Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold726
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: 990522
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.25
Warning! 295012 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:445654 original size:20 final size:20
Alignment explanation
Indices: 445631--445692 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
445621 TATGTGATAT
445631 AAATTATATAATATATATAA
1 AAATTATATAATATATATAA
* * *
445651 AAATAATACAATATATATAT
1 AAATTATATAATATATATAA
445671 AAA-TATAATACATATTATATAA
1 AAATTAT-ATA-ATA-TATATAA
445693 CCATATTAGG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 2 0.06
20 22 0.67
21 3 0.09
22 6 0.18
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATTATATAATATATATAA
Found at i:445698 original size:22 final size:22
Alignment explanation
Indices: 445641--445692 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
445631 AAATTATATA
*
445641 ATATATATAAAAATAATACAAT
1 ATATATATAAATATAATACAAT
445663 ATATATATAAATATAATAC-AT
1 ATATATATAAATATAATACAAT
445684 AT-TATATAA
1 ATATATATAA
445693 CCATATTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 4 0.14
22 18 0.62
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
ATATATATAAATATAATACAAT
Found at i:445833 original size:18 final size:18
Alignment explanation
Indices: 445791--445835 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
445781 TTTATTATTT
445791 TTTAAA-AATTTTTTAAA
1 TTTAAATAATTTTTTAAA
* *
445808 TATCAAATAATTTTTTTAA
1 T-TTAAATAATTTTTTAAA
445827 TTTAAATAA
1 TTTAAATAA
445836 GTAACTCGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 1 0.04
18 11 0.48
19 11 0.48
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAAATAATTTTTTAAA
Found at i:446602 original size:19 final size:19
Alignment explanation
Indices: 446554--446617 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 19
446544 AAACATAAAT
446554 AATAATTTATATTATAAT-TTA
1 AATAATTT-TA-TA-AATATTA
446575 AATTAATTTTATAAATATTA
1 AA-TAATTTTATAAATATTA
* * *
446595 AATAATTTAAAAAATATAA
1 AATAATTTTATAAATATTA
446614 AATA
1 AATA
446618 TTTATCCATA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
19 21 0.55
20 7 0.18
21 4 0.11
22 6 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATAATTTTATAAATATTA
Found at i:446651 original size:15 final size:15
Alignment explanation
Indices: 446626--446660 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
446616 TATTTATCCA
446626 TATTA-ATTTTTCTT
1 TATTATATTTTTCTT
446640 TATTATATTTTTCTT
1 TATTATATTTTTCTT
*
446655 TTTTAT
1 TATTAT
446661 CCTCTTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTATATTTTTCTT
Found at i:447899 original size:17 final size:18
Alignment explanation
Indices: 447877--447919 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
447867 CTATGGGTGA
447877 AAAAAATAAATATT-TTT
1 AAAAAATAAATATTGTTT
* *
447894 AAAAAAT-TATTTTGTTT
1 AAAAAATAAATATTGTTT
447911 AAAAAATAA
1 AAAAAATAA
447920 CAAGTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
AAAAAATAAATATTGTTT
Found at i:448160 original size:22 final size:22
Alignment explanation
Indices: 448135--448192 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
448125 TTTGTTTATA
* *
448135 TATAAATATAAATTTTCATAAT
1 TATAAATATAAATATTCAAAAT
* *
448157 TATAAATATTTAGTATTCAAAAT
1 TATAAATA-TAAATATTCAAAAT
448180 T-TAAATATAAATA
1 TATAAATATAAATA
448193 AATAAAATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 4 0.14
22 14 0.48
23 11 0.38
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (22 bp):
TATAAATATAAATATTCAAAAT
Found at i:448221 original size:9 final size:10
Alignment explanation
Indices: 448181--448209 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
448171 ATTCAAAATT
448181 TAAATATAAA
1 TAAATATAAA
448191 TAAATA-AAA
1 TAAATATAAA
448200 TAAATATAAA
1 TAAATATAAA
448210 ATATAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAATATAAA
Found at i:449305 original size:17 final size:18
Alignment explanation
Indices: 449270--449306 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
449260 TATTTTTTTG
449270 ATAATAGTATAATTTATA
1 ATAATAGTATAATTTATA
449288 ATAAT-GTAT-ATTTAATA
1 ATAATAGTATAATTT-ATA
449305 AT
1 AT
449307 TTACCGAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.22
17 9 0.50
18 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (18 bp):
ATAATAGTATAATTTATA
Found at i:451176 original size:20 final size:18
Alignment explanation
Indices: 451134--451177 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
451124 ACTGTGTTTT
*
451134 AAATTAATTTTATTTTCA
1 AAATTAATTTTATATTCA
*
451152 TAATTCAATTTTAATATTCA
1 AAATT-AATTTT-ATATTCA
451172 AAATTA
1 AAATTA
451178 GTTATTTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
18 4 0.19
19 7 0.33
20 10 0.48
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATTAATTTTATATTCA
Found at i:451459 original size:25 final size:25
Alignment explanation
Indices: 451425--451474 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
451415 AACTCAAATA
* *
451425 AATTTAAATTTGATCTCGAATCAAC
1 AATTTAAATTCGATCTCAAATCAAC
* *
451450 AATTTGAATTCGGTCTCAAATCAAC
1 AATTTAAATTCGATCTCAAATCAAC
451475 TCAGCCGTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (25 bp):
AATTTAAATTCGATCTCAAATCAAC
Found at i:459730 original size:25 final size:25
Alignment explanation
Indices: 459659--459735 Score: 61
Period size: 25 Copynumber: 3.0 Consensus size: 25
459649 CTCGTAATTA
*
459659 AAAATATATATTTTTATTTTTAA--TT
1 AAAATA-ATATTTTTA-TATTAATTTT
* * *
459684 AAATTATTATTATTTA-AATAATTTT
1 AAAATAATATT-TTTATATTAATTTT
459709 AAAATAATATTTTTATATTAATATTT
1 AAAATAATATTTTTATATTAAT-TTT
459735 A
1 A
459736 TATAATTATA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
23 3 0.08
24 8 0.20
25 25 0.62
26 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
AAAATAATATTTTTATATTAATTTT
Found at i:459758 original size:48 final size:44
Alignment explanation
Indices: 459673--459773 Score: 105
Period size: 48 Copynumber: 2.2 Consensus size: 44
459663 TATATATTTT
* * *
459673 TATTTTTAATTAAATTATTATTATTTAAATAATTTTAAA-ATAA
1 TATTTTTAATTAAATTATTATTATATAAATAAATTTAAATAAAA
*
459716 TATTTTTATATTAATATTTATATAATTATATAATTAAATTTAAATAAAA
1 TATTTTTA-ATTAA-A-TTAT-T-ATTATATAAATAAATTTAAATAAAA
459765 TATATTTTA
1 TAT-TTTTA
459774 CATAAATAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
43 8 0.17
44 5 0.11
45 1 0.02
46 4 0.09
47 1 0.02
48 17 0.36
49 6 0.13
50 5 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (44 bp):
TATTTTTAATTAAATTATTATTATATAAATAAATTTAAATAAAA
Found at i:459768 original size:23 final size:23
Alignment explanation
Indices: 459725--459769 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
459715 ATATTTTTAT
* *
459725 ATTAATATTTATATAATTATATA
1 ATTAATATTTAAATAAATATATA
459748 ATTAA-ATTTAAATAAAATATAT
1 ATTAATATTTAAAT-AAATATAT
459770 TTTACATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTAATATTTAAATAAATATATA
Found at i:460318 original size:21 final size:21
Alignment explanation
Indices: 460265--460328 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
460255 ATTTTATTAT
* *
460265 TTTATATATAAACTATTTTAAA
1 TTTATATTTAAATTATTTT-AA
* *
460287 TTAATTATTTAAATTAATTTAA
1 TTTA-TATTTAAATTATTTTAA
460309 TTTATATTTAAATTATTTTA
1 TTTATATTTAAATTATTTTA
460329 TAACATAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
21 15 0.43
22 8 0.23
23 12 0.34
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTATATTTAAATTATTTTAA
Found at i:460328 original size:16 final size:16
Alignment explanation
Indices: 460210--460393 Score: 100
Period size: 16 Copynumber: 11.8 Consensus size: 16
460200 AATATTTAAA
* *
460210 TTAATTTATTTTA-AA
1 TTAAATTATTTTATAT
460225 TT-AATTATATTTAATAT
1 TTAAATTAT-TTT-ATAT
460242 TTAATATTATTTTAT-T
1 TTAA-ATTATTTTATAT
460258 TT--ATTATTTTATAT
1 TTAAATTATTTTATAT
* * *
460272 ATAAACTATTTTA-AA
1 TTAAATTATTTTATAT
*
460287 TT-AATTA-TTTA-AA
1 TTAAATTATTTTATAT
* *
460300 TTAATTTAATTTATAT
1 TTAAATTATTTTATAT
460316 TTAAATTATTTTATA-
1 TTAAATTATTTTATAT
** * *
460331 ACATAATCATTTTAAAT
1 TTA-AATTATTTTATAT
* *
460348 TTTAATTATTTTAAAT
1 TTAAATTATTTTATAT
* *
460364 TTTAATTATTTTAAAT
1 TTAAATTATTTTATAT
*
460380 TTAATTTATATTTA
1 TTAAATTAT-TTTA
460394 AAATAAACTA
Statistics
Matches: 134, Mismatches: 21, Indels: 26
0.74 0.12 0.14
Matches are distributed among these distances:
13 18 0.13
14 15 0.11
15 12 0.09
16 71 0.53
17 9 0.07
18 4 0.03
19 5 0.04
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAAATTATTTTATAT
Found at i:460351 original size:7 final size:7
Alignment explanation
Indices: 460339--460381 Score: 50
Period size: 7 Copynumber: 5.6 Consensus size: 7
460329 TAACATAATC
460339 ATTTTAA
1 ATTTTAA
460346 ATTTTAA
1 ATTTTAA
460353 TTATTTTAA
1 --ATTTTAA
460362 ATTTTAA
1 ATTTTAA
460369 TTATTTTAA
1 --ATTTTAA
460378 ATTT
1 ATTT
460382 AATTTATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
7 18 0.56
9 14 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (7 bp):
ATTTTAA
Found at i:460360 original size:9 final size:9
Alignment explanation
Indices: 460287--460377 Score: 59
Period size: 9 Copynumber: 10.4 Consensus size: 9
460277 CTATTTTAAA
460287 TTAATTATT
1 TTAATTATT
* *
460296 TAAATTAAT
1 TTAATTATT
460305 TTAATTTATAT
1 TTAA-TTAT-T
460316 TTAAATTATT
1 TT-AATTATT
**
460326 TT-A-TAAC
1 TTAATTATT
* *
460333 ATAATCATT
1 TTAATTATT
460342 TTAA--ATT
1 TTAATTATT
460349 TTAATTATT
1 TTAATTATT
460358 TTAA--ATT
1 TTAATTATT
460365 TTAATTATT
1 TTAATTATT
460374 TTAA
1 TTAA
460378 ATTTAATTTA
Statistics
Matches: 62, Mismatches: 11, Indels: 18
0.68 0.12 0.20
Matches are distributed among these distances:
7 17 0.27
8 2 0.03
9 28 0.45
10 6 0.10
11 7 0.11
12 2 0.03
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (9 bp):
TTAATTATT
Found at i:460540 original size:15 final size:15
Alignment explanation
Indices: 460522--460571 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
460512 AACAGGAAAG
460522 GAAAAGAGAGAAAAA
1 GAAAAGAGAGAAAAA
*
460537 GAAAGGTAGA-AAAAA
1 GAAAAG-AGAGAAAAA
*
460552 GAAACGAGAGAAAAA
1 GAAAAGAGAGAAAAA
460567 GAAAA
1 GAAAA
460572 AAATATATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 3 0.10
15 24 0.80
16 3 0.10
ACGTcount: A:0.70, C:0.02, G:0.26, T:0.02
Consensus pattern (15 bp):
GAAAAGAGAGAAAAA
Found at i:460771 original size:11 final size:11
Alignment explanation
Indices: 460746--460809 Score: 85
Period size: 11 Copynumber: 5.6 Consensus size: 11
460736 TATTAGTAAA
460746 TATTTTTATATT
1 TATTTTTATA-T
460758 TATTTTTATAT
1 TATTTTTATAT
460769 TATTTTT-TAAT
1 TATTTTTAT-AT
460780 TAATTTTTATAT
1 T-ATTTTTATAT
*
460792 TATGTTTATAT
1 TATTTTTATAT
460803 TATTTTT
1 TATTTTT
460810 TGTATATTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
10 1 0.02
11 26 0.55
12 19 0.40
13 1 0.02
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (11 bp):
TATTTTTATAT
Found at i:460772 original size:23 final size:23
Alignment explanation
Indices: 460746--460809 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
460736 TATTAGTAAA
460746 TATTTTTATATTTATTTTTATAT
1 TATTTTTATATTTATTTTTATAT
*
460769 TATTTTT-TAATTAATTTTTATAT
1 TATTTTTAT-ATTTATTTTTATAT
*
460792 TATGTTTATA-TTATTTTT
1 TATTTTTATATTTATTTTT
460810 TGTATATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.22
23 27 0.75
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (23 bp):
TATTTTTATATTTATTTTTATAT
Found at i:460810 original size:23 final size:22
Alignment explanation
Indices: 460749--460818 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 22
460739 TAGTAAATAT
460749 TTTTATATT-TATTTTTATATTA
1 TTTTATATTAT-TTTTTATATTA
* *
460771 TTTTTTAATTAATTTTTATATTA
1 TTTTAT-ATTATTTTTTATATTA
*
460794 TGTTTATATTATTTTTTGTA-TA
1 T-TTTATATTATTTTTTATATTA
460816 TTT
1 TTT
460819 AAAATATTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
21 2 0.05
22 8 0.20
23 26 0.65
24 4 0.10
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (22 bp):
TTTTATATTATTTTTTATATTA
Found at i:461360 original size:15 final size:14
Alignment explanation
Indices: 461340--461377 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
461330 TAAATTATTT
*
461340 TTAATTTTTAATTAA
1 TTAATTTTAAATT-A
461355 TTAATTTTAAATTA
1 TTAATTTTAAATTA
461369 TTAATTTTA
1 TTAATTTTA
461378 TTTTAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTAATTTTAAATTA
Found at i:461361 original size:22 final size:21
Alignment explanation
Indices: 461332--461425 Score: 64
Period size: 22 Copynumber: 4.9 Consensus size: 21
461322 CACTAGTTTA
* *
461332 AATTATTTTTAATTTTTAATT
1 AATTATTTTAAATTATTAATT
461353 AATTAATTTTAAATTATTAATT
1 AATT-ATTTTAAATTATTAATT
461375 --TTATTTT-AATTA--AATT
1 AATTATTTTAAATTATTAATT
* *
461391 -A-TA-TTTAAATT-TAAATA
1 AATTATTTTAAATTATTAATT
*
461408 AATTATTTAAAATT-TTAA
1 AATTATTTTAAATTATTAA
461426 ATTCAAATTA
Statistics
Matches: 60, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
15 3 0.05
16 10 0.17
17 3 0.05
18 6 0.10
19 7 0.12
20 12 0.20
21 4 0.07
22 15 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AATTATTTTAAATTATTAATT
Found at i:461364 original size:14 final size:14
Alignment explanation
Indices: 461340--461387 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
461330 TAAATTATTT
461340 TTAATTTTTAATTAA
1 TTAA-TTTTAATTAA
461355 TTAATTTTAAATT-A
1 TTAATTTT-AATTAA
*
461369 TTAATTTTATTTTAA
1 TTAATTTTA-ATTAA
461384 TTAA
1 TTAA
461388 ATTATATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 1 0.03
14 15 0.52
15 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTAATTTTAATTAA
Found at i:461403 original size:21 final size:21
Alignment explanation
Indices: 461361--461422 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
461351 TTAATTAATT
* *
461361 TTAAATTATTAATTTTATTTTAA
1 TTAAATTA-T-ATTTAAATTTAA
461384 TTAAATTATATTTAAATTTAA
1 TTAAATTATATTTAAATTTAA
* *
461405 ATAAATTAT-TTAAAATTT
1 TTAAATTATATTTAAATTT
461423 TAAATTCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.23
21 18 0.51
22 1 0.03
23 8 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTAAATTATATTTAAATTTAA
Found at i:461424 original size:21 final size:22
Alignment explanation
Indices: 461377--461427 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
461367 TATTAATTTT
* *
461377 ATTTTAATTAAATTATATTTAA
1 ATTTTAAATAAATTATATTAAA
461399 A-TTTAAATAAATTAT-TTAAA
1 ATTTTAAATAAATTATATTAAA
461419 ATTTTAAAT
1 ATTTTAAAT
461428 TCAAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 5 0.19
21 20 0.77
22 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTTAAATAAATTATATTAAA
Found at i:461730 original size:21 final size:21
Alignment explanation
Indices: 461706--461757 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
461696 AATTATTTTT
461706 ATTTAATATTTTATTATAATA
1 ATTTAATATTTTATTATAATA
461727 ATTTAATATTTTATTATAATA
1 ATTTAATATTTTATTATAATA
461748 ATTTAATATT
1 ATTTAATATT
461758 AAATTTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTTAATATTTTATTATAATA
Found at i:461787 original size:8 final size:8
Alignment explanation
Indices: 461776--461800 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
461766 ATTTATTTAT
461776 TTAAAATA
1 TTAAAATA
461784 TTAAAATA
1 TTAAAATA
461792 TTAAAATA
1 TTAAAATA
461800 T
1 T
461801 ATTAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TTAAAATA
Found at i:467554 original size:16 final size:16
Alignment explanation
Indices: 467530--467564 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
467520 ATAACCATAC
*
467530 TTTCATTATGGTGAAG
1 TTTCATTATAGTGAAG
*
467546 TTTCGTTATAGTGAAG
1 TTTCATTATAGTGAAG
467562 TTT
1 TTT
467565 TGAAATAGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.49
Consensus pattern (16 bp):
TTTCATTATAGTGAAG
Found at i:468033 original size:16 final size:16
Alignment explanation
Indices: 468005--468043 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
467995 AACAACCAAT
468005 CTAAAAC-TAAAATTA
1 CTAAAACTTAAAATTA
468020 CTAAAACTTAAAATTA
1 CTAAAACTTAAAATTA
*
468036 CTTAAACT
1 CTAAAACT
468044 CGATTAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (16 bp):
CTAAAACTTAAAATTA
Found at i:469139 original size:24 final size:24
Alignment explanation
Indices: 469107--469155 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
469097 GGGTTTCCGA
469107 TACTTATTCCTATGTCACTCAGAC
1 TACTTATTCCTATGTCACTCAGAC
469131 TACTTATTCCTATGTCACTCAGAC
1 TACTTATTCCTATGTCACTCAGAC
469155 T
1 T
469156 CGGGTATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.29, G:0.08, T:0.39
Consensus pattern (24 bp):
TACTTATTCCTATGTCACTCAGAC
Found at i:474491 original size:19 final size:19
Alignment explanation
Indices: 474469--474505 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
474459 ATTTAACATT
474469 TTAATTAAAATTTTATAAG
1 TTAATTAAAATTTTATAAG
**
474488 TTAATTAATTTTTTATAA
1 TTAATTAAAATTTTATAA
474506 TTTTATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
TTAATTAAAATTTTATAAG
Found at i:475308 original size:13 final size:13
Alignment explanation
Indices: 475287--475316 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
475277 ATTAAAATAT
*
475287 AATATAATATAAA
1 AATACAATATAAA
475300 AATACAATATAAA
1 AATACAATATAAA
475313 AATA
1 AATA
475317 TTTTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (13 bp):
AATACAATATAAA
Found at i:475648 original size:25 final size:25
Alignment explanation
Indices: 475620--475668 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
475610 AATCAATATA
475620 TTTT-AATATAAATATAAATTTTAATT
1 TTTTAAATATAAA-A-AAATTTTAATT
475646 TTTTAAATATAAAAAAATTTTAA
1 TTTTAAATATAAAAAAATTTTAA
475669 AAATTAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 9 0.41
26 5 0.23
27 8 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTTAAATATAAAAAAATTTTAATT
Found at i:475869 original size:12 final size:12
Alignment explanation
Indices: 475849--475879 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
475839 AAAAATATAT
475849 ATTTAAATTTTAA
1 ATTT-AATTTTAA
475862 ATTTAATTTTAA
1 ATTTAATTTTAA
475874 ATTTAA
1 ATTTAA
475880 CTCGAGTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTAATTTTAA
Found at i:475941 original size:14 final size:14
Alignment explanation
Indices: 475922--475956 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
475912 ACATAATAAA
475922 TTTTATAAAAATAT
1 TTTTATAAAAATAT
**
475936 TTTTATATTAATAT
1 TTTTATAAAAATAT
475950 TTTTATA
1 TTTTATA
475957 TTTTATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTATAAAAATAT
Found at i:475957 original size:14 final size:14
Alignment explanation
Indices: 475931--475958 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
475921 ATTTTATAAA
475931 AATATTTTTATATT
1 AATATTTTTATATT
475945 AATATTTTTATATT
1 AATATTTTTATATT
475959 TTATATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:479798 original size:42 final size:42
Alignment explanation
Indices: 479739--479851 Score: 190
Period size: 42 Copynumber: 2.7 Consensus size: 42
479729 TGAACATTCT
*
479739 GGTGACTTTTGTTGGTCCCAAGAACTATTCATTGCAGTTGTC
1 GGTGACTTTTGTTGGTCCCAAGAACTATTCATTGCAGTTGTA
* * *
479781 GGTGACTTTTGTTGGTCCAAATAACTATTCATTGTAGTTGTA
1 GGTGACTTTTGTTGGTCCCAAGAACTATTCATTGCAGTTGTA
479823 GGTGACTTTTGTTGGTCCCAAGAACTATT
1 GGTGACTTTTGTTGGTCCCAAGAACTATT
479852 TATTATAGGT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (42 bp):
GGTGACTTTTGTTGGTCCCAAGAACTATTCATTGCAGTTGTA
Found at i:480200 original size:201 final size:200
Alignment explanation
Indices: 479838--480564 Score: 832
Period size: 201 Copynumber: 3.6 Consensus size: 200
479828 CTTTTGTTGG
* *
479838 TCCCAAGAACTATTTATTATAGGTGACTCATCCTTAGTCCAGCCTGCAGCAGTTGAAGAAACCCA
1 TCCCAAGAACTATTCATTATAGGTGAATCATCCTTAGTCCAGCCTGCAGCAGTTGAAGAAACCCA
* * * * * *
479903 TCCAGACGTGGACTGAACTGGCTTTTCCTGATTAGTTTTTTTATCCCAACCAGAAGTC-GACTGA
66 ACCAGATGT-AACTGAACTGGCTTTTCCTCAGTAGCTTTTTTATCCCAACCAGAAGTCAG-CTGA
* * * * * *
479967 ATTGTATTTTCCTCAGTCACTTTGTTATTCCAACCGGATATCAACTGCACTGGTTTTTGTTGATT
129 ACTGTCTTTTCCTCAGTCACTTTGTTATTCCAACCAGATGTCAACTGCACTGGCTTTTGTTGACT
* *
480032 TGCATGA
194 TGCGTTA
* * * * *
480039 TCCCAAGAACTATTCATTATAGGAGACTCATCCTTAGTCCAGCCTGTAGCAGTTGGAGAAACCCT
1 TCCCAAGAACTATTCATTATAGGTGAATCATCCTTAGTCCAGCCTGCAGCAGTTGAAGAAACCCA
*
480104 ACCAGATGTCAACTGAACTGGCTTTTCCTCAGTAGCTTTTTTATCCCAACCAGAAGTCAGCTGGA
66 ACCAGATGT-AACTGAACTGGCTTTTCCTCAGTAGCTTTTTTATCCCAACCAGAAGTCAGCTGAA
*** * * *
480169 CTGTCTTTTCCTC-GCTTGGTTTGTCATTCCAACAAGATGTCAACCGCACTGGCTTTTGTTGACT
130 CTGTCTTTTCCTCAG-TCACTTTGTTATTCCAACCAGATGTCAACTGCACTGGCTTTTGTTGACT
480233 TGCGTTA
194 TGCGTTA
* * ** * * * *
480240 TCCCAAGAACTATTCGTTATAAGTGAATCATCCTTAGTAGAGCATGTAGCATTTGGAGAAACCCA
1 TCCCAAGAACTATTCATTATAGGTGAATCATCCTTAGTCCAGCCTGCAGCAGTTGAAGAAACCCA
* * * **
480305 ACCAGATGTAGACTGAACTGGCTTTTCCTGAGTAGCTTTTTTATCCCAATCAGATGTCAATTGAA
66 ACCAGATGTA-ACTGAACTGGCTTTTCCTCAGTAGCTTTTTTATCCCAACCAGAAGTCAGCTGAA
* * * * *
480370 CTGAC-TTTCCTTCTGTCACTTTGTTATTCCAAGCAGATGTCAATTGCACTGGCTTTCGTTGACT
130 CTGTCTTTTCC-TCAGTCACTTTGTTATTCCAACCAGATGTCAACTGCACTGGCTTTTGTTGACT
*
480434 TGTGTTA
194 TGCGTTA
* * * * * *
480441 CCCCAAGAACTATTCGTTATAGGTGAATCATCGTTGGTCCAGCCTGCAGTAGTTGAAGACACCCA
1 TCCCAAGAACTATTCATTATAGGTGAATCATCCTTAGTCCAGCCTGCAGCAGTTGAAGAAACCCA
* * * * *
480506 ACCAGATGTTGACTGAACTGGCTTTTCC-CGAGAACCTTTTTTATCCCATCCAGACGTCA
66 ACCAGATG-TAACTGAACTGGCTTTTCCTC-AGTAGCTTTTTTATCCCAACCAGAAGTCA
480565 CCTTTTCCTC
Statistics
Matches: 447, Mismatches: 72, Indels: 14
0.84 0.14 0.03
Matches are distributed among these distances:
200 7 0.02
201 437 0.98
202 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.33
Consensus pattern (200 bp):
TCCCAAGAACTATTCATTATAGGTGAATCATCCTTAGTCCAGCCTGCAGCAGTTGAAGAAACCCA
ACCAGATGTAACTGAACTGGCTTTTCCTCAGTAGCTTTTTTATCCCAACCAGAAGTCAGCTGAAC
TGTCTTTTCCTCAGTCACTTTGTTATTCCAACCAGATGTCAACTGCACTGGCTTTTGTTGACTTG
CGTTA
Found at i:480370 original size:48 final size:49
Alignment explanation
Indices: 480301--480425 Score: 123
Period size: 48 Copynumber: 2.6 Consensus size: 49
480291 TTTGGAGAAA
* * *
480301 CCCAACCAGATGT-AGACTGAACTGGCTTTTCC-TGAGT-AGCTTTTTTAT
1 CCCAACCAGATGTCA-ATTGAACTGGCTTTTCCTTCAGTCA-CTTTGTTAT
* * *
480349 CCCAATCAGATGTCAATTGAACTGAC-TTTCCTTCTGTCACTTTGTTAT
1 CCCAACCAGATGTCAATTGAACTGGCTTTTCCTTCAGTCACTTTGTTAT
* * *
480397 TCCAAGCAGATGTCAATTGCACTGGCTTT
1 CCCAACCAGATGTCAATTGAACTGGCTTT
480426 CGTTGACTTG
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
47 5 0.08
48 54 0.86
49 4 0.06
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (49 bp):
CCCAACCAGATGTCAATTGAACTGGCTTTTCCTTCAGTCACTTTGTTAT
Found at i:485405 original size:21 final size:20
Alignment explanation
Indices: 485377--485420 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
485367 TAAAATTTAT
*
485377 AAAAAAAT-TATTAAACATAA
1 AAAAAAATAAATTAAA-ATAA
485397 AAAATAAATAAATTAAAATAA
1 AAAA-AAATAAATTAAAATAA
485418 AAA
1 AAA
485421 TTTTATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 11 0.52
22 6 0.29
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAAAAATAAATTAAAATAA
Found at i:485539 original size:19 final size:19
Alignment explanation
Indices: 485515--485609 Score: 104
Period size: 19 Copynumber: 4.9 Consensus size: 19
485505 TTTCACGTAA
485515 CATTTCATGCATGCATTTT
1 CATTTCATGCATGCATTTT
485534 CATTTCATGCATGCATTTT
1 CATTTCATGCATGCATTTT
* **
485553 CATTTCATGCATTTCA-CAT
1 CATTTCATGCA-TGCATTTT
* *
485572 AATTTTCATTTCATGCA-TTT
1 CA-TTTCA-TGCATGCATTTT
485592 CATTTCATGCATGCATTT
1 CATTTCATGCATGCATTT
485610 CATAAACATT
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
18 7 0.11
19 39 0.63
20 13 0.21
21 3 0.05
ACGTcount: A:0.23, C:0.21, G:0.08, T:0.47
Consensus pattern (19 bp):
CATTTCATGCATGCATTTT
Found at i:485695 original size:16 final size:16
Alignment explanation
Indices: 485674--485714 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
485664 AATTCATGCA
485674 TGCATTTCACATAATT
1 TGCATTTCACATAATT
485690 TGCATTTCACATAATT
1 TGCATTTCACATAATT
*
485706 TTCATTTCA
1 TGCATTTCA
485715 TAAACATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.46
Consensus pattern (16 bp):
TGCATTTCACATAATT
Found at i:485703 original size:89 final size:88
Alignment explanation
Indices: 485537--485698 Score: 220
Period size: 89 Copynumber: 1.8 Consensus size: 88
485527 GCATTTTCAT
** * ** *
485537 TTCATGCATGCATTTTCATTTCATGCATTTCACATAATTTTCATTTCATGCATTTCATTTCATGC
1 TTCATGCATGCATTTTCATTTCATGCATTTCACATAAAATTCATTGCATGCATTTCACATAAT-C
485602 ATGCATTTCATAAACATTTCAAGC
65 ATGCATTTCATAAACATTTCAAGC
*
485626 TTCATGCATGCATTTTCATTTCATGCATTTCACGTAACAATTCA-TGCATGCATTTCACATAAT-
1 TTCATGCATGCATTTTCATTTCATGCATTTCACATAA-AATTCATTGCATGCATTTCACATAATC
*
485689 TTGCATTTCA
65 ATGCATTTCA
485699 CATAATTTTC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 9 0.14
89 51 0.80
90 4 0.06
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.43
Consensus pattern (88 bp):
TTCATGCATGCATTTTCATTTCATGCATTTCACATAAAATTCATTGCATGCATTTCACATAATCA
TGCATTTCATAAACATTTCAAGC
Found at i:487362 original size:88 final size:91
Alignment explanation
Indices: 487200--487367 Score: 261
Period size: 93 Copynumber: 1.9 Consensus size: 91
487190 ATCTTCATTG
* * *
487200 TTGCTTTGCTTTGCTGTTCCATGTTGCTTTGTCTTTATCATTGCTGTTTTTTTTTTTCACGTTAC
1 TTGCTTTGCTTTGCTGTTCCATATTGCTTTGTCTTCATCATTGCTGTTTTTTTTCTTCACGTTAC
487265 TTTGTCTTCCACTTTCTTCATTGTTGCT
66 --TGTCTTCCACTTTCTTCATTGTTGCT
*
487293 TTGCTTTGCTTTGCTGTTTCATATTGCTTTGTCTTCATCATTGCTGTTTTTTTTCTTCACGTT-C
1 TTGCTTTGCTTTGCTGTTCCATATTGCTTTGTCTTCATCATTGCTGTTTTTTTTCTTCACGTTAC
487357 -G-CTTCCACTTT
66 TGTCTTCCACTTT
487368 AATTTATTTG
Statistics
Matches: 71, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
88 10 0.14
89 1 0.01
92 1 0.01
93 59 0.83
ACGTcount: A:0.08, C:0.21, G:0.14, T:0.57
Consensus pattern (91 bp):
TTGCTTTGCTTTGCTGTTCCATATTGCTTTGTCTTCATCATTGCTGTTTTTTTTCTTCACGTTAC
TGTCTTCCACTTTCTTCATTGTTGCT
Found at i:487817 original size:21 final size:20
Alignment explanation
Indices: 487778--487821 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
487768 TTTTATAAAA
*
487778 TTTTTATTTTAATTTATTTAT
1 TTTTTATTTTAATTAATTT-T
487799 TTTTTATGTTTAA-TAATTTT
1 TTTTTAT-TTTAATTAATTTT
487819 TTT
1 TTT
487822 ATAAACTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 12 0.57
22 5 0.24
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (20 bp):
TTTTTATTTTAATTAATTTT
Found at i:488338 original size:43 final size:42
Alignment explanation
Indices: 488250--488663 Score: 254
Period size: 43 Copynumber: 9.8 Consensus size: 42
488240 AAGAAAATAT
* * * *
488250 TCTCTCGGGTCAAAGCC-AAAGGGCATACTTAGGGA-AAGAAAG
1 TCTCTAGGGTCAAAGCCGACA-GGCAGAC-TAAGGATAAGAAAG
*
488292 TCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAAGAAAG
1 TCTCTAGGGTCAAAGCCGACAGGCAGACT-AAGGATAAGAAAG
* *** * * * *
488335 TCTCCAAAATCAAAGCCGATAGGCATACTTAGGACTAGGAAAG
1 TCTCTAGGGTCAAAGCCGACAGGCAGACTAAGGA-TAAGAAAG
* * * * * *
488378 TCTCCAAGCTCAAAGCCGACAAGCAGACTTAGGA-AAAAAAG
1 TCTCTAGGGTCAAAGCCGACAGGCAGACTAAGGATAAGAAAG
* * *
488419 TCTTTAGGATCAAAACCGACAGGCAGACTAAGGGAT-AGAAAAG
1 TCTCTAGGGTCAAAGCCGACAGGCAGACTAA-GGATAAG-AAAG
* * * * * *
488462 TTTTTAGGGTCAAAGCCGATAAGCAGACTCAGGGATAAAAAAG
1 TCTCTAGGGTCAAAGCCGACAGGCAGACT-AAGGATAAGAAAG
* * *
488505 TCTCTAGGGTTAAAGCCGACAGGCAAACTAAGGGA-AGGGAAAG
1 TCTCTAGGGTCAAAGCCGACAGGCAGACTAA-GGATA-AGAAAG
* * *
488548 TCTCTAGAGTCAAAGCCAACAGGCAGACTGAA--AAAAGGAAAG
1 TCTCTAGGGTCAAAGCCGACAGGCAGACT-AAGGATAA-GAAAG
* * * *
488590 TCT-TGAGGGACGAAGCCAACAGGCAGACTAAGAGATTA-AAAG
1 TCTCT-AGGGTCAAAGCCGACAGGCAGACTAAG-GATAAGAAAG
* * * *
488632 TCTCGAGGGACGAAA-CCAACAGACAGACTAAG
1 TCTCTAGGGTC-AAAGCCGACAGGCAGACTAAG
488664 AGAAAACAGA
Statistics
Matches: 296, Mismatches: 56, Indels: 40
0.76 0.14 0.10
Matches are distributed among these distances:
41 34 0.11
42 94 0.32
43 162 0.55
44 6 0.02
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.15
Consensus pattern (42 bp):
TCTCTAGGGTCAAAGCCGACAGGCAGACTAAGGATAAGAAAG
Found at i:488606 original size:42 final size:42
Alignment explanation
Indices: 488560--488664 Score: 131
Period size: 42 Copynumber: 2.5 Consensus size: 42
488550 TCTAGAGTCA
* *
488560 AAGCCAACAGGCAGACTGAA-AAAAGGAAAGTCTTGAGGGACG
1 AAGCCAACAGGCAGACT-AAGAAAAGAAAAGTCTCGAGGGACG
* **
488602 AAGCCAACAGGCAGACTAAGAGATTAAAAGTCTCGAGGGACG
1 AAGCCAACAGGCAGACTAAGAAAAGAAAAGTCTCGAGGGACG
* *
488644 AAACCAACAGACAGACTAAGA
1 AAGCCAACAGGCAGACTAAGA
488665 GAAAACAGAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 2 0.04
42 53 0.96
ACGTcount: A:0.45, C:0.19, G:0.27, T:0.10
Consensus pattern (42 bp):
AAGCCAACAGGCAGACTAAGAAAAGAAAAGTCTCGAGGGACG
Found at i:488665 original size:42 final size:42
Alignment explanation
Indices: 488586--488666 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
488576 TGAAAAAAGG
* * *
488586 AAAGTCTTGAGGGACGAAGCCAACAGGCAGACTAAGAGATTA
1 AAAGTCTCGAGGGACGAAACCAACAGACAGACTAAGAGATTA
488628 AAAGTCTCGAGGGACGAAACCAACAGACAGACTAAGAGA
1 AAAGTCTCGAGGGACGAAACCAACAGACAGACTAAGAGA
488667 AAACAGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.43, C:0.19, G:0.27, T:0.11
Consensus pattern (42 bp):
AAAGTCTCGAGGGACGAAACCAACAGACAGACTAAGAGATTA
Found at i:500534 original size:85 final size:86
Alignment explanation
Indices: 500390--500546 Score: 271
Period size: 85 Copynumber: 1.8 Consensus size: 86
500380 TTAAAAAAAA
* * * *
500390 TCTTTATTGTTGCTTTGCTTTGCTGTTCCATGTTGCTTTGTCTTCATCATTGCTGTTTTTTTT-T
1 TCTTCATTGTTACTTCGCTTTGCTGTTCCATATTGCTTTGTCTTCATCATTGCTGTTTTTTTTCT
500454 TCACGTTACTGTCTTCCACTT
66 TCACGTTACTGTCTTCCACTT
500475 TCTTCATTGTTACTTCGCTTTGCTGTTCCATATTGCTTTGTCTTCATCATTGCTGTTTTTTTTCT
1 TCTTCATTGTTACTTCGCTTTGCTGTTCCATATTGCTTTGTCTTCATCATTGCTGTTTTTTTTCT
500540 TCACGTT
66 TCACGTT
500547 GGCTTCCACT
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
85 59 0.88
86 8 0.12
ACGTcount: A:0.09, C:0.22, G:0.13, T:0.56
Consensus pattern (86 bp):
TCTTCATTGTTACTTCGCTTTGCTGTTCCATATTGCTTTGTCTTCATCATTGCTGTTTTTTTTCT
TCACGTTACTGTCTTCCACTT
Found at i:501595 original size:2 final size:2
Alignment explanation
Indices: 501582--501623 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
501572 AACAGTAATC
* *
501582 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
501624 CCCATTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:505360 original size:2 final size:2
Alignment explanation
Indices: 505353--505395 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
505343 CACATGTGAA
505353 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
505395 A
1 A
505396 ACATGTTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:507551 original size:19 final size:20
Alignment explanation
Indices: 507523--507561 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
507513 TGTACTTCTC
*
507523 TTTTTCTTTTTCCTT-TTTT
1 TTTTTCTTTTCCCTTGTTTT
*
507542 TTTTTTTTTTCCCTTGTTTT
1 TTTTTCTTTTCCCTTGTTTT
507562 CAACTTTAAT
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:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (20 bp):
TTTTTCTTTTCCCTTGTTTT
Found at i:507561 original size:18 final size:18
Alignment explanation
Indices: 507523--507561 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
507513 TGTACTTCTC
* *
507523 TTTTTCTTTTTCCTTTTT
1 TTTTTCTTTTTCCCTTGT
*
507541 TTTTTTTTTTTCCCTTGT
1 TTTTTCTTTTTCCCTTGT
507559 TTT
1 TTT
507562 CAACTTTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTTTCTTTTTCCCTTGT
Found at i:510378 original size:16 final size:19
Alignment explanation
Indices: 510344--510411 Score: 93
Period size: 19 Copynumber: 3.5 Consensus size: 19
510334 TCGATTTGAA
510344 TTATATTTTTATAATAATAT
1 TTATA-TTTTATAATAATAT
510364 TTATATTTTATAATAATAT
1 TTATATTTTATAATAATAT
*
510383 TTATATTTTACAAT-ATAAT
1 TTATATTTTATAATAAT-AT
510402 TATATATTTT
1 T-TATATTTT
510412 TTTATAATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
18 2 0.04
19 30 0.67
20 13 0.29
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATATTTTATAATAATAT
Found at i:510408 original size:39 final size:39
Alignment explanation
Indices: 510344--510420 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
510334 TCGATTTGAA
*
510344 TTATATTTTTATAATAATATTTATATTTTATAATAATAT
1 TTATATTTTTACAATAATATTTATATTTTATAATAATAT
* *
510383 TTATA-TTTTACAAT-ATAATTATATATTTTTTTATAATA
1 TTATATTTTTACAATAAT-ATT-TATATTTTATAATAATA
510421 ATGGTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 2 0.06
38 11 0.33
39 20 0.61
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (39 bp):
TTATATTTTTACAATAATATTTATATTTTATAATAATAT
Found at i:510556 original size:15 final size:15
Alignment explanation
Indices: 510506--510557 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
510496 AAACATTGAC
*
510506 AAAAATATT-TAATA
1 AAAAATATTAAAATA
*
510520 AAAATATATTAAATTA
1 AAAA-ATATTAAAATA
**
510536 GTAAATATTAAAATA
1 AAAAATATTAAAATA
510551 AAAAATA
1 AAAAATA
510558 ATATAAATAT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
14 4 0.14
15 20 0.69
16 5 0.17
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (15 bp):
AAAAATATTAAAATA
Found at i:510753 original size:17 final size:17
Alignment explanation
Indices: 510733--510775 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
510723 ATTCATGTAT
*
510733 TTTTTATATTATAATTA
1 TTTTTATATAATAATTA
510750 TTTTTA-A-AATAATTA
1 TTTTTATATAATAATTA
*
510765 TATTTATATAA
1 TTTTTATATAA
510776 ATTTTAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 12 0.55
16 2 0.09
17 8 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTTATATAATAATTA
Found at i:510785 original size:18 final size:18
Alignment explanation
Indices: 510764--510833 Score: 58
Period size: 18 Copynumber: 4.0 Consensus size: 18
510754 TAAAATAATT
510764 ATATTTATATAAATTTTA
1 ATATTTATATAAATTTTA
* *
510782 ATATGTAAAT-AA-TTT-
1 ATATTTATATAAATTTTA
*
510797 ATATTT-CATAAATTTTAA
1 ATATTTATATAAATTTT-A
*
510815 TATATTTATATATATTTTA
1 -ATATTTATATAAATTTTA
510834 TGATATATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
14 2 0.05
15 7 0.17
16 6 0.15
17 2 0.05
18 8 0.20
19 7 0.17
20 8 0.20
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (18 bp):
ATATTTATATAAATTTTA
Found at i:510792 original size:32 final size:32
Alignment explanation
Indices: 510756--510817 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
510746 ATTATTTTTA
*
510756 AAATAA-TTATATTTATATAAATTTTAATATGT
1 AAATAATTTATATTT-CATAAATTTTAATATGT
510788 AAATAATTTATATTTCATAAATTTTAATAT
1 AAATAATTTATATTTCATAAATTTTAATAT
510818 ATTTATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 20 0.71
33 8 0.29
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (32 bp):
AAATAATTTATATTTCATAAATTTTAATATGT
Found at i:510839 original size:12 final size:11
Alignment explanation
Indices: 510796--510855 Score: 60
Period size: 9 Copynumber: 5.9 Consensus size: 11
510786 GTAAATAATT
*
510796 TATATTTCATA
1 TATATTTTATA
510807 -A-ATTTTA-A
1 TATATTTTATA
510815 TATA-TTTATA
1 TATATTTTATA
510825 TATATTTTATGA
1 TATATTTTAT-A
510837 TATATTTTA-A
1 TATATTTTATA
510847 T-TATTTTAT
1 TATATTTTAT
510856 GTGTCTAACC
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
8 1 0.02
9 17 0.40
10 9 0.21
11 5 0.12
12 10 0.24
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (11 bp):
TATATTTTATA
Found at i:511031 original size:4 final size:4
Alignment explanation
Indices: 511022--511094 Score: 51
Period size: 4 Copynumber: 17.0 Consensus size: 4
511012 TATGTGGTTA
* *
511022 TAAT TAAT TAAT TAATT TAAT TAAT AATAT TAA- T-AT TAAT ATCATT
1 TAAT TAAT TAAT TAA-T TAAT TAAT TA-AT TAAT TAAT TAAT -T-AAT
511068 TATAT TATAT TAAT TAATT TAAT TAAT
1 TA-AT TA-AT TAAT TAA-T TAAT TAAT
511095 ACGATCAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
2 1 0.02
3 2 0.04
4 31 0.54
5 21 0.37
6 2 0.04
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:511043 original size:9 final size:9
Alignment explanation
Indices: 511022--511094 Score: 62
Period size: 9 Copynumber: 7.9 Consensus size: 9
511012 TATGTGGTTA
511022 TAATTAA-T
1 TAATTAATT
511030 TAATTAATT
1 TAATTAATT
511039 TAATTAA-T
1 TAATTAATT
*
511047 AATATTAATAT
1 TA-ATTAAT-T
*
511058 TAATATCATT
1 TAAT-TAATT
511068 TATATT-ATAT
1 TA-ATTAAT-T
511078 TAATTAATT
1 TAATTAATT
511087 TAATTAAT
1 TAATTAAT
511095 ACGATCAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
8 9 0.17
9 27 0.50
10 11 0.20
11 7 0.13
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (9 bp):
TAATTAATT
Found at i:512198 original size:10 final size:10
Alignment explanation
Indices: 512183--512223 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
512173 CATCAATATA
512183 AAAATTTTTC
1 AAAATTTTTC
*
512193 AAAATTTTTT
1 AAAATTTTTC
512203 AAAATTTTT-
1 AAAATTTTTC
512212 AAAATATTTTC
1 AAAAT-TTTTC
512223 A
1 A
512224 TTATAATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 5 0.18
10 22 0.79
11 1 0.04
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (10 bp):
AAAATTTTTC
Found at i:512703 original size:42 final size:42
Alignment explanation
Indices: 512655--512740 Score: 104
Period size: 42 Copynumber: 2.0 Consensus size: 42
512645 TTTATAATTA
* *
512655 AAATTAAATAAAAATGTT-ATTATT-TAATTAATATTTTGAATC
1 AAATTAAAT-AAAATGTTAATTATTAAAATT-ATATTTTAAATC
* *
512697 AAATTAAATTAAATTTTAATTATTAAAATTATATTTTAAATC
1 AAATTAAATAAAATGTTAATTATTAAAATTATATTTTAAATC
512739 AA
1 AA
512741 TCTAATTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
41 6 0.16
42 28 0.74
43 4 0.11
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (42 bp):
AAATTAAATAAAATGTTAATTATTAAAATTATATTTTAAATC
Found at i:512837 original size:18 final size:18
Alignment explanation
Indices: 512795--512839 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
512785 AAAACTTAAA
*
512795 TTAATATTTAAAATATATT
1 TTAATA-TTAAAAAATATT
**
512814 AAAATATTAAAAAATATT
1 TTAATATTAAAAAATATT
512832 TTAATATT
1 TTAATATT
512840 TATATAATTA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATATTAAAAAATATT
Found at i:512886 original size:39 final size:35
Alignment explanation
Indices: 512821--512899 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 35
512811 ATTAAAATAT
* * *
512821 TAAAAAATATTTTAATATTTATATAATTAAATTTAAA
1 TAAAAAATATTTTAATAATTAAATAA-T-AATTCAAA
512858 TAAAAATATTATTTTAATAATTAAATAATAATTCAAA
1 TAAAAA-A-TATTTTAATAATTAAATAATAATTCAAA
512895 TAAAA
1 TAAAA
512900 TCAAACCAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 18 0.49
38 2 0.05
39 17 0.46
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (35 bp):
TAAAAAATATTTTAATAATTAAATAATAATTCAAA
Found at i:514983 original size:23 final size:21
Alignment explanation
Indices: 514969--515010 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
514959 TCTCGTACTT
514969 TCTTTTCTTTTTTTCTCTTTC
1 TCTTTTCTTTTTTTCTCTTTC
*
514990 TCTTTTCTATTTTT-TCTTTC
1 TCTTTTCTTTTTTTCTCTTTC
515010 T
1 T
515011 TATTCGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTTTTCTCTTTC
Found at i:515596 original size:9 final size:9
Alignment explanation
Indices: 515552--515601 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
515542 AATTTTAAAT
*
515552 TATTTATTT
1 TATTTATTA
515561 TATTATATTA
1 TATT-TATTA
*
515571 TATTT-TAA
1 TATTTATTA
*
515579 TAATT-TTA
1 TATTTATTA
515587 TATTTATTA
1 TATTTATTA
515596 TATTTA
1 TATTTA
515602 AAATTATCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
8 12 0.35
9 14 0.41
10 8 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TATTTATTA
Found at i:515600 original size:16 final size:15
Alignment explanation
Indices: 515554--515600 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
515544 TTTTAAATTA
515554 TTTATTTTATTATAT
1 TTTATTTTATTATAT
* *
515569 TATATTTTAATA-AT
1 TTTATTTTATTATAT
515583 TTTATATTTATTATAT
1 TTTAT-TTTATTATAT
515599 TT
1 TT
515601 AAAATTATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 6 0.23
15 16 0.62
16 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTATTTTATTATAT
Found at i:515875 original size:15 final size:15
Alignment explanation
Indices: 515842--515875 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
515832 TAAGTTTGGG
**
515842 TAAATTATTTTAAGT
1 TAAATTATTTTAAAA
515857 TAAATTATTTTAAAA
1 TAAATTATTTTAAAA
515872 TAAA
1 TAAA
515876 AATAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
TAAATTATTTTAAAA
Found at i:515888 original size:26 final size:27
Alignment explanation
Indices: 515859--515910 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
515849 TTTTAAGTTA
515859 AATTATTTT-AAAATAAAAATAATTTT
1 AATTATTTTGAAAATAAAAATAATTTT
* *
515885 AATTATTTTGAAATTAAAATTAATTT
1 AATTATTTTGAAAATAAAAATAATTT
515911 CTATTTGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
AATTATTTTGAAAATAAAAATAATTTT
Found at i:516907 original size:4 final size:4
Alignment explanation
Indices: 516848--516923 Score: 62
Period size: 4 Copynumber: 19.0 Consensus size: 4
516838 GAAGAATCAA
* * * * * * * * *
516848 ATAT ACAT ATAC ATAT ACAT ATAC ATAT ACAT ATAC ATAC ATAC ATAC
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
516896 ATAC ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT
516924 TGCAAGATAA
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 60 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (4 bp):
ATAT
Found at i:516923 original size:6 final size:6
Alignment explanation
Indices: 516848--516922 Score: 87
Period size: 6 Copynumber: 11.8 Consensus size: 6
516838 GAAGAATCAA
516848 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATACATAC ATACATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC AT--ATAC AT--ATAC
* * *
516900 ATATAT ATATAT ATATAT ATATA
1 ATATAC ATATAC ATATAC ATATA
516923 TTGCAAGATA
Statistics
Matches: 66, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
6 52 0.79
8 14 0.21
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATAC
Found at i:517068 original size:17 final size:17
Alignment explanation
Indices: 517027--517080 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
517017 TAAATTAATT
517027 TAATTTAATCT-TAATAA
1 TAATTTAAT-TATAATAA
*
517044 TTATTTTAATTATAATAA
1 -TAATTTAATTATAATAA
*
517062 TAATTTAATTATAAAAA
1 TAATTTAATTATAATAA
517079 TA
1 TA
517081 TATAAATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 18 0.56
18 14 0.44
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATTTAATTATAATAA
Found at i:517659 original size:18 final size:18
Alignment explanation
Indices: 517636--517671 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
517626 TTATACCGTT
517636 CTTATCTCCTATGAAGCA
1 CTTATCTCCTATGAAGCA
517654 CTTATCTCCTATGAAGCA
1 CTTATCTCCTATGAAGCA
517672 TGTATACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.33
Consensus pattern (18 bp):
CTTATCTCCTATGAAGCA
Found at i:519288 original size:21 final size:21
Alignment explanation
Indices: 519246--519284 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
519236 TATTTTTATT
519246 TAAATTAAATTATAAAATATA
1 TAAATTAAATTATAAAATATA
*
519267 TAAATTTAA-TATAAAATA
1 TAAATTAAATTATAAAATA
519285 ATATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATTAAATTATAAAATATA
Found at i:519630 original size:17 final size:20
Alignment explanation
Indices: 519608--519649 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
519598 AAAATATATA
519608 AATA-TTAA-TATAA-AAAT
1 AATATTTAATTATAATAAAT
519625 AATATTTTAATTATAATAAAT
1 AATA-TTTAATTATAATAAAT
519646 AATA
1 AATA
519650 ATTCAAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.19
19 4 0.19
20 5 0.24
21 8 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATATTTAATTATAATAAAT
Found at i:521371 original size:17 final size:18
Alignment explanation
Indices: 521337--521379 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
521327 ATGAAATATG
*
521337 ATATTTT-AAATATATAA
1 ATATTTTAAAAAATATAA
521354 ATATTTTAAAAAAT-TAA
1 ATATTTTAAAAAATATAA
521371 ATATATTTA
1 ATAT-TTTA
521380 TATTAAATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATTTTAAAAAATATAA
Found at i:521386 original size:15 final size:16
Alignment explanation
Indices: 521366--521399 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
521356 ATTTTAAAAA
521366 ATTAAAT-ATATTTAT
1 ATTAAATAATATTTAT
521381 ATTAAATACATATTTAT
1 ATTAAATA-ATATTTAT
521398 AT
1 AT
521400 CTTACAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
17 10 0.59
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAAATAATATTTAT
Found at i:525070 original size:30 final size:29
Alignment explanation
Indices: 525017--525088 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 29
525007 ACTATAATTT
525017 TTTAAAGATAAATGATACTTATCTCTCTAAATC-
1 TTTAAA-A-AAATGATACTTATCTCT-T-AA-CG
*
525050 TTTAAAAAAAT-ATATTTATCTCTTAACG
1 TTTAAAAAAATGATACTTATCTCTTAACG
525078 TTTAAAAAAAT
1 TTTAAAAAAAT
525089 TCACTTACTC
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
27 1 0.03
28 13 0.35
29 1 0.03
30 11 0.30
31 4 0.11
32 1 0.03
33 6 0.16
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.40
Consensus pattern (29 bp):
TTTAAAAAAATGATACTTATCTCTTAACG
Found at i:525100 original size:29 final size:29
Alignment explanation
Indices: 525017--525100 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 29
525007 ACTATAATTT
525017 TTTAAAGATAAATGATACTTATCTCTCTAAATC
1 TTTAAA-A-AAAT-ATACTTA-CTCTCTAAATC
* *
525050 TTTAAAAAAATATATTTA-TCTCTTAA-C
1 TTTAAAAAAATATACTTACTCTCTAAATC
525077 GTTTAAAAAAAT-TCACTTACTCTC
1 -TTTAAAAAAATAT-ACTTACTCTC
525101 GTGAAGTTCA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
27 2 0.04
28 22 0.49
29 4 0.09
30 6 0.13
31 4 0.09
32 1 0.02
33 6 0.13
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.40
Consensus pattern (29 bp):
TTTAAAAAAATATACTTACTCTCTAAATC
Found at i:525288 original size:16 final size:16
Alignment explanation
Indices: 525263--525294 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
525253 AGTTATTTTT
525263 AATTACTATTAAATTA
1 AATTACTATTAAATTA
*
525279 AATTATTATTAAATTA
1 AATTACTATTAAATTA
525295 TATTTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTACTATTAAATTA
Found at i:526258 original size:2 final size:2
Alignment explanation
Indices: 526251--526286 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
526241 CTTTGCATCA
526251 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
526287 TGACAAAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:528337 original size:2 final size:2
Alignment explanation
Indices: 528330--528368 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
528320 TACATCAATG
528330 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
528369 AAGAAACAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:529200 original size:18 final size:19
Alignment explanation
Indices: 529177--529244 Score: 83
Period size: 18 Copynumber: 3.8 Consensus size: 19
529167 CTTAAAATTT
529177 ATATAAATATA-AAATATA
1 ATATAAATATATAAATATA
*
529195 ATAT-AAT-TAT-AATATG
1 ATATAAATATATAAATATA
*
529211 ATATAAA-ATATAAATTTA
1 ATATAAATATATAAATATA
529229 ATATAAATATATAAAT
1 ATATAAATATATAAAT
529245 TATTAAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
16 11 0.26
17 8 0.19
18 15 0.36
19 8 0.19
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (19 bp):
ATATAAATATATAAATATA
Found at i:529214 original size:28 final size:26
Alignment explanation
Indices: 529183--529253 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 26
529173 ATTTATATAA
529183 ATATAAAATAT-AATATAATTATAATAT
1 ATATAAAATATAAATATAA-TATAA-AT
*
529210 GATATAAAATATAAATTTAATATAAAT
1 -ATATAAAATATAAATATAATATAAAT
*
529237 ATATAAATTATTAAATA
1 ATATAAAATA-TAAATA
529254 AAAAAATCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
26 9 0.24
27 7 0.18
28 16 0.42
29 6 0.16
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (26 bp):
ATATAAAATATAAATATAATATAAAT
Found at i:530171 original size:16 final size:18
Alignment explanation
Indices: 530150--530191 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
530140 AAAGAGTTTG
530150 AAAAAATAATGAGT-G-T
1 AAAAAATAATGAGTAGAT
*
530166 AAAAAAT-ATGATTAGAT
1 AAAAAATAATGAGTAGAT
530183 AAAAAATAA
1 AAAAAATAA
530192 AATTTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.23
16 8 0.36
17 8 0.36
18 1 0.05
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (18 bp):
AAAAAATAATGAGTAGAT
Found at i:530176 original size:15 final size:17
Alignment explanation
Indices: 530150--530190 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
530140 AAAGAGTTTG
530150 AAAAAATAATGAGT-G-T
1 AAAAAAT-ATGAGTAGAT
*
530166 AAAAAATATGATTAGAT
1 AAAAAATATGAGTAGAT
530183 AAAAAATA
1 AAAAAATA
530191 AAATTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 5 0.23
16 8 0.36
17 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.24
Consensus pattern (17 bp):
AAAAAATATGAGTAGAT
Found at i:531778 original size:2 final size:2
Alignment explanation
Indices: 531771--531811 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
531761 ACAGGAAAAG
531771 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
531812 AAGTTCAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:532119 original size:27 final size:27
Alignment explanation
Indices: 532089--532150 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 27
532079 ATTTTGTTAC
532089 TTAAA-TTATATTAAAATATTTTA-AATT
1 TTAAATTTATATT--AATATTTTATAATT
532116 TTAAATTTTATATTAATATTTTATAA--
1 TTAAA-TTTATATTAATATTTTATAATT
532142 TTAAATTTA
1 TTAAATTTA
532151 AATAAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
25 4 0.12
26 5 0.16
27 14 0.44
28 2 0.06
29 7 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TTAAATTTATATTAATATTTTATAATT
Found at i:532144 original size:14 final size:13
Alignment explanation
Indices: 532116--532149 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
532106 ATTTTAAATT
532116 TTAAATTTTAT-A
1 TTAAATTTTATAA
532128 TTAATATTTTATAA
1 TTAA-ATTTTATAA
532142 TTAAATTT
1 TTAAATTT
532150 AAATAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 11 0.55
14 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTAAATTTTATAA
Found at i:532169 original size:20 final size:20
Alignment explanation
Indices: 532146--532184 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
532136 TTATAATTAA
532146 ATTTAAATAAATAA-AATTTT
1 ATTT-AATAAATAATAATTTT
*
532166 ATTTATTAAATAATAATTT
1 ATTTAATAAATAATAATTT
532185 AAATTGATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTAATAAATAATAATTTT
Found at i:534582 original size:19 final size:19
Alignment explanation
Indices: 534558--534604 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
534548 CCAAATGAGT
534558 TAAAAAT-TTATTTTATTAA
1 TAAAAATATT-TTTTATTAA
*
534577 TAAAAATATTTTTTATTAT
1 TAAAAATATTTTTTATTAA
534596 TAAATAATA
1 TAAA-AATA
534605 ATTTAAATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAAAAATATTTTTTATTAA
Found at i:535269 original size:29 final size:30
Alignment explanation
Indices: 535242--535299 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
535232 TTTAAATTAG
535242 TATAAAATTATTATTTAATATAATATTAAAAA
1 TATAAAATTATTATTTAATATAATATT--AAA
535274 TATAAAATTATT-TTT-ATATTAATATT
1 TATAAAATTATTATTTAATA-TAATATT
535300 TATGATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
30 3 0.12
31 10 0.40
32 12 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
TATAAAATTATTATTTAATATAATATTAAA
Found at i:538331 original size:20 final size:19
Alignment explanation
Indices: 538308--538355 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 19
538298 TAAAATATTT
538308 TAAATATGATTATTATATAATA
1 TAAATAT-ATTA--ATATAATA
538330 -AAATATATTAATATAATA
1 TAAATATATTAATATAATA
538348 TAAATATA
1 TAAATATA
538356 AAAATTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 8 0.32
19 7 0.28
20 4 0.16
21 6 0.24
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TAAATATATTAATATAATA
Found at i:538354 original size:29 final size:24
Alignment explanation
Indices: 538329--538394 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 24
538319 ATTATATAAT
538329 AAAATATATTAATATAATATAAATATA
1 AAAAT-TATTAA-A-AATATAAATATA
*
538356 AAAATTATTAAAAATATAAAGTAGA
1 AAAATTATTAAAAATATAAA-TATA
* *
538381 AGAATGATTAAAAA
1 AAAATTATTAAAAA
538395 GGAGGGAGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.23
25 16 0.46
26 6 0.17
27 5 0.14
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (24 bp):
AAAATTATTAAAAATATAAATATA
Found at i:538588 original size:103 final size:104
Alignment explanation
Indices: 538409--538609 Score: 266
Period size: 106 Copynumber: 1.9 Consensus size: 104
538399 GGAGGACACA
538409 TTTTTTTTCCAAAACATTTTCTATAACAAAGGTTATACATGATTAAACCTTGGGTCATAATTTCA
1 TTTTTTTTCCAAAACATTTTCTATAACAAAGGTTATA-ATGATTAAACCTTGGGTCATAATTTCA
* *
538474 TGGTAAGTTTTTTTAGTAATTATTGTTTTGGAATGAATTTT
65 AGGTAAG-TTTTTTACTAATTATTGTTTTGGAATGAATTTT
** * * *
538515 TTTTTTTTTGAAAACATTTTCCT-TAACAATGGTTAT-AT-ATTAATCTTTGGGTCATAATTTCA
1 TTTTTTTTCCAAAACATTTT-CTATAACAAAGGTTATAATGATTAAACCTTGGGTCATAATTTCA
*
538577 AGATTAA-TTTTTTACTAATTATTGTTTTGGAAT
65 AG-GTAAGTTTTTTACTAATTATTGTTTTGGAAT
538610 ACTAATTGCT
Statistics
Matches: 85, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
102 25 0.29
103 23 0.27
104 5 0.06
106 30 0.35
107 2 0.02
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (104 bp):
TTTTTTTTCCAAAACATTTTCTATAACAAAGGTTATAATGATTAAACCTTGGGTCATAATTTCAA
GGTAAGTTTTTTACTAATTATTGTTTTGGAATGAATTTT
Found at i:541580 original size:45 final size:44
Alignment explanation
Indices: 541496--541581 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 44
541486 CTCTTATGAA
* *
541496 CATGGAATGAAAAATACTAAATACAATAATTAATGTAATATAAG
1 CATGGAATGAAAAATACTAAATACAATAATCAATATAATATAAG
* * *
541540 CATGGAATGAAAAATCCTAAAATACGATAATCGATATAATAT
1 CATGGAATGAAAAATACT-AAATACAATAATCAATATAATAT
541582 TTGCTTAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 17 0.47
45 19 0.53
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (44 bp):
CATGGAATGAAAAATACTAAATACAATAATCAATATAATATAAG
Found at i:542739 original size:23 final size:26
Alignment explanation
Indices: 542696--542745 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
542686 ATAAAATTAC
542696 AATATTACTTAAATATATTTT-ATTT
1 AATATTACTTAAATATATTTTAATTT
*
542721 AATATTA-TT-AATATTTTTTAATTT
1 AATATTACTTAAATATATTTTAATTT
542745 A
1 A
542746 CTTTAATTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 9 0.39
24 7 0.30
25 7 0.30
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (26 bp):
AATATTACTTAAATATATTTTAATTT
Found at i:543114 original size:42 final size:41
Alignment explanation
Indices: 543068--543146 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 41
543058 TAATTTACTT
* *
543068 ATATTATTTATTTTATTATTTATAATTAATA-AAAATATATTA
1 ATATTATATATTTTA-TAATTA-AATTAATATAAAATATATTA
*
543110 ATATTATATATTTTATAATTAAATTTATATAAAATAT
1 ATATTATATATTTTATAATTAAATTAATATAAAATAT
543147 TTTTTACTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 7 0.21
41 12 0.36
42 14 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (41 bp):
ATATTATATATTTTATAATTAAATTAATATAAAATATATTA
Found at i:543228 original size:2 final size:2
Alignment explanation
Indices: 543221--543256 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
543211 CTCGTCAACA
* *
543221 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
543257 TCATCGAGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:543705 original size:19 final size:19
Alignment explanation
Indices: 543663--543707 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 19
543653 ATAATAAATT
543663 AAAATAAAAATAATATTTTA
1 AAAATAAAAAT-ATATTTTA
543683 AAAATAATAAAT-TATTTTA
1 AAAATAA-AAATATATTTTA
543702 AAAATA
1 AAAATA
543708 TACTCATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.54
20 7 0.29
21 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATAAAAATATATTTTA
Found at i:544210 original size:21 final size:20
Alignment explanation
Indices: 544178--544219 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
544168 TAATTTTATT
544178 TAAATTTAAATATAAAATATA
1 TAAATTTAAATATAAAA-ATA
544199 TAAATATT-AATATAAAAATA
1 TAAAT-TTAAATATAAAAATA
544219 T
1 T
544220 TTTTAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 14 0.70
22 2 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATTTAAATATAAAAATA
Found at i:547437 original size:16 final size:17
Alignment explanation
Indices: 547416--547450 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
547406 CTTCATTTAA
547416 TTATATTT-TTTATTTT
1 TTATATTTATTTATTTT
547432 TTATATTTATTTATTTT
1 TTATATTTATTTATTTT
547449 TT
1 TT
547451 GTCGCTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (17 bp):
TTATATTTATTTATTTT
Found at i:547708 original size:38 final size:36
Alignment explanation
Indices: 547636--547756 Score: 108
Period size: 38 Copynumber: 3.3 Consensus size: 36
547626 AAATTTTTAG
*
547636 TTAATTAATATTTA-AAAATATAAA-ATATT-A-TTT
1 TTAATTAATATTTATAAATTATAAATAT-TTAATTTT
* *
547669 TTATATTAATATTTA-AATATTATACATTTTATAATTTT
1 TTA-ATTAATATTTATAA-ATTATAAATATT-TAATTTT
*
547707 TTAAATAATATATTATAAATTATAAATATTTAATTTT
1 TTAATTAATAT-TTATAAATTATAAATATTTAATTTT
*
547744 TTAAATTTATATT
1 TT-AATTAATATT
547757 AAAAATCATA
Statistics
Matches: 71, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
33 3 0.04
34 13 0.18
35 7 0.10
36 2 0.03
37 18 0.25
38 26 0.37
39 2 0.03
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (36 bp):
TTAATTAATATTTATAAATTATAAATATTTAATTTT
Found at i:547716 original size:37 final size:37
Alignment explanation
Indices: 547666--547836 Score: 104
Period size: 37 Copynumber: 4.6 Consensus size: 37
547656 TAAAATATTA
* * *
547666 TTTTTATATTAATAT-TTA-AATATTATACATTTTATAAT
1 TTTTTA-AATAATATATTATAA-ATTATAAATATT-TAAT
547704 TTTTTAAATAATATATTATAAATTATAAATATTTAAT
1 TTTTTAAATAATATATTATAAATTATAAATATTTAAT
* * * *
547741 TTTTTAAAT-TTATATTAAAAATCAT-ATTATTTAAT
1 TTTTTAAATAATATATTATAAATTATAAATATTTAAT
* * * * * * *
547776 TATATATATAATTTATTAAATAATTAT-TATATTTATT
1 TTTTTAAATAATATATTATA-AATTATAAATATTTAAT
*
547813 TATTATTAAA-ATTATATT-TAAATT
1 T-TT-TTAAATAATATATTATAAATT
547837 TTGTATTTTA
Statistics
Matches: 105, Mismatches: 22, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
35 15 0.14
36 25 0.24
37 34 0.32
38 26 0.25
39 5 0.05
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (37 bp):
TTTTTAAATAATATATTATAAATTATAAATATTTAAT
Found at i:547720 original size:45 final size:47
Alignment explanation
Indices: 547670--547784 Score: 114
Period size: 45 Copynumber: 2.4 Consensus size: 47
547660 ATATTATTTT
*
547670 TATATTA-ATATT-TAAATATTATACATTTTAT-AATTT-T-TTAAATAA
1 TATATTATAAATTATAAATATT-TA-ATTTTATAAATTTATATTAAA-AA
*
547715 TATATTATAAATTATAAATATTTAATTTTTTAAATTTATATTAAAAA
1 TATATTATAAATTATAAATATTTAATTTTATAAATTTATATTAAAAA
* *
547762 TCATATTATTTAATTATATATAT
1 T-ATATTA-TAAATTATAAATAT
547785 AATTTATTAA
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
45 13 0.22
46 11 0.19
47 12 0.20
48 11 0.19
49 12 0.20
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (47 bp):
TATATTATAAATTATAAATATTTAATTTTATAAATTTATATTAAAAA
Found at i:547755 original size:36 final size:36
Alignment explanation
Indices: 547636--547810 Score: 110
Period size: 37 Copynumber: 4.9 Consensus size: 36
547626 AAATTTTTAG
* *
547636 TTAATTAATAT-TTAAAAAT-ATAAAATATT-A-TTT
1 TTAAATAATATATTAAAAATCATAATAT-TTAATTTT
* * * *
547669 TTATATTAATAT-TTAAATATTATACATTTTATAATTTT
1 TTA-AATAATATATTAAAAATCATA-ATATT-TAATTTT
* *
547707 TTAAATAATATATTATAAATTATAAATATTTAATTTT
1 TTAAATAATATATTAAAAATCAT-AATATTTAATTTT
* * *
547744 TTAAAT-TTATATTAAAAATCATATTATTTAATTAT
1 TTAAATAATATATTAAAAATCATAATATTTAATTTT
* * * * *
547779 ATATATAATTTATTAAATAATTATTATATTTA
1 TTAAATAATATATTAAA-AATCATAATATTTA
547811 TTTATTATTA
Statistics
Matches: 113, Mismatches: 19, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
33 3 0.03
34 15 0.13
35 19 0.17
36 24 0.21
37 32 0.28
38 19 0.17
39 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (36 bp):
TTAAATAATATATTAAAAATCATAATATTTAATTTT
Found at i:547799 original size:24 final size:24
Alignment explanation
Indices: 547772--547817 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
547762 TCATATTATT
547772 TAATTA-TATATATAATTTATTAAA
1 TAATTATTATAT-TAATTTATTAAA
*
547796 TAATTATTATATTTATTTATTA
1 TAATTATTATATTAATTTATTA
547818 TTAAAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TAATTATTATATTAATTTATTAAA
Found at i:547850 original size:32 final size:31
Alignment explanation
Indices: 547811--547895 Score: 85
Period size: 31 Copynumber: 2.9 Consensus size: 31
547801 ATTATATTTA
547811 TTTATTATTAAAATT-ATATTTAAATTTTGTAT
1 TTTATTATT--AATTAATATTTAAATTTTGTAT
*
547843 TTTATTA-TAATTACATATTTAAATTTTTTAT
1 TTTATTATTAATTA-ATATTTAAATTTTGTAT
547874 TTT-TTA-T--TTAATATTT-AATTTT
1 TTTATTATTAATTAATATTTAAATTTT
547896 AAAATTATAT
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
26 6 0.12
27 6 0.12
28 3 0.06
29 4 0.08
30 4 0.08
31 20 0.40
32 7 0.14
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (31 bp):
TTTATTATTAATTAATATTTAAATTTTGTAT
Found at i:547861 original size:31 final size:27
Alignment explanation
Indices: 547826--547922 Score: 90
Period size: 27 Copynumber: 3.5 Consensus size: 27
547816 TATTAAAATT
547826 ATATTTAAATTTTGTATTTTATTATAATTA
1 ATATTTAAATTTTGTATTTT-TTAT--TTA
*
547856 CATATTTAAATTTTTTATTTTTTATTTA
1 -ATATTTAAATTTTGTATTTTTTATTTA
** * *
547884 ATATTT-AATTTTAAAATTATATATTTA
1 ATATTTAAATTTT-GTATTTTTTATTTA
547911 ATATTT-AATTTT
1 ATATTTAAATTTT
547923 AAAAATATAT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.10
27 28 0.47
28 3 0.05
30 4 0.07
31 19 0.32
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (27 bp):
ATATTTAAATTTTGTATTTTTTATTTA
Found at i:547888 original size:7 final size:7
Alignment explanation
Indices: 547878--547948 Score: 69
Period size: 7 Copynumber: 10.4 Consensus size: 7
547868 TTTTATTTTT
547878 TATTTAA
1 TATTTAA
547885 TATTTAA
1 TATTTAA
547892 T-TTTAA
1 TATTTAA
*
547898 -AATTATA
1 TATTTA-A
547905 TATTTAA
1 TATTTAA
547912 TATTTAA
1 TATTTAA
547919 T-TTTAA
1 TATTTAA
**
547925 -AAATATA
1 TATTTA-A
547932 TATTTAA
1 TATTTAA
547939 TATTTAA
1 TATTTAA
547946 TAT
1 TAT
547949 AATTAATTAG
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
6 15 0.29
7 30 0.58
8 7 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
TATTTAA
Found at i:547890 original size:27 final size:26
Alignment explanation
Indices: 547826--547946 Score: 89
Period size: 27 Copynumber: 4.3 Consensus size: 26
547816 TATTAAAATT
*
547826 ATATTTAAATTTTGTATTTTATTATAATTA
1 ATATTT-AATTTTATATTTT-TTAT--TTA
*
547856 CATATTTAAATTTTTTATTTTTTATTTA
1 -ATATTT-AATTTTATATTTTTTATTTA
* * *
547884 ATATTTAATTTTAAAATTATATATTTA
1 ATATTTAATTTT-ATATTTTTTATTTA
* * * *
547911 ATATTTAATTTTAAAAATATATATTTA
1 ATATTTAATTTT-ATATTTTTTATTTA
547938 ATATTTAAT
1 ATATTTAAT
547947 ATAATTAATT
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
26 6 0.07
27 51 0.61
28 3 0.04
30 4 0.05
31 19 0.23
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.59
Consensus pattern (26 bp):
ATATTTAATTTTATATTTTTTATTTA
Found at i:549711 original size:2 final size:2
Alignment explanation
Indices: 549704--549735 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
549694 ACGAGTATTC
549704 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
549736 ACAATAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:550035 original size:23 final size:22
Alignment explanation
Indices: 549998--550047 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
549988 TGCTCTTATA
* *
549998 TTTTTTTATTTTTTTAAAAATT
1 TTTTTTTAGTATTTTAAAAATT
*
550020 TATTTTTTAGTATTTTAATAATT
1 T-TTTTTTAGTATTTTAAAAATT
550043 TTTTT
1 TTTTT
550048 ATTAAGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTTTTTAGTATTTTAAAAATT
Found at i:550143 original size:27 final size:25
Alignment explanation
Indices: 550083--550143 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 25
550073 TAATATATTT
*
550083 TTTAATG-TTTATATAAAAATATTA
1 TTTAATGTTTTATATAAAAAAATTA
*
550107 TAT-AT-TTTTATATAATAAAAATTA
1 TTTAATGTTTTATATAA-AAAAATTA
550131 TTTAATGTATTTA
1 TTTAATGT-TTTA
550144 AATATGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
23 11 0.38
24 11 0.38
25 2 0.07
26 1 0.03
27 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (25 bp):
TTTAATGTTTTATATAAAAAAATTA
Found at i:550500 original size:3 final size:3
Alignment explanation
Indices: 550492--550529 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
550482 AATAAATTGT
550492 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
550530 TGCAAGAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:550861 original size:14 final size:14
Alignment explanation
Indices: 550842--550885 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
550832 TAAGTGTCAA
550842 TTTAGTATTAAATT
1 TTTAGTATTAAATT
*
550856 TTTAGTAATAAATT
1 TTTAGTATTAAATT
*
550870 TATTAGAATTAAATT
1 T-TTAGTATTAAATT
550885 T
1 T
550886 GTTTGATGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTAGTATTAAATT
Done.