCTTAA-TTATTTTATATTT
1040228 TTTTACATAA
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
36 9 0.14
37 17 0.27
38 24 0.38
39 14 0.22
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (37 bp):
TATTTGTTTATATCATGTCTTAATTATTTTATATTTA
Found at i:1041122 original size:6 final size:6
Alignment explanation
Indices: 1041113--1041166 Score: 54
Period size: 6 Copynumber: 8.5 Consensus size: 6
1041103 TATTTGTATT
* * *
1041113 TTTTAA TTTTTAA TTTTAA TTTTAT TTTTAAA TTATATA TTTTAA TGTTAA
1 TTTTAA -TTTTAA TTTTAA TTTTAA TTTT-AA TTTTA-A TTTTAA TTTTAA
1041164 TTT
1 TTT
1041167 GCATTGTCGT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
6 24 0.62
7 15 0.38
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:1041154 original size:26 final size:27
Alignment explanation
Indices: 1041095--1041158 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
1041085 TAAAAACTTC
* *
1041095 ATAT-TTTTTATTTGTATTTTTTAATT
1 ATATATTTTAATTTGTATTTTTAAATT
*
1041121 -TTTAATTTTAATTT-TATTTTTAAATT
1 ATAT-ATTTTAATTTGTATTTTTAAATT
1041147 ATATATTTTAAT
1 ATATATTTTAAT
1041159 GTTAATTTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
25 2 0.06
26 19 0.61
27 10 0.32
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (27 bp):
ATATATTTTAATTTGTATTTTTAAATT
Found at i:1042158 original size:21 final size:20
Alignment explanation
Indices: 1042116--1042164 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1042106 AATCACATTT
*
1042116 AATAAAATAATATTATTATA
1 AATAAAATATTATTATTATA
*
1042136 AATAAAATATTAATTA-TATT
1 AATAAAATATT-ATTATTATA
1042156 AA-AAAATAT
1 AATAAAATAT
1042165 ATTTAAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 7 0.27
20 15 0.58
21 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATAAAATATTATTATTATA
Found at i:1042440 original size:25 final size:23
Alignment explanation
Indices: 1042389--1042443 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
1042379 AAGAGTTTGC
*
1042389 TTAAATTTTAATTTATTTAAAAT
1 TTAAATTTTAATATATTTAAAAT
1042412 TTAATATTTTAAATATATTATAAAA-
1 TTAA-ATTTT-AATATATT-TAAAAT
1042437 TTAAATT
1 TTAAATT
1042444 AAAATTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 4 0.14
24 8 0.29
25 11 0.39
26 5 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTAAATTTTAATATATTTAAAAT
Found at i:1042456 original size:21 final size:21
Alignment explanation
Indices: 1042431--1042490 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
1042421 TAAATATATT
1042431 ATAAAATTAAATTAAAATTAA
1 ATAAAATTAAATTAAAATTAA
* * *
1042452 ATAAAATTATATTTAAATTGA
1 ATAAAATTAAATTAAAATTAA
*
1042473 ATCAAACTTAAATTAAAA
1 AT-AAAATTAAATTAAAA
1042491 AAATTATCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (21 bp):
ATAAAATTAAATTAAAATTAA
Found at i:1042458 original size:10 final size:10
Alignment explanation
Indices: 1042431--1042460 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
1042421 TAAATATATT
1042431 ATAAAATTAA
1 ATAAAATTAA
1042441 ATTAAAATTAA
1 A-TAAAATTAA
1042452 ATAAAATTA
1 ATAAAATTA
1042461 TATTTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
ATAAAATTAA
Found at i:1042649 original size:15 final size:15
Alignment explanation
Indices: 1042622--1042682 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 15
1042612 ATGTATGAAA
1042622 TATATTA-AT-AATT
1 TATATTATATAAATT
1042635 TATATTATATAAATT
1 TATATTATATAAATT
* *
1042650 T-TAATATATTTAATT
1 TATATTATA-TAAATT
*
1042665 TATATTATGTTAAATT
1 TATATTAT-ATAAATT
1042681 TA
1 TA
1042683 ATTTTTATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
13 7 0.18
14 8 0.21
15 11 0.29
16 12 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
TATATTATATAAATT
Found at i:1042666 original size:30 final size:32
Alignment explanation
Indices: 1042620--1042681 Score: 92
Period size: 30 Copynumber: 2.0 Consensus size: 32
1042610 ATATGTATGA
1042620 AATATATTAATAATTTATATTAT-ATAAATTTT
1 AATATATT-ATAATTTATATTATGATAAATTTT
*
1042652 AATATATT-TAATTTATATTATGTTAAATTT
1 AATATATTATAATTTATATTATGATAAATTT
1042682 AATTTTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 13 0.46
31 7 0.25
32 8 0.29
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (32 bp):
AATATATTATAATTTATATTATGATAAATTTT
Found at i:1042682 original size:16 final size:15
Alignment explanation
Indices: 1042631--1042682 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
1042621 ATATATTAAT
*
1042631 AATTTATATTATATA
1 AATTTATATTATTTA
1042646 AATTT-TAATATATTT-
1 AATTTAT-AT-TATTTA
1042661 AATTTATATTATGTTA
1 AATTTATATTAT-TTA
1042677 AATTTA
1 AATTTA
1042683 ATTTTTATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
14 4 0.13
15 16 0.52
16 11 0.35
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
AATTTATATTATTTA
Found at i:1043511 original size:16 final size:16
Alignment explanation
Indices: 1043472--1043512 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
1043462 AAGTTAAATA
*
1043472 TTATTTAAATAATTTT
1 TTATTAAAATAATTTT
*
1043488 TTA-AAAAATAATTTT
1 TTATTAAAATAATTTT
1043503 TTATTAAAAT
1 TTATTAAAAT
1043513 TTTTAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATTAAAATAATTTT
Found at i:1044227 original size:18 final size:19
Alignment explanation
Indices: 1044179--1044230 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
1044169 TATTAAATTA
* * *
1044179 TATTTATATTATTTTTTAT
1 TATTTATGTAATTATTTAT
1044198 TATTTATGTAATTATTTAT
1 TATTTATGTAATTATTTAT
1044217 T-TTTAAT-TAATTAT
1 TATTT-ATGTAATTAT
1044231 ATTAATTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 10 0.34
19 19 0.66
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTTATGTAATTATTTAT
Found at i:1044298 original size:34 final size:31
Alignment explanation
Indices: 1044226--1044301 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 31
1044216 TTTTTAATTA
1044226 ATTATATTAATTATATAATAATAAAATACAT
1 ATTATATTAATTATATAATAATAAAATACAT
**
1044257 ATT-TATTAATTA-ACTATATAATAAAATTTATTT
1 ATTATATTAATTATA-TA-ATAATAAAA--TACAT
1044290 ATTATATTAATT
1 ATTATATTAATT
1044302 GAAACTGCTG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 1 0.03
30 11 0.29
31 12 0.32
33 6 0.16
34 8 0.21
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (31 bp):
ATTATATTAATTATATAATAATAAAATACAT
Found at i:1045149 original size:26 final size:25
Alignment explanation
Indices: 1045085--1045151 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 25
1045075 ATATATATAT
*
1045085 AAAA-ATTTATATATTATTAATAAA
1 AAAATATTTATATTTTATTAATAAA
*
1045109 AAAATAATTATTATTTTATTAA-AATA
1 AAAATATTTA-TATTTTATTAATAA-A
*
1045135 AAAGTTATTTATATTTT
1 AAA-ATATTTATATTTT
1045152 TTATAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 4 0.11
25 6 0.17
26 20 0.57
27 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (25 bp):
AAAATATTTATATTTTATTAATAAA
Found at i:1045211 original size:61 final size:60
Alignment explanation
Indices: 1045090--1045220 Score: 142
Period size: 61 Copynumber: 2.1 Consensus size: 60
1045080 TATATAAAAA
* *
1045090 TTTATATATTATTAATAAAAAAATAATTATTATTTTATTAAAATAAAAGTTATTTATATTT
1 TTTATA-ATTATTAATAAAAAAATAATTATTATTTTATTAAAATAAAAATTATATATATTT
* *
1045151 TTTATAATTTTTAATAAATAAAATAATT-TTA-TTTATTAATAATATATAAATT-TATGTATTT
1 TTTATAATTATTAATAAA-AAAATAATTATTATTTTATTAA-AATA-A-AAATTATATATATTT
* *
1045212 ATTAAAATT
1 TTTATAATT
1045221 GATTTTTAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
59 8 0.13
60 18 0.30
61 30 0.50
62 4 0.07
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (60 bp):
TTTATAATTATTAATAAAAAAATAATTATTATTTTATTAAAATAAAAATTATATATATTT
Found at i:1045256 original size:18 final size:18
Alignment explanation
Indices: 1045226--1045260 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
1045216 AAATTGATTT
1045226 TTAAAATTATATTTATAAA
1 TTAAAATTATA-TTATAAA
1045245 TTAAAA-TATATTATAA
1 TTAAAATTATATTATAA
1045261 TTTTAAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAAAATTATATTATAAA
Found at i:1045266 original size:18 final size:20
Alignment explanation
Indices: 1045224--1045266 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
1045214 TAAAATTGAT
1045224 TTTTAAAATTATATTTATAA
1 TTTTAAAATTATATTTATAA
*
1045244 -ATTAAAA-TATA-TTATAA
1 TTTTAAAATTATATTTATAA
1045261 TTTTAA
1 TTTTAA
1045267 GAAGCATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
17 6 0.30
18 8 0.40
19 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTAAAATTATATTTATAA
Found at i:1046536 original size:14 final size:14
Alignment explanation
Indices: 1046513--1046548 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1046503 ATTTATTATT
1046513 TATTTT-TTAAATA
1 TATTTTATTAAATA
1046526 TATTTTATTAAATA
1 TATTTTATTAAATA
*
1046540 TATGTTATT
1 TATTTTATT
1046549 TTAAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (14 bp):
TATTTTATTAAATA
Found at i:1046653 original size:15 final size:14
Alignment explanation
Indices: 1046622--1046654 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1046612 ATATAATTTA
1046622 TTTTAAAAATTGAT
1 TTTTAAAAATTGAT
1046636 TTTTAATAAATT-AT
1 TTTTAA-AAATTGAT
1046650 TTTTA
1 TTTTA
1046655 CATTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (14 bp):
TTTTAAAAATTGAT
Found at i:1052472 original size:21 final size:21
Alignment explanation
Indices: 1052437--1052488 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
1052427 AAATGACATC
*
1052437 ATAAAAAAGTATTTTTT--AA
1 ATAAAAAATTATTTTTTAAAA
*
1052456 TTAAAAAATTATTTTTTAAAA
1 ATAAAAAATTATTTTTTAAAA
1052477 ATAAAAAATTAT
1 ATAAAAAATTAT
1052489 AAATATCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 15 0.54
21 13 0.46
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
ATAAAAAATTATTTTTTAAAA
Found at i:1053181 original size:14 final size:16
Alignment explanation
Indices: 1053152--1053184 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1053142 ATATTTTAAA
1053152 TAATAAAATAAAATTT
1 TAATAAAATAAAATTT
*
1053168 TAAT-AAATAAATTTT
1 TAATAAAATAAAATTT
1053183 TA
1 TA
1053185 TTTGATTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATAAAATAAAATTT
Done.