Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000260.1 Hibiscus syriacus cultivar Beakdansim tig00000477_pilon, whole genome shotgun sequence
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: 5583615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 26
Found at i:441682 original size:52 final size:52
Alignment explanation
Indices: 441622--441735 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 52
441612 AAAAAAACAA
*
441622 AAGAAAAAAAATAGAAGAA-GA-AAAAAAATAGAAAAAGA-AAATGAAAATGA-AG
1 AAGAAAAAAAAT-GAA-AACGAGAAAAAAA-AGAAAAAGAGAAA-AAAAATGAGAG
*
441674 AAG-AAAAAAATGAAAACGAGAAAGAAAAGAAAAAGAGAAAAAAAATGAGAG
1 AAGAAAAAAAATGAAAACGAGAAAAAAAAGAAAAAGAGAAAAAAAATGAGAG
*
441725 ATGAAAAAAAA
1 AAGAAAAAAAA
441736 AATTCACTCG
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
49 2 0.04
50 21 0.39
51 21 0.39
52 10 0.19
ACGTcount: A:0.75, C:0.01, G:0.18, T:0.06
Consensus pattern (52 bp):
AAGAAAAAAAATGAAAACGAGAAAAAAAAGAAAAAGAGAAAAAAAATGAGAG
Found at i:441698 original size:21 final size:21
Alignment explanation
Indices: 441651--441701 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
441641 GAAAAAAAAT
* *
441651 AGAAA-AAGAAAATGAAAATG
1 AGAAAGAAAAAAATGAAAACG
441671 A-AGAAGAAAAAAATGAAAACG
1 AGA-AAGAAAAAAATGAAAACG
441692 AGAAAGAAAA
1 AGAAAGAAAA
441702 GAAAAAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 1 0.04
20 3 0.12
21 21 0.81
22 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.06
Consensus pattern (21 bp):
AGAAAGAAAAAAATGAAAACG
Found at i:441705 original size:17 final size:17
Alignment explanation
Indices: 441620--441717 Score: 82
Period size: 17 Copynumber: 5.8 Consensus size: 17
441610 GAAAAAAAAC
441620 AAAAGA-AAAAAAATAGA
1 AAAAGAGAAAAAAAT-GA
*
441637 AGAAGA-AAAAAAATAGA
1 AAAAGAGAAAAAAAT-GA
441654 AAAAGA-AAATGAAAATG-
1 AAAAGAGAAA--AAAATGA
*
441671 AAGA-AGAAAAAAATGA
1 AAAAGAGAAAAAAATGA
*
441687 AAACGAGAAAGAAAA-GA
1 AAAAGAGAAA-AAAATGA
441704 AAAAGAGAAAAAAA
1 AAAAGAGAAAAAAA
441718 ATGAGAGATG
Statistics
Matches: 69, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
15 6 0.09
16 7 0.10
17 46 0.67
18 5 0.07
19 5 0.07
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.05
Consensus pattern (17 bp):
AAAAGAGAAAAAAATGA
Found at i:441709 original size:50 final size:52
Alignment explanation
Indices: 441626--441734 Score: 129
Period size: 51 Copynumber: 2.1 Consensus size: 52
441616 AAACAAAAGA
*
441626 AAAAAAATAGAAGAAGAAAAAAAATAGAAAAAGA-AAATGAAAATGA-AGAAG
1 AAAAAAATAGAAGAAGAAAAAAAATAGAAAAAGAGAAA-AAAAATGAGAGAAG
* *
441677 AAAAAAAT-GAA-AACGAGAAAGAAA-AGAAAAAGAGAAAAAAAATGAGAGATG
1 AAAAAAATAGAAGAA-GA-AAAAAAATAGAAAAAGAGAAAAAAAATGAGAGAAG
441728 AAAAAAA
1 AAAAAAA
441735 AAATTCACTC
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
49 2 0.04
50 21 0.41
51 28 0.55
ACGTcount: A:0.74, C:0.01, G:0.18, T:0.06
Consensus pattern (52 bp):
AAAAAAATAGAAGAAGAAAAAAAATAGAAAAAGAGAAAAAAAATGAGAGAAG
Found at i:441718 original size:17 final size:17
Alignment explanation
Indices: 441610--441718 Score: 77
Period size: 17 Copynumber: 6.5 Consensus size: 17
441600 TTATAAGAAG
*
441610 GAAAAAAAA-CAAAAGA
1 GAAAAAAAAGAAAAAGA
*
441626 -AAAAAAATAGAAGAAGA
1 GAAAAAAA-AGAAAAAGA
441643 -AAAAAAATAGAAAAAGA
1 GAAAAAAA-AGAAAAAGA
* *
441660 -AAATGAAAATG-AAGA-A
1 GAAA--AAAAAGAAAAAGA
* *
441676 GAAAAAAATGAAAACGA
1 GAAAAAAAAGAAAAAGA
*
441693 GAAAGAAAAGAAAAAGA
1 GAAAAAAAAGAAAAAGA
441710 GAAAAAAAA
1 GAAAAAAAA
441719 TGAGAGATGA
Statistics
Matches: 75, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
15 13 0.17
16 4 0.05
17 53 0.71
18 1 0.01
19 4 0.05
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.05
Consensus pattern (17 bp):
GAAAAAAAAGAAAAAGA
Found at i:445953 original size:47 final size:45
Alignment explanation
Indices: 445859--445984 Score: 182
Period size: 47 Copynumber: 2.8 Consensus size: 45
445849 GTATGCATAC
* * *
445859 AAATAAGCTTACGAGCTTTTGGAAT-AATGGCAAGTCTATGGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATGGGTA
* *
445903 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATGGGTA
445950 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
445985 GGATTTTATA
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
44 23 0.31
45 11 0.15
46 1 0.01
47 39 0.53
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATGGGTA
Found at i:450881 original size:79 final size:79
Alignment explanation
Indices: 450750--450923 Score: 339
Period size: 79 Copynumber: 2.2 Consensus size: 79
450740 AATACGTGAA
450750 GTCACAAGATCAAGTTGCCGATATTTTTACCAAACCACTGAAAAGTGAAGACTTCATAAGATTAA
1 GTCACAAGATCAAGTTGCCGATATTTTTACCAAACCACTGAAAAGTGAAGACTTCATAAGATTAA
450815 GGAACTTACTAGGG
66 GGAACTTACTAGGG
*
450829 GTCACAAGATCAAGTTGCCGATATTTTTACCAAGCCACTGAAAAGTGAAGACTTCATAAGATTAA
1 GTCACAAGATCAAGTTGCCGATATTTTTACCAAACCACTGAAAAGTGAAGACTTCATAAGATTAA
450894 GGAACTTACTAGGG
66 GGAACTTACTAGGG
450908 GTCACAAGATCAAGTT
1 GTCACAAGATCAAGTT
450924 TAAGGGGGGT
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 94 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (79 bp):
GTCACAAGATCAAGTTGCCGATATTTTTACCAAACCACTGAAAAGTGAAGACTTCATAAGATTAA
GGAACTTACTAGGG
Found at i:453902 original size:43 final size:43
Alignment explanation
Indices: 453828--454010 Score: 228
Period size: 43 Copynumber: 4.3 Consensus size: 43
453818 GTGGCACCAT
* * * *
453828 TAAAAACAATAGAATTAGCGGCATTTATGGCAATAAATGCCAC
1 TAAAGACAAGAGAATTAGCGGCATTTGTGGCAATAAACGCCAC
* * * *
453871 TAAAGGCAAGAGAATTAGCAGCGTTTGTGGCAA-AAATGCCAC
1 TAAAGACAAGAGAATTAGCGGCATTTGTGGCAATAAACGCCAC
* *
453913 TAAA-A-AAGATAATTAGCGGCATCTGTGGCAATAAACGCCAC
1 TAAAGACAAGAGAATTAGCGGCATTTGTGGCAATAAACGCCAC
* **
453954 TAAAGATAAGAGAATTAGTTGCATTTGTGGCAATAAACGCCAC
1 TAAAGACAAGAGAATTAGCGGCATTTGTGGCAATAAACGCCAC
453997 TAAAGACAAGAGAA
1 TAAAGACAAGAGAA
454011 CAAACATCGC
Statistics
Matches: 120, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
40 22 0.18
41 12 0.10
42 14 0.12
43 72 0.60
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.21
Consensus pattern (43 bp):
TAAAGACAAGAGAATTAGCGGCATTTGTGGCAATAAACGCCAC
Found at i:453942 original size:83 final size:84
Alignment explanation
Indices: 453840--454000 Score: 234
Period size: 83 Copynumber: 1.9 Consensus size: 84
453830 AAAACAATAG
* * * *
453840 AATTAGCGGCATTTATGGCAATAAATGCCACTAAAGGCAAGAGAATTAGCAGCGTTTGTGGCAA-
1 AATTAGCGGCATCTATGGCAATAAACGCCACTAAAGACAAGAGAATTAGCAGCATTTGTGGCAAT
*
453904 AAATGCCACTAAAAAAGAT
66 AAACGCCACTAAAAAAGAT
* * **
453923 AATTAGCGGCATCTGTGGCAATAAACGCCACTAAAGATAAGAGAATTAGTTGCATTTGTGGCAAT
1 AATTAGCGGCATCTATGGCAATAAACGCCACTAAAGACAAGAGAATTAGCAGCATTTGTGGCAAT
453988 AAACGCCACTAAA
66 AAACGCCACTAAA
454001 GACAAGAGAA
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
83 56 0.82
84 12 0.18
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (84 bp):
AATTAGCGGCATCTATGGCAATAAACGCCACTAAAGACAAGAGAATTAGCAGCATTTGTGGCAAT
AAACGCCACTAAAAAAGAT
Found at i:455551 original size:21 final size:20
Alignment explanation
Indices: 455517--455555 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
455507 AAAACTCACA
* *
455517 CAAACAACTTTTATTGAAACT
1 CAAACAAATATTA-TGAAACT
455538 CAAACAAATATTATGAAA
1 CAAACAAATATTATGAAA
455556 GCACTCTCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.28
Consensus pattern (20 bp):
CAAACAAATATTATGAAACT
Found at i:455797 original size:29 final size:29
Alignment explanation
Indices: 455754--455836 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
455744 CTCACCTAAC
455754 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
455784 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
*
455813 TAAATGATGTAAGCAATGAAATCA
1 TAAATGATGTAAGCAATGACATCA
455837 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:459217 original size:15 final size:15
Alignment explanation
Indices: 459197--459226 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
459187 TTTTCTCATA
459197 ATTGTTGTTGGAATT
1 ATTGTTGTTGGAATT
*
459212 ATTGTTGTTGTAATT
1 ATTGTTGTTGGAATT
459227 CCAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (15 bp):
ATTGTTGTTGGAATT
Found at i:460545 original size:29 final size:29
Alignment explanation
Indices: 460509--460584 Score: 134
Period size: 29 Copynumber: 2.6 Consensus size: 29
460499 AACTAAATTG
460509 ATGTAAGCAATGACATCATTACTTAAATA
1 ATGTAAGCAATGACATCATTACTTAAATA
* *
460538 ATGTAAGCAATGACATCTTTACTTAAATG
1 ATGTAAGCAATGACATCATTACTTAAATA
460567 ATGTAAGCAATGACATCA
1 ATGTAAGCAATGACATCA
460585 ATTTAGTTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (29 bp):
ATGTAAGCAATGACATCATTACTTAAATA
Found at i:474817 original size:18 final size:18
Alignment explanation
Indices: 474796--474830 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
474786 AGAAAAGAAA
*
474796 TTAATACTAAAAAAAATT
1 TTAAAACTAAAAAAAATT
*
474814 TTAAAACTAAAATAAAT
1 TTAAAACTAAAAAAAAT
474831 GTAATAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAAACTAAAAAAAATT
Found at i:475947 original size:26 final size:26
Alignment explanation
Indices: 475912--476009 Score: 119
Period size: 26 Copynumber: 3.8 Consensus size: 26
475902 TGGCAGCAGT
*
475912 GGTGGCTGTTGAGTGGTCCAAGCGAC
1 GGTGGCTGTTGAGTGGTCCAAGCGGC
* ** *
475938 GGTGGTTGTTGAGCAGTCCAAGCGGT
1 GGTGGCTGTTGAGTGGTCCAAGCGGC
*
475964 GGTGGCTGATGAGTGGTCCAAGCGGC
1 GGTGGCTGTTGAGTGGTCCAAGCGGC
*
475990 GGTGGC--ATGAGTGGTCCAAG
1 GGTGGCTGTTGAGTGGTCCAAG
476010 TGGTGGCGGT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
24 14 0.23
26 48 0.77
ACGTcount: A:0.16, C:0.17, G:0.44, T:0.22
Consensus pattern (26 bp):
GGTGGCTGTTGAGTGGTCCAAGCGGC
Found at i:476233 original size:18 final size:18
Alignment explanation
Indices: 476206--476247 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
476196 TAAATCTGTA
476206 AAATAA-AAT-ATAATTAT
1 AAATAATAATAATAA-TAT
476223 AAATAATAATAATAATAT
1 AAATAATAATAATAATAT
476241 AAATAAT
1 AAATAAT
476248 GACGGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAATAATAATAATAT
Found at i:477615 original size:42 final size:41
Alignment explanation
Indices: 477569--477720 Score: 157
Period size: 42 Copynumber: 3.7 Consensus size: 41
477559 CACAACGCCG
* * * *
477569 CTAAAGGTTATGTTTTTTAGCGGTGTTTTTTTACAAACGCAT
1 CTAAAGGTAATGATATTTAGCGGCGTTTTTTTACAAACGC-T
** * *
477611 CTAAAGGTAATGATA-TTAATGGC--ATTTTTACAAACGCCG
1 CTAAAGGTAATGATATTTAGCGGCGTTTTTTTACAAACG-CT
* *
477650 CTAAAGGTAATGATATTTAGCGGCATTTTTTTACAATCGCT
1 CTAAAGGTAATGATATTTAGCGGCGTTTTTTTACAAACGCT
*
477691 GCTAAAGGTTATGATATTTAGCGGCGTTTT
1 -CTAAAGGTAATGATATTTAGCGGCGTTTT
477721 CTCCAAACGC
Statistics
Matches: 90, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
39 27 0.30
40 7 0.08
41 6 0.07
42 50 0.56
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (41 bp):
CTAAAGGTAATGATATTTAGCGGCGTTTTTTTACAAACGCT
Found at i:477647 original size:39 final size:39
Alignment explanation
Indices: 477595--477708 Score: 131
Period size: 39 Copynumber: 2.8 Consensus size: 39
477585 TTAGCGGTGT
*
477595 TTTTTTACAAACGCATCTAAAGGTAATGATATTAATGGCA
1 TTTTTTACAAACGC-TCTAAAGGTAATGATATTAACGGCA
* *
477635 -TTTTTACAAACGCCGCTAAAGGTAATGATATTTAGCGGCA
1 TTTTTTACAAACG-CTCTAAAGGTAATGATA-TTAACGGCA
* *
477675 TTTTTTTACAATCGCTGCTAAAGGTTATGATATT
1 -TTTTTTACAAACGCT-CTAAAGGTAATGATATT
477709 TAGCGGCGTT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
39 27 0.43
40 8 0.13
41 3 0.05
42 25 0.40
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (39 bp):
TTTTTTACAAACGCTCTAAAGGTAATGATATTAACGGCA
Found at i:477697 original size:81 final size:83
Alignment explanation
Indices: 477562--477735 Score: 219
Period size: 81 Copynumber: 2.1 Consensus size: 83
477552 TGTCGTTCAC
* * * **
477562 AACGCCGCTAAAGGTTATGTTTTTTAGCGGTGTTTTTTTACAAACGCATCTAAAGGTAATGATA-
1 AACGCCGCTAAAGGTAATGATATTTAGCGGCATTTTTTTACAAACGCATCTAAAGGTAATGATAT
*
477626 TTAATGGCATTTT-TACA
66 TTAACGGCATTTTCTACA
* *
477643 AACGCCGCTAAAGGTAATGATATTTAGCGGCATTTTTTTACAATCGC-TGCTAAAGGTTATGATA
1 AACGCCGCTAAAGGTAATGATATTTAGCGGCATTTTTTTACAAACGCAT-CTAAAGGTAATGATA
* * *
477707 TTTAGCGGCGTTTTCTCCA
65 TTTAACGGCATTTTCTACA
477726 AACGCCGCTA
1 AACGCCGCTA
477736 TTTATCTTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
80 1 0.01
81 55 0.70
82 10 0.13
83 13 0.16
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (83 bp):
AACGCCGCTAAAGGTAATGATATTTAGCGGCATTTTTTTACAAACGCATCTAAAGGTAATGATAT
TTAACGGCATTTTCTACA
Found at i:477810 original size:44 final size:42
Alignment explanation
Indices: 477754--477838 Score: 107
Period size: 44 Copynumber: 2.0 Consensus size: 42
477744 TTCTTTTGTG
*
477754 GCATTTGGTCCCAAAAACGCCGCTAAATGTTCTGACATATAGTA
1 GCATTTGGTCCCAAAAACGCCGCT--ATGTTATGACATATAGTA
* * * *
477798 GCATTTGTTCCCAAAGACGTCGCTATGTTATGTCATATAGT
1 GCATTTGGTCCCAAAAACGCCGCTATGTTATGACATATAGT
477839 GGTTTTTGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 15 0.42
44 21 0.58
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (42 bp):
GCATTTGGTCCCAAAAACGCCGCTATGTTATGACATATAGTA
Found at i:481627 original size:121 final size:118
Alignment explanation
Indices: 481420--481897 Score: 318
Period size: 121 Copynumber: 3.9 Consensus size: 118
481410 AAGTACGATT
* * * * * *
481420 ATTTAGCAGCGTTTGTATAAAAACTCCACCAAAGTACGAGTTTTTGGCGGCATTTGTACACAAAC
1 ATTTAGCAACGTTTATATAAAAACGCCACTAAAGTACGAGTATTTGAC-G--TTTGTACACAAAC
* *
481485 ACCACTAAAGTACAATATTTAGCTGTGTTTATAAAAAAAATGCCACTAAACTATGAGC
63 ACCACTAAAGTACAATATTTAGCAGCGTTTAT-AAAAAAATGCCACTAAACTAT-AGC
* * * * * * *
481543 ATTTAGTAACGTTTGTGCTTAAAACGCCACTAAAGTACGTGTATTTGACGTTTGTATACAAACGC
1 ATTTAGCAACGTTTAT-ATAAAAACGCCACTAAAGTACGAGTATTTGACGTTTGTACACAAACAC
* * * * * * *
481608 CATTAAAGTATAGTTTTTAGCAGCGTTTATATAAAAATGCCACTAAAGTATAGT
65 CACTAAAGTACAATATTTAGCAGCGTTTATAAAAAAATGCCACTAAACTATAGC
* * * * ** * *
481662 GTTTAGCACCGTTTATATAAAAATGCCACTAAAGTACGAGTATTTAGTGGCGTTTGTTTAAAAAT
1 ATTTAGCAACGTTTATATAAAAACGCCACTAAAGTACGAGTA-TT--TGACGTTTGTACACAAAC
* * * * * * * **
481727 ACCACTAAAGTACAAGTCTTTGGC-GACGTTTGTATACAAACGCCACTAAAGTATAAT
63 ACCACTAAAGTACAA-TATTTAGCAG-CGTTTATAAAAAAATGCCACTAAACTATAGC
* ** * * *
481784 ATTTAGCGATATTTATAT-AAAACGACACTAAAGTATG-GATATTT-ACCGGCATTTGTGCTTA-
1 ATTTAGCAACGTTTATATAAAAACGCCACTAAAGTACGAG-TATTTGA-C-G--TTTGTAC--AC
** * *
481845 AAATGCCACTAAAGTACAATATTTAGCGGCGTTTATATAAAAATGCCACTAAA
59 AAACACCACTAAAGTACAATATTTAGCAGCGTTTATAAAAAAATGCCACTAAA
481898 GTACAAGTAT
Statistics
Matches: 282, Mismatches: 59, Indels: 30
0.76 0.16 0.08
Matches are distributed among these distances:
118 24 0.09
119 17 0.06
120 22 0.08
121 113 0.40
122 65 0.23
123 16 0.06
124 25 0.09
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (118 bp):
ATTTAGCAACGTTTATATAAAAACGCCACTAAAGTACGAGTATTTGACGTTTGTACACAAACACC
ACTAAAGTACAATATTTAGCAGCGTTTATAAAAAAATGCCACTAAACTATAGC
Found at i:481655 original size:40 final size:40
Alignment explanation
Indices: 481394--481939 Score: 291
Period size: 41 Copynumber: 13.4 Consensus size: 40
481384 TATATATATA
* * * *
481394 TATATAAATACCACTAAAGTACGATTATTTAGCAGCGTTTG
1 TATAAAAATGCCACTAAAGTA-TAGTATTTAGCAGCGTTTG
* * * * * *
481435 TATAAAAACT-CCACCAAAGTACGAGTTTTTGGCGGCATTTG
1 TATAAAAA-TGCCACTAAAGTA-TAGTATTTAGCAGCGTTTG
* * ** * * * * *
481476 TACACAAACACCACTAAAGTACAATATTTAGCTGTGTTTA
1 TATAAAAATGCCACTAAAGTATAGTATTTAGCAGCGTTTG
* * * * *
481516 TAAAAAAAATGCCACTAAACTATGAGCATTTAGTAACGTTTG
1 T-ATAAAAATGCCACTAAAGTAT-AGTATTTAGCAGCGTTTG
* * *
481558 TGCTTAAAACGCCACTAAAGTACGT-GTATTT-G-A-CGTTTG
1 T-ATAAAAATGCCACTAAAGTA--TAGTATTTAGCAGCGTTTG
* * * * *
481597 TATACAAACGCCATTAAAGTATAGTTTTTAGCAGCGTTTA
1 TATAAAAATGCCACTAAAGTATAGTATTTAGCAGCGTTTG
* * *
481637 TATAAAAATGCCACTAAAGTATAGTGTTTAGCACCGTTTA
1 TATAAAAATGCCACTAAAGTATAGTATTTAGCAGCGTTTG
* **
481677 TATAAAAATGCCACTAAAGTACGAGTATTTAGTGGCGTTTG
1 TATAAAAATGCCACTAAAGTA-TAGTATTTAGCAGCGTTTG
* * * * *
481718 TTTAAAAATACCACTAAAGTACAAGTCTTTGGC-GACGTTTG
1 TATAAAAATGCCACTAAAGTA-TAGTATTTAGCAG-CGTTTG
* * * *
481759 TATACAAACGCCACTAAAGTATAATATTTAGC-G-ATATT-
1 TATAAAAATGCCACTAAAGTATAGTATTTAGCAGCGT-TTG
* * * * * *
481797 TATATAAAACGACACTAAAGTATGGATATTTACCGGCATTTG
1 TATA-AAAATGCCACTAAAGTATAG-TATTTAGCAGCGTTTG
* * * * * *
481839 TGCTTAAAATGCCACTAAAGTACAATATTTAGCGGCGTTTA
1 T-ATAAAAATGCCACTAAAGTATAGTATTTAGCAGCGTTTG
* * * *
481880 TATAAAAATGCCACTAAAGTACAAGTATCTACCGGCGTTTG
1 TATAAAAATGCCACTAAAGTA-TAGTATTTAGCAGCGTTTG
* *
481921 TTTAAAAAAGGCCACTAAA
1 TAT-AAAAATGCCACTAAA
481940 AATTCCGCAA
Statistics
Matches: 389, Mismatches: 95, Indels: 41
0.74 0.18 0.08
Matches are distributed among these distances:
36 1 0.00
37 5 0.01
38 22 0.06
39 26 0.07
40 108 0.28
41 160 0.41
42 65 0.17
43 1 0.00
44 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (40 bp):
TATAAAAATGCCACTAAAGTATAGTATTTAGCAGCGTTTG
Found at i:481787 original size:81 final size:80
Alignment explanation
Indices: 481589--481905 Score: 255
Period size: 81 Copynumber: 3.9 Consensus size: 80
481579 ACGTGTATTT
* * *
481589 GACGTTTGTATACAAACGCCATTAAAGTATAGTTTTTAGCAGCGTTTATATAAAAATGCCACTAA
1 GACGTTTGTATACAAACGCCACTAAAGTATAGTATTTAGCAGCGTTTATATAAAAATACCACTAA
* *
481654 AGTATAGTGTTTAGC
66 AGTAAAGTCTTTAGC
* * * * ** * *
481669 -ACCGTTTATATAAAAATGCCACTAAAGTACGAGTATTTAGTGGCGTTTGTTTAAAAATACCACT
1 GA-CGTTTGTATACAAACGCCACTAAAGTA-TAGTATTTAGCAGCGTTTATATAAAAATACCACT
*
481733 AAAGTACAAGTCTTTGGC
64 AAAGTA-AAGTCTTTAGC
* ** **
481751 GACGTTTGTATACAAACGCCACTAAAGTATAATATTTAGC-GATATTTATATAAAACGA-CACTA
1 GACGTTTGTATACAAACGCCACTAAAGTATAGTATTTAGCAG-CGTTTATATAAAAATACCACTA
** * *
481814 AAGTATGGATATTTACC
65 AAGTAAAG-TCTTTAGC
* * * * * * * *
481831 GGCATTTGTGCTTA-AAATGCCACTAAAGTACAATATTTAGCGGCGTTTATATAAAAATGCCACT
1 GACGTTTGT--ATACAAACGCCACTAAAGTATAGTATTTAGCAGCGTTTATATAAAAATACCACT
481895 AAAGTACAAGT
64 AAAGTA-AAGT
481906 ATCTACCGGC
Statistics
Matches: 183, Mismatches: 43, Indels: 20
0.74 0.17 0.08
Matches are distributed among these distances:
79 2 0.01
80 46 0.25
81 87 0.48
82 46 0.25
83 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (80 bp):
GACGTTTGTATACAAACGCCACTAAAGTATAGTATTTAGCAGCGTTTATATAAAAATACCACTAA
AGTAAAGTCTTTAGC
Found at i:482486 original size:15 final size:15
Alignment explanation
Indices: 482452--482493 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
482442 AATATATTCA
*
482452 CTTGATTTAA-TTCC
1 CTTGATTTAAGCTCC
*
482466 CTTGATTTAAGCTCT
1 CTTGATTTAAGCTCC
*
482481 CTTGATTTGAGCT
1 CTTGATTTAAGCT
482494 TAATTAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.48
Consensus pattern (15 bp):
CTTGATTTAAGCTCC
Found at i:484432 original size:3 final size:3
Alignment explanation
Indices: 484424--484502 Score: 61
Period size: 3 Copynumber: 26.0 Consensus size: 3
484414 TCCATTTCAT
* * *
484424 TTA TTA TTA TT- TTA TTA TTTA ATA TTA TTA TTA TTT TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
** * * *
484469 ACA TTA TTA TTTA TTA TTA ATA ATA ATA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
484503 ATACTATTAC
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
2 2 0.03
3 55 0.87
4 6 0.10
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:484451 original size:21 final size:22
Alignment explanation
Indices: 484425--484501 Score: 86
Period size: 22 Copynumber: 3.5 Consensus size: 22
484415 CCATTTCATT
484425 TATTATTATTTTATTATT-TAA
1 TATTATTATTTTATTATTATAA
*
484446 TATTATTATTATTTTTATTAATAA
1 TATTATTATT-TTATTATT-ATAA
*
484470 CATTATTA-TTTATTATTAATAA
1 TATTATTATTTTATTATT-ATAA
*
484492 TAATATTATT
1 TATTATTATT
484502 AATACTATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
21 10 0.21
22 25 0.53
23 2 0.04
24 10 0.21
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTATTATTTTATTATTATAA
Found at i:484478 original size:37 final size:37
Alignment explanation
Indices: 484435--484505 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
484425 TATTATTATT
* * * *
484435 TTATTATTTAATATTATTATTATTTTTATTAATAACA
1 TTATTATTTAATATTAATAATAATATTATTAATAACA
*
484472 TTATTATTTATTATTAATAATAATATTATTAATA
1 TTATTATTTAATATTAATAATAATATTATTAATA
484506 CTATTACATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (37 bp):
TTATTATTTAATATTAATAATAATATTATTAATAACA
Found at i:484671 original size:34 final size:34
Alignment explanation
Indices: 484628--484694 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
484618 TATCCCATGC
484628 ACCCAGCCGCTGCTTCTATCAACCGTTGGATCTA
1 ACCCAGCCGCTGCTTCTATCAACCGTTGGATCTA
484662 ACCCAGCCGCTGCTTCTATCAACCGTTGGATCT
1 ACCCAGCCGCTGCTTCTATCAACCGTTGGATCT
484695 GATTAGATCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.19, C:0.36, G:0.18, T:0.27
Consensus pattern (34 bp):
ACCCAGCCGCTGCTTCTATCAACCGTTGGATCTA
Found at i:485783 original size:2 final size:2
Alignment explanation
Indices: 485776--485820 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
485766 TTTGAGTCAC
485776 AT AT AT AT AT AT AT AT AT AT AT AT A- 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
485817 AT AT
1 AT AT
485821 TTGATTAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:492847 original size:24 final size:24
Alignment explanation
Indices: 492815--492886 Score: 135
Period size: 24 Copynumber: 3.0 Consensus size: 24
492805 TTGGGGAATT
492815 TTAAAGGCCACTTCAGACAGATCC
1 TTAAAGGCCACTTCAGACAGATCC
492839 TTAAAGGCCACTTCAGACAGATCC
1 TTAAAGGCCACTTCAGACAGATCC
*
492863 TTAAAGGCCACTTCAGACAAATCC
1 TTAAAGGCCACTTCAGACAGATCC
492887 ATATGAGGCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.21
Consensus pattern (24 bp):
TTAAAGGCCACTTCAGACAGATCC
Found at i:494028 original size:54 final size:55
Alignment explanation
Indices: 493933--494036 Score: 156
Period size: 54 Copynumber: 1.9 Consensus size: 55
493923 ATTAACAAAC
493933 ATCTGTACAGAAGCCACAAGAAAATGATGAATATGCTGTCAAATATTTTACGATT
1 ATCTGTACAGAAGCCACAAGAAAATGATGAATATGCTGTCAAATATTTTACGATT
* * * * *
493988 ATCTGTGCAGAAGCCAC-AGGAAATGATGAATGTGTTGTCAAATGTTTTA
1 ATCTGTACAGAAGCCACAAGAAAATGATGAATATGCTGTCAAATATTTTA
494037 TGAACCAGTG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
54 28 0.64
55 16 0.36
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (55 bp):
ATCTGTACAGAAGCCACAAGAAAATGATGAATATGCTGTCAAATATTTTACGATT
Found at i:495250 original size:47 final size:47
Alignment explanation
Indices: 495101--495964 Score: 1018
Period size: 47 Copynumber: 18.7 Consensus size: 47
495091 TTATTTCCTA
* * *
495101 CATCCGTAAGACCTTCAGTGCATGATGTTTTC-AAAA-CCTTTGGGT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
** *
495146 CATCTGTAAGACCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGGT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
** * * *
495191 CATCTGTAAGACCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
* *
495238 CATCCATAAGACCTTCAGTGCATGATGTTTTC-AAAA-CCTTCAGGT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
** *
495283 CATCTGTAAGACCTAT-AGTGCAGGATGTTTTCAAAAAGCTTTCGGGT
1 CATCCATAAGACCT-TCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
**
495330 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCATGT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
*
495377 CATCCATAAGACCTTCAGTGCAAGATGTTTTCAAAAAGCCTTCGGGT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
** * * * *
495424 CATTTATAAGACCTACAGTGCAGGATGTTTTCAAAAAACATTTGGGT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
* * * *
495471 TATCCATAAGACCTTCAGTGCAAGATGTTTTTAAAAAGCTTTCGGGT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
*
495518 CATCCATAAGACCTTCAGTGCAGGATGTTTTTAAAAAGCCTTCGGGT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
*
495565 AATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
*
495612 CATCCATAAGACCTTCAGTGCAGGATATTTTCAAAAAGCCTTCGGGT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
*
495659 CATCCATAAGACCTTCAGTGCAAGATGTTTTCAAAAAGCCTTCGGGT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
** * *
495706 CATCTTTAAGACCTTCAGTGCAAGATG--TT---AAAGTCCTTCGGGC
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAG-CCTTCGGGT
* ** ** *
495749 CATCCATAAGACCTACAGTGCAGGATGTTTTCTTAATTCCTTCGGAT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
** * *
495796 CATCTGTAAGACCTTCAGTGTAAGATG--TT---AAAGTCCTTCGGG-
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAG-CCTTCGGGT
*** *
495838 CAATCCATAAGACCTTCAGTGCAGGATGTTTTTTTTAAAGCCTTCAGGT
1 C-ATCCATAAGACCTTCAGTGCAGGATG-TTTTCAAAAAGCCTTCGGGT
* *
495887 CATCTATAAGACCTTCAGTGCAAGATG--TT---AAAGTCCTTCGGGT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAG-CCTTCGGGT
* *
495930 CATCCATAAGACCTTCTGTGCAGGTTGTTTTCAAA
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAA
495965 GGAGATTTTA
Statistics
Matches: 714, Mismatches: 78, Indels: 51
0.85 0.09 0.06
Matches are distributed among these distances:
42 11 0.02
43 91 0.13
45 118 0.17
46 16 0.02
47 439 0.61
48 34 0.05
49 5 0.01
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (47 bp):
CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
Found at i:496288 original size:18 final size:18
Alignment explanation
Indices: 496265--496308 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
496255 TTTCTCTATT
496265 TTATTTATAGTTA-TTTTA
1 TTATTTATA-TTATTTTTA
496283 TTATTTAATATTATTTTTA
1 TTATTT-ATATTATTTTTA
496302 TT-TTTAT
1 TTATTTAT
496309 TAATAACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 2 0.08
18 12 0.50
19 10 0.42
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
TTATTTATATTATTTTTA
Found at i:496306 original size:25 final size:25
Alignment explanation
Indices: 496294--496346 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
496284 TATTTAATAT
*
496294 TATT-TTTATTTTTATTAATAACAT
1 TATTGTTTATTTTTATTAATAATAT
* *
496318 TATTGTTTATTATTAATAATAATAT
1 TATTGTTTATTTTTATTAATAATAT
496343 TATT
1 TATT
496347 AATACTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TATTGTTTATTTTTATTAATAATAT
Found at i:496799 original size:11 final size:11
Alignment explanation
Indices: 496783--496815 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
496773 AATAGAAACG
496783 AAGAACGAAGC
1 AAGAACGAAGC
496794 AAGAACGAAGC
1 AAGAACGAAGC
496805 AAGAACGAAGC
1 AAGAACGAAGC
496816 CACACCAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.55, C:0.18, G:0.27, T:0.00
Consensus pattern (11 bp):
AAGAACGAAGC
Found at i:497303 original size:14 final size:14
Alignment explanation
Indices: 497286--497328 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
497276 ATCATTTCAA
497286 TTTAGTCTTTATAT
1 TTTAGTCTTTATAT
*
497300 TTTA---TTTATAA
1 TTTAGTCTTTATAT
497311 TTTAGTCTTTATAT
1 TTTAGTCTTTATAT
497325 TTTA
1 TTTA
497329 TTTATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
11 10 0.42
14 14 0.58
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.65
Consensus pattern (14 bp):
TTTAGTCTTTATAT
Found at i:497313 original size:25 final size:25
Alignment explanation
Indices: 497284--497341 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
497274 TAATCATTTC
497284 AATTTAGTCTTTATATTTTATTTAT
1 AATTTAGTCTTTATATTTTATTTAT
497309 AATTTAGTCTTTATATTTTATTTAT
1 AATTTAGTCTTTATATTTTATTTAT
497334 AATTTAGT
1 AATTTAGT
497342 AATCACCTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.62
Consensus pattern (25 bp):
AATTTAGTCTTTATATTTTATTTAT
Found at i:497682 original size:24 final size:24
Alignment explanation
Indices: 497655--497703 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
497645 ATATATATAT
497655 ATATATATATATGATTAAATATTA
1 ATATATATATATGATTAAATATTA
* * **
497679 ATATTTATTTATTTTTAAATATTA
1 ATATATATATATGATTAAATATTA
497703 A
1 A
497704 GAGATGATTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
ATATATATATATGATTAAATATTA
Found at i:500604 original size:29 final size:29
Alignment explanation
Indices: 500564--500619 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
500554 TAAACATTAA
500564 TTTTATTCATTTATATTTCTACTCTTTAC
1 TTTTATTCATTTATATTTCTACTCTTTAC
*
500593 TTTTATGT-ATTTATATTTCTATTCTTT
1 TTTTAT-TCATTTATATTTCTACTCTTT
500620 TATTTATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.20, C:0.12, G:0.02, T:0.66
Consensus pattern (29 bp):
TTTTATTCATTTATATTTCTACTCTTTAC
Found at i:500627 original size:4 final size:4
Alignment explanation
Indices: 500618--500656 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
500608 TTTCTATTCT
*
500618 TTTA TTTA TTTA TTTA TTTA TTGGTA TTTA TTTT TTTA T
1 TTTA TTTA TTTA TTTA TTTA TT--TA TTTA TTTA TTTA T
500657 CTAATATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 27 0.87
6 4 0.13
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:501428 original size:16 final size:16
Alignment explanation
Indices: 501407--501438 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
501397 TGGCGACTCC
501407 AAAGCATTTCCTTAAA
1 AAAGCATTTCCTTAAA
501423 AAAGCATTTCCTTAAA
1 AAAGCATTTCCTTAAA
501439 CAACATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (16 bp):
AAAGCATTTCCTTAAA
Found at i:503455 original size:12 final size:13
Alignment explanation
Indices: 503430--503472 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
503420 TTCTTGTATT
503430 TTTGCATCTTTGCA
1 TTTGCA-CTTTGCA
503444 TTTGCA-TTTGCA
1 TTTGCACTTTGCA
*
503456 TTCGCATCTTTGCA
1 TTTGCA-CTTTGCA
503470 TTT
1 TTT
503473 TTACGTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 11 0.44
14 14 0.56
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.51
Consensus pattern (13 bp):
TTTGCACTTTGCA
Found at i:506116 original size:7 final size:7
Alignment explanation
Indices: 506104--506194 Score: 85
Period size: 7 Copynumber: 12.4 Consensus size: 7
506094 CTCATTCATT
506104 AAAAAAG
1 AAAAAAG
506111 AAAAAAG
1 AAAAAAG
506118 AAGAAAAAG
1 -A-AAAAAG
*
506127 AAAATAG
1 AAAAAAG
506134 ATGAAAAAG
1 A--AAAAAG
506143 AAGAAAA-
1 AA-AAAAG
*
506150 AGAAAAG
1 AAAAAAG
* *
506157 GAAAAGG
1 AAAAAAG
*
506164 AAATAAG
1 AAAAAAG
506171 AAAAAAG
1 AAAAAAG
506178 AAAAAAG
1 AAAAAAG
506185 AAAAAAG
1 AAAAAAG
506192 AAA
1 AAA
506195 TTGAATCAAG
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
6 4 0.06
7 46 0.68
8 6 0.09
9 12 0.18
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:506124 original size:9 final size:9
Alignment explanation
Indices: 506112--506153 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
506102 TTAAAAAAGA
506112 AAAAAGAAG
1 AAAAAGAAG
506121 AAAAAG-A-
1 AAAAAGAAG
* *
506128 AAATAGATG
1 AAAAAGAAG
506137 AAAAAGAAG
1 AAAAAGAAG
506146 AAAAAGAA
1 AAAAAGAA
506154 AAGGAAAAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
7 5 0.19
8 1 0.04
9 21 0.78
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:506127 original size:6 final size:6
Alignment explanation
Indices: 506105--506194 Score: 60
Period size: 6 Copynumber: 14.5 Consensus size: 6
506095 TCATTCATTA
* * *
506105 AAAAAG -AAAA- AAGAAG AAAAAG AAAATAG ATGAAA- AAGAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA-AG A-AAAAG AAAAAG AAAAAG
* *
506152 AAAAGG AAAAGG AAATAAG AAAAAAG AAAAAAG AAAAAAG AAA
1 AAAAAG AAAAAG AAA-AAG -AAAAAG -AAAAAG -AAAAAG AAA
506195 TTGAATCAAG
Statistics
Matches: 69, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
5 9 0.13
6 32 0.46
7 23 0.33
8 5 0.07
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:507772 original size:101 final size:102
Alignment explanation
Indices: 507621--507816 Score: 288
Period size: 101 Copynumber: 1.9 Consensus size: 102
507611 AAGGTCTATA
* * * *
507621 TAATCCATGTGGGGTATCTTTAAGACTCACATCAGTAGAAAAATATAGAAGTAATCCATGTAGGG
1 TAATCCATGTGGGGTATCTTGAAGACTCACATCAGCAGAAAAAGACAGAAGTAATCCATGTAGGG
*
507686 CATCTTGAAGGCTCACATCAACATGAAAAGAAAGAAG
66 CATCTTGAAGGCTCACACCAACATGAAAAGAAAGAAG
* * *
507723 TAATCCATGT-GGGTATCTTGAAGGCTCACATCTGCATG-AAAAGACAGAAGTAATCCATGTGGG
1 TAATCCATGTGGGGTATCTTGAAGACTCACATCAGCA-GAAAAAGACAGAAGTAATCCATGTAGG
*
507786 GCATCTTGAAGGCTCACACCAGCATGAAAAG
65 GCATCTTGAAGGCTCACACCAACATGAAAAG
507817 GTTGAGATAT
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
101 73 0.87
102 11 0.13
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (102 bp):
TAATCCATGTGGGGTATCTTGAAGACTCACATCAGCAGAAAAAGACAGAAGTAATCCATGTAGGG
CATCTTGAAGGCTCACACCAACATGAAAAGAAAGAAG
Found at i:507816 original size:51 final size:51
Alignment explanation
Indices: 507621--507816 Score: 263
Period size: 51 Copynumber: 3.9 Consensus size: 51
507611 AAGGTCTATA
* * * *
507621 TAATCCATGTGGGGTATCTTTAAGACTCACATCAGTA-GAAAA-ATATAGAAG
1 TAATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGA-A-AGAAG
* *
507672 TAATCCATGTAGGGCATCTTGAAGGCTCACATCAACATGAAAAGAAAGAAG
1 TAATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGAAAGAAG
* * *
507723 TAATCCATGT-GGGTATCTTGAAGGCTCACATCTGCATGAAAAGACAGAAG
1 TAATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGAAAGAAG
*
507773 TAATCCATGTGGGGCATCTTGAAGGCTCACACCAGCATGAAAAG
1 TAATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAG
507817 GTTGAGATAT
Statistics
Matches: 129, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
50 46 0.36
51 76 0.59
52 6 0.05
53 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (51 bp):
TAATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGAAAGAAG
Found at i:508383 original size:54 final size:54
Alignment explanation
Indices: 508277--508388 Score: 161
Period size: 54 Copynumber: 2.1 Consensus size: 54
508267 CAATTATTGA
* ** * * *
508277 GAACATCTGTGCAGAAACCACAGGAAGTGATGAATGTGTTGTCAAATGTTTTAT
1 GAACATCTGTGCAGAAACCACAAGAAAAGATGAATGTGTTGCCAAATATTTTAC
*
508331 GAACATCTGTGCAGAAACCACAAGAAAAGATGAATGTGTTGCCAATTATTTTAC
1 GAACATCTGTGCAGAAACCACAAGAAAAGATGAATGTGTTGCCAAATATTTTAC
508385 GAAC
1 GAAC
508389 CAGTTATTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (54 bp):
GAACATCTGTGCAGAAACCACAAGAAAAGATGAATGTGTTGCCAAATATTTTAC
Found at i:509619 original size:73 final size:73
Alignment explanation
Indices: 509497--509830 Score: 587
Period size: 73 Copynumber: 4.6 Consensus size: 73
509487 GGATGTTTTC
* * *
509497 AAATAGCAATTTATGTCACTTGAGATTGTTTTTCTTAAAACAAAATGTTTCTCGCTAGAGAAAGT
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCGCTGGAGAAAGT
*
509562 TTCACTTG
66 TTCACTCG
*
509570 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAATAAATTGTTTCTCGCTGGAGAAAGT
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCGCTGGAGAAAGT
*
509635 TTCACTTG
66 TTCACTCG
509643 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCGCTGGAGAAAGT
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCGCTGGAGAAAGT
509708 TTCACTCG
66 TTCACTCG
509716 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCGCTGGAGAAAGT
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCGCTGGAGAAAGT
509781 TTCACTCG
66 TTCACTCG
* * *
509789 AAATAGCAATTTGTCTCACCTGAAATTGTTTTTCTTAAAACA
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
509831 TTTCCATATA
Statistics
Matches: 252, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 252 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (73 bp):
AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCGCTGGAGAAAGT
TTCACTCG
Found at i:509901 original size:39 final size:39
Alignment explanation
Indices: 509842--510131 Score: 341
Period size: 39 Copynumber: 7.4 Consensus size: 39
509832 TTCCATATAT
*
509842 AGTTCATAATCTGAATAACTCATTTGAAGAGGAAGAAGG
1 AGTTCATAATCTGAAGAACTCATTTGAAGAGGAAGAAGG
* * * *
509881 AGTTCATAGTTTGAAGAACTCGTCTT-AAGAGGAAGAAGA
1 AGTTCATAATCTGAAGAACTCAT-TTGAAGAGGAAGAAGG
* * * * *
509920 AGTTCATAGTCTGAAGAACTCGTCTGAAGAGGAAAAATG
1 AGTTCATAATCTGAAGAACTCATTTGAAGAGGAAGAAGG
*
509959 AGTTCATAATCTGAAGAACTCATATGAAGAGGAAGAAGG
1 AGTTCATAATCTGAAGAACTCATTTGAAGAGGAAGAAGG
* *
509998 AGTTCATAATCTGAAGAACTCGTCTT-AAGAGGAAAAAGG
1 AGTTCATAATCTGAAGAACTCAT-TTGAAGAGGAAGAAGG
* * * *
510037 AGTTCATAATCTTAAGAACTCATATGAAGAGGAAAAAAG
1 AGTTCATAATCTGAAGAACTCATTTGAAGAGGAAGAAGG
* * * *
510076 AGTTCACAATCTGAAGAACTAATCTGAAGAGGAAGAAGA
1 AGTTCATAATCTGAAGAACTCATTTGAAGAGGAAGAAGG
* *
510115 AATTCATAGTCTGAAGA
1 AGTTCATAATCTGAAGA
510132 GGAAGAAGAA
Statistics
Matches: 215, Mismatches: 32, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
38 2 0.01
39 210 0.98
40 3 0.01
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.23
Consensus pattern (39 bp):
AGTTCATAATCTGAAGAACTCATTTGAAGAGGAAGAAGG
Found at i:510054 original size:117 final size:117
Alignment explanation
Indices: 509842--510786 Score: 1122
Period size: 117 Copynumber: 8.3 Consensus size: 117
509832 TTCCATATAT
* * * * *
509842 AGTTCATAATCTGAATAACTCATTTGAAGAGGAAGAAGGAGTTCATAGTTTGAAGAACTCGTCTT
1 AGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCGTCTG
* * * * *
509907 AAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTCGTCTGAAGAGGAAAAATG
66 AAGAGGAAAAAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAAAAAG
* *
509959 AGTTCATAATCTGAAGAACTCATATGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCGTCTT
1 AGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCGTCTG
* *
510024 AAGAGGAAAAAGGAGTTCATAATCTTAAGAACTCATATGAAGAGGAAAAAAG
66 AAGAGGAAAAAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAAAAAG
* * * *
510076 AGTTCACAATCTGAAGAACTAATCTGAAGAGGAAG-A--AG---A-AAT-T----CA-TAGTCTG
1 AGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCGTCTG
* * * * *
510128 AAGAGGAAGAAGAAGTCCATAGTCTGAAGAACTCATATGAAGAGGAAAAAAG
66 AAGAGGAAAAAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAAAAAG
* ** * *
510180 AGTTCATAATCTGAAAAACTTGTCTGAAGAGGAAAAAGGAGTTCATAATCTGAGGAACTCGTCTG
1 AGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCGTCTG
* * *
510245 AAGAGGAAAAAGGAGTTCATAATCTGAATAACTCATATGAAGAGGAAAAATG
66 AAGAGGAAAAAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAAAAAG
* * * * *
510297 AGTTCATAATCTAAAGAACTCGTCTGAAGAGGAA-AATGAGTTCGTAATCTGAAGAACTCATCTG
1 AGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCGTCTG
* * *
510361 AAGAGGTAAAATGAGTTCATAATCT---G-----A---G-AGA--AAAAATG
66 AAGAGGAAAAAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAAAAAG
* * *
510399 AGTTCATAATCTGAAGAACTCATCTGAAGAGGAAAAATGAGTTCATAATCTGAAGAACTTGTCTG
1 AGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCGTCTG
* * *
510464 AAGAGGAAAAAAGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAAG
66 AAGAGGAAAAAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAAAAAG
* * *
510516 AGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAATGAGTTCATAATCTGAAGAACTCATCTG
1 AGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCGTCTG
* * *
510581 AAGAGGAAGAAGGAGTTCATAATCTGAATAACTCATCTGAAGATGAAAAAAG
66 AAGAGGAAAAAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAAAAAG
* *
510633 AGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAAGAGTTCATAATCTGAAGAACTCGTCTG
1 AGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCGTCTG
* * * *
510698 AAGAGGAAGAAA-GAGTTCATAATCTGAAGAACTCGTCCGAAGAAG-AAGAAG
66 AAGAGGAA-AAAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAAAAAG
* * *
510749 AAGCTCATAATCTGAAGAACTCATATGAAAAGGAAGAA
1 -AGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAA
510787 TGAGAAAGAA
Statistics
Matches: 721, Mismatches: 77, Indels: 60
0.84 0.09 0.07
Matches are distributed among these distances:
102 39 0.05
103 50 0.07
104 85 0.12
105 3 0.00
106 1 0.00
107 2 0.00
108 1 0.00
109 1 0.00
110 4 0.01
111 4 0.01
112 1 0.00
114 3 0.00
115 3 0.00
116 56 0.08
117 466 0.65
118 2 0.00
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (117 bp):
AGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCGTCTG
AAGAGGAAAAAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAAAAAG
Found at i:510128 original size:26 final size:26
Alignment explanation
Indices: 510098--510157 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
510088 GAAGAACTAA
*
510098 TCTGAAGAGGAAGAAGAAATTCATAG
1 TCTGAAGAGGAAGAAGAAATCCATAG
*
510124 TCTGAAGAGGAAGAAGAAGTCCATAG
1 TCTGAAGAGGAAGAAGAAATCCATAG
510150 TCTGAAGA
1 TCTGAAGA
510158 ACTCATATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.43, C:0.10, G:0.28, T:0.18
Consensus pattern (26 bp):
TCTGAAGAGGAAGAAGAAATCCATAG
Found at i:510163 original size:104 final size:104
Alignment explanation
Indices: 510019--510332 Score: 315
Period size: 104 Copynumber: 2.9 Consensus size: 104
510009 TGAAGAACTC
* * * *
510019 GTCTTAAGAGGAAAAAGGAGTTCATAATCTTAAGAACTCATATGAAGAGGAAAAAAGAGTTCACA
1 GTCTGAAGAGGAAAAAGAAGTCCATAATCTGAAGAACTCATATGAAGAGGAAAAAAGAGTTCACA
* *
510084 ATCTGAAGAACTAATCTGAAGAGGAAGAAGAAATTCATA
66 ATCTGAAAAACTAATCTGAAGAGGAAAAAGAAATTCATA
* * *
510123 GTCTGAAGAGGAAGAAGAAGTCCATAGTCTGAAGAACTCATATGAAGAGGAAAAAAGAGTTCATA
1 GTCTGAAGAGGAAAAAGAAGTCCATAATCTGAAGAACTCATATGAAGAGGAAAAAAGAGTTCACA
** * *
510188 ATCTGAAAAACTTGTCTGAAGAGGAAAAAGGAGTTCATAATCTGAGGAACTC
66 ATCTGAAAAACTAATCTGAAGAGG-AAAA--AG---A-AAT-T----CA-TA
* * * * *
510240 GTCTGAAGAGGAAAAAGGAGTTCATAATCTGAATAACTCATATGAAGAGGAAAAATGAGTTCATA
1 GTCTGAAGAGGAAAAAGAAGTCCATAATCTGAAGAACTCATATGAAGAGGAAAAAAGAGTTCACA
**
510305 ATCT-AAAGAACTCGTCTGAAGAGGAAAA
66 ATCTGAAA-AACTAATCTGAAGAGGAAAA
510333 TGAGTTCGTA
Statistics
Matches: 176, Mismatches: 20, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
104 79 0.45
105 3 0.02
107 2 0.01
110 1 0.01
111 3 0.02
112 1 0.01
116 8 0.05
117 79 0.45
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.21
Consensus pattern (104 bp):
GTCTGAAGAGGAAAAAGAAGTCCATAATCTGAAGAACTCATATGAAGAGGAAAAAAGAGTTCACA
ATCTGAAAAACTAATCTGAAGAGGAAAAAGAAATTCATA
Found at i:510169 original size:39 final size:38
Alignment explanation
Indices: 510124--510783 Score: 641
Period size: 39 Copynumber: 17.3 Consensus size: 38
510114 AAATTCATAG
* * *
510124 TCTGAAGAGGAAGAAGAAGTCCATAGTCTGAAGAACTCA
1 TCTGAAGAGGAAAAAG-AGTTCATAATCTGAAGAACTCA
* * **
510163 TATGAAGAGGAAAAAAGAGTTCATAATCTGAAAAACTTG
1 TCTGAAGAGG-AAAAAGAGTTCATAATCTGAAGAACTCA
* *
510202 TCTGAAGAGGAAAAAGGAGTTCATAATCTGAGGAACTCG
1 TCTGAAGAGGAAAAA-GAGTTCATAATCTGAAGAACTCA
*
510241 TCTGAAGAGGAAAAAGGAGTTCATAATCTGAATAACTCA
1 TCTGAAGAGGAAAAA-GAGTTCATAATCTGAAGAACTCA
* * *
510280 TATGAAGAGGAAAAATGAGTTCATAATCTAAAGAACTCG
1 TCTGAAGAGGAAAAA-GAGTTCATAATCTGAAGAACTCA
* *
510319 TCTGAAGAGGAAAATGAGTTCGTAATCTGAAGAACTCA
1 TCTGAAGAGGAAAAAGAGTTCATAATCTGAAGAACTCA
* *
510357 TCTGAAGAGGTAAAATGAGTTCATAATCTGAGAGAA--AA
1 TCTGAAGAGG-AAAAAGAGTTCATAATCTGA-AGAACTCA
** *** ** ** *
510395 AATG-AGTTCATAATCTGAAGAAC-TCATCTGAAG-----A
1 TCTGAAGAGGA-AA-AAG-AGTTCATAATCTGAAGAACTCA
* **
510429 ---G--GA--AAAATGAGTTCATAATCTGAAGAACTTG
1 TCTGAAGAGGAAAAAGAGTTCATAATCTGAAGAACTCA
*
510460 TCTGAAGAGGAAAAAAGAGTTCATAATCTGAAGAACTCG
1 TCTGAAGAGG-AAAAAGAGTTCATAATCTGAAGAACTCA
*
510499 TCTGAAGAGGAAGAAAGAGTTCATAATCTGAAGAACTCG
1 TCTGAAGAGGAA-AAAGAGTTCATAATCTGAAGAACTCA
*
510538 TCTGAAGAGGAAGAATGAGTTCATAATCTGAAGAACTCA
1 TCTGAAGAGGAA-AAAGAGTTCATAATCTGAAGAACTCA
* *
510577 TCTGAAGAGGAAGAAGGAGTTCATAATCTGAATAACTCA
1 TCTGAAGAGGAA-AAAGAGTTCATAATCTGAAGAACTCA
* *
510616 TCTGAAGATGAAAAAAGAGTTCATAATCTGAAGAACTCG
1 TCTGAAGA-GGAAAAAGAGTTCATAATCTGAAGAACTCA
*
510655 TCTGAAGAGGAAGAAAGAGTTCATAATCTGAAGAACTCG
1 TCTGAAGAGGAA-AAAGAGTTCATAATCTGAAGAACTCA
*
510694 TCTGAAGAGGAAGAAAGAGTTCATAATCTGAAGAACTCG
1 TCTGAAGAGGAA-AAAGAGTTCATAATCTGAAGAACTCA
* * * *
510733 TCCGAAGAAGAAGAAGAAGCTCATAATCTGAAGAACTCA
1 TCTGAAGAGGAAAAAG-AGTTCATAATCTGAAGAACTCA
* *
510772 TATGAAAAGGAA
1 TCTGAAGAGGAA
510784 GAATGAGAAA
Statistics
Matches: 535, Mismatches: 61, Indels: 50
0.83 0.09 0.08
Matches are distributed among these distances:
25 3 0.01
26 11 0.02
27 2 0.00
28 1 0.00
30 1 0.00
31 1 0.00
34 2 0.00
36 3 0.01
37 6 0.01
38 55 0.10
39 438 0.82
40 12 0.02
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (38 bp):
TCTGAAGAGGAAAAAGAGTTCATAATCTGAAGAACTCA
Found at i:510397 original size:64 final size:63
Alignment explanation
Indices: 510319--510455 Score: 229
Period size: 64 Copynumber: 2.1 Consensus size: 63
510309 AAAGAACTCG
* * *
510319 TCTGAAGAGGAAAATGAGTTCGTAATCTGAAGAACTCATCTGAAGAGGTAAAATGAGTTCATAA
1 TCTGAAGA-AAAAATGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAAAATGAGTTCATAA
510383 TCTGAGAGAAAAAATGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAAAATGAGTTCATAA
1 TCTGA-AGAAAAAATGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAAAATGAGTTCATAA
510447 TCTGAAGAA
1 TCTGAAGAA
510456 CTTGTCTGAA
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
63 4 0.06
64 62 0.90
65 3 0.04
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (63 bp):
TCTGAAGAAAAAATGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAAAATGAGTTCATAA
Found at i:510416 original size:24 final size:25
Alignment explanation
Indices: 510368--510416 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
510358 CTGAAGAGGT
510368 AAAATGAGTTCATAATCTGAGAGAA
1 AAAATGAGTTCATAATCTGAGAGAA
510393 AAAATGAGTTCATAATCTGA-AGAA
1 AAAATGAGTTCATAATCTGAGAGAA
510417 CTCATCTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.24
Consensus pattern (25 bp):
AAAATGAGTTCATAATCTGAGAGAA
Found at i:510481 original size:103 final size:102
Alignment explanation
Indices: 510285--510494 Score: 332
Period size: 103 Copynumber: 2.1 Consensus size: 102
510275 ACTCATATGA
* * *
510285 AGAGGAAAAATGAGTTCATAATCTAAAGAACTCGTCTGAAGAGGAAAATGAGTTCGTAATCTGAA
1 AGAGAAAAAATGAGTTCATAATCTAAAGAACTCATCTGAAGAGGAAAATGAGTTCATAATCTGAA
* *
510350 GAACTCATCTGAAGAGGTAAAATGAGTTCATAATCTG
66 GAACTCATCTGAAGAGGAAAAAAGAGTTCATAATCTG
*
510387 AGAGAAAAAATGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAAAATGAGTTCATAATCTGA
1 AGAGAAAAAATGAGTTCATAATCTAAAGAACTCATCTGAAGAGG-AAAATGAGTTCATAATCTGA
**
510452 AGAACTTGTCTGAAGAGGAAAAAAGAGTTCATAATCTG
65 AGAACTCATCTGAAGAGGAAAAAAGAGTTCATAATCTG
510490 A-AGAA
1 AGAGAA
510495 CTCGTCTGAA
Statistics
Matches: 99, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
102 45 0.45
103 54 0.55
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (102 bp):
AGAGAAAAAATGAGTTCATAATCTAAAGAACTCATCTGAAGAGGAAAATGAGTTCATAATCTGAA
GAACTCATCTGAAGAGGAAAAAAGAGTTCATAATCTG
Found at i:510689 original size:20 final size:20
Alignment explanation
Indices: 510664--510728 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
510654 GTCTGAAGAG
510664 GAAGAAAGAGTTCATAATCT
1 GAAGAAAGAGTTCATAATCT
*** ***
510684 GAAGAACTCG-TC-TGAAGAG
1 GAAGAAAGAGTTCAT-AATCT
510703 GAAGAAAGAGTTCATAATCT
1 GAAGAAAGAGTTCATAATCT
510723 GAAGAA
1 GAAGAA
510729 CTCGTCCGAA
Statistics
Matches: 30, Mismatches: 12, Indels: 6
0.62 0.25 0.12
Matches are distributed among these distances:
18 1 0.03
19 11 0.37
20 17 0.57
21 1 0.03
ACGTcount: A:0.45, C:0.11, G:0.25, T:0.20
Consensus pattern (20 bp):
GAAGAAAGAGTTCATAATCT
Found at i:511917 original size:29 final size:30
Alignment explanation
Indices: 511862--511927 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 30
511852 TAAACATTAA
511862 TTTTATTCATTTATATTTCTTCCC-TTTAC
1 TTTTATTCATTTATATTTCTTCCCTTTTAC
* *
511891 TTTTATGT-ATTTATATTTCTAT-TCTTTTAT
1 TTTTAT-TCATTTATATTTCT-TCCCTTTTAC
511921 TTTTATT
1 TTTTATT
511928 TTTTTGTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 20 0.62
30 12 0.38
ACGTcount: A:0.18, C:0.12, G:0.02, T:0.68
Consensus pattern (30 bp):
TTTTATTCATTTATATTTCTTCCCTTTTAC
Found at i:512991 original size:27 final size:26
Alignment explanation
Indices: 512932--513023 Score: 123
Period size: 27 Copynumber: 3.5 Consensus size: 26
512922 CAACACGCTT
*
512932 AGAGGCATCTCACAATTCTTT-GGTAC
1 AGAGGCATCTCACAGTT-TTTAGGTAC
512958 AGAGGCATCTCACAGTTTTGTAGGTAC
1 AGAGGCATCTCACAGTTTT-TAGGTAC
512985 AGAGGCATCTCACAGTTTTATAGGTAC
1 AGAGGCATCTCACAGTTTT-TAGGTAC
* *
513012 AGAAGCAACTCA
1 AGAGGCATCTCA
513024 ACATTTCTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
25 2 0.03
26 17 0.28
27 41 0.68
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (26 bp):
AGAGGCATCTCACAGTTTTTAGGTAC
Found at i:513143 original size:32 final size:31
Alignment explanation
Indices: 513106--513169 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 31
513096 AAAAGAAAAT
*
513106 TAGCACTCTTTTAACCGTAGGGTAAGGGCATC
1 TAGCACTCTTTTAACCGTAGAGTAA-GGCATC
513138 TAGCACTCTTTTAACCGTAGAGTAAGGCATC
1 TAGCACTCTTTTAACCGTAGAGTAAGGCATC
513169 T
1 T
513170 TCATTATGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 7 0.23
32 24 0.77
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (31 bp):
TAGCACTCTTTTAACCGTAGAGTAAGGCATC
Found at i:514406 original size:19 final size:20
Alignment explanation
Indices: 514382--514427 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
514372 AACTGGCTGA
514382 GAACCGGC-AAAACCGGGGT
1 GAACCGGCGAAAACCGGGGT
* *
514401 GAACCGGCTGAAATCCGGTGT
1 GAACCGGC-GAAAACCGGGGT
514422 GAACCG
1 GAACCG
514428 TCGGTTCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 8 0.35
21 15 0.65
ACGTcount: A:0.28, C:0.26, G:0.35, T:0.11
Consensus pattern (20 bp):
GAACCGGCGAAAACCGGGGT
Found at i:519804 original size:24 final size:24
Alignment explanation
Indices: 519772--519817 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
519762 ACCCCAAGGC
519772 TTTTGATTGATAATGTTAAATCAT
1 TTTTGATTGATAATGTTAAATCAT
*
519796 TTTTTATTGATAATGTTAAATC
1 TTTTGATTGATAATGTTAAATC
519818 TATTAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.52
Consensus pattern (24 bp):
TTTTGATTGATAATGTTAAATCAT
Found at i:520005 original size:23 final size:23
Alignment explanation
Indices: 519962--520007 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
519952 ATTTATAATT
*
519962 TAAATTTTATAAAACATTATATA
1 TAAATTTTATAAAACAGTATATA
*
519985 TAAATTTTATTATAA-AGTATATA
1 TAAATTTTA-TAAAACAGTATATA
520008 AATTTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
TAAATTTTATAAAACAGTATATA
Found at i:521094 original size:22 final size:22
Alignment explanation
Indices: 521055--521098 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
521045 ATGTTTAGAG
***
521055 ATAATCATAATTTTATTTAAAA
1 ATAATCATAATAAAATTTAAAA
521077 ATAATCATAATAAAATTTAAAA
1 ATAATCATAATAAAATTTAAAA
521099 GTTTCAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
ATAATCATAATAAAATTTAAAA
Found at i:521768 original size:35 final size:35
Alignment explanation
Indices: 521729--521800 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
521719 AAAAATAAGT
**
521729 TACTAATAATTTAGTTTTAAAAATAACGTTACTAA
1 TACTAATAATTTAACTTTAAAAATAACGTTACTAA
521764 TACTAATAATTTAACTTTAAAAATAACGTTACTAA
1 TACTAATAATTTAACTTTAAAAATAACGTTACTAA
521799 TA
1 TA
521801 ATTATTAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (35 bp):
TACTAATAATTTAACTTTAAAAATAACGTTACTAA
Found at i:521796 original size:29 final size:29
Alignment explanation
Indices: 521719--521803 Score: 91
Period size: 35 Copynumber: 2.8 Consensus size: 29
521709 TTTTCATATA
**
521719 AAAAATAA-GTTACTAATAATTTAGTTTT
1 AAAAATAACGTTACTAATAATTTAACTTT
521747 AAAAATAACGTTACTAATACTAATAATTTAACTTT
1 AAAAATAACG----T--TACTAATAATTTAACTTT
521782 AAAAATAACGTTACTAATAATT
1 AAAAATAACGTTACTAATAATT
521804 ATTAACATGT
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
28 8 0.17
29 12 0.25
31 1 0.02
33 1 0.02
35 26 0.54
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (29 bp):
AAAAATAACGTTACTAATAATTTAACTTT
Found at i:529039 original size:23 final size:20
Alignment explanation
Indices: 528985--529043 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 20
528975 TTTTGGTGCA
*
528985 GAGGGAATCGA-TCCCCCTT
1 GAGGGAACCGATTCCCCCTT
529004 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC-TT
*
529025 GAAGGAGAACTGATTCCCC
1 G-AGG-GAACCGATTCCCC
529044 TCACATGGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.29
20 6 0.18
21 3 0.09
22 3 0.09
23 12 0.35
ACGTcount: A:0.24, C:0.31, G:0.25, T:0.20
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCTT
Found at i:531784 original size:21 final size:21
Alignment explanation
Indices: 531758--531798 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
531748 CCAGTATGCT
*
531758 CAGGGGGAACTGATTCCCCCC
1 CAGGGGGAACCGATTCCCCCC
*
531779 CAGGGGGTACCGATTCCCCC
1 CAGGGGGAACCGATTCCCCC
531799 TTGTATAACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.39, G:0.29, T:0.15
Consensus pattern (21 bp):
CAGGGGGAACCGATTCCCCCC
Found at i:535718 original size:17 final size:17
Alignment explanation
Indices: 535687--535732 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
535677 CTTATATTAA
535687 AATATATATATATATATAT
1 AATATA-ATA-ATATATAT
* *
535706 ATTATAATAATATATTT
1 AATATAATAATATATAT
535723 AATATAATAA
1 AATATAATAA
535733 AATTAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 16 0.67
18 3 0.12
19 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATATAATAATATATAT
Found at i:550838 original size:82 final size:82
Alignment explanation
Indices: 550686--550839 Score: 211
Period size: 85 Copynumber: 1.9 Consensus size: 82
550676 AGGGAAATTT
* * *
550686 AATATTATAATAATTAATAAGATTTTTTATTAATATTACAATTAGTTATTATAATTCAATTTTAA
1 AATATTATAACAATTAATAAGAATTTTTATTAATATTACAATTAG-T-TTATAATTCAATTTCAA
550751 AAATATTATTTATATTTAA
64 AAATATTATTTATATTTAA
* * * *
550770 AATATTATAACAATTAATAGGAAATTTTTATTAGTATTACAATTAG-TTGTAATTCAATTTCATA
1 AATATTATAACAATTAATAAG-AATTTTTATTAATATTACAATTAGTTTATAATTCAATTTCAAA
550834 AATATT
65 AATATT
550840 TGAAATATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
82 21 0.34
84 19 0.31
85 22 0.35
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (82 bp):
AATATTATAACAATTAATAAGAATTTTTATTAATATTACAATTAGTTTATAATTCAATTTCAAAA
ATATTATTTATATTTAA
Found at i:550848 original size:82 final size:82
Alignment explanation
Indices: 550686--550849 Score: 197
Period size: 82 Copynumber: 2.0 Consensus size: 82
550676 AGGGAAATTT
* * *
550686 AATATTATAATAATTAATAAGATTTTTTATTAATATTACAATTAGTTATTATAATTCAATTTTAA
1 AATATTATAACAATTAATAAGAATTTTTATTAATATTACAATTAG-T-TTATAATTCAATTTCAA
**
550751 AAATATTATTTATATTTAA
64 AAATATTATAAATATTTAA
* * * *
550770 AATATTATAACAATTAATAGGAAATTTTTATTAGTATTACAATTAG-TTGTAATTCAATTTCATA
1 AATATTATAACAATTAATAAG-AATTTTTATTAATATTACAATTAGTTTATAATTCAATTTCAAA
550834 AATATT-TGAAATATTT
65 AATATTAT-AAATATTT
550850 GATTTTTTTA
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
81 1 0.01
82 27 0.39
84 19 0.28
85 22 0.32
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.48
Consensus pattern (82 bp):
AATATTATAACAATTAATAAGAATTTTTATTAATATTACAATTAGTTTATAATTCAATTTCAAAA
ATATTATAAATATTTAA
Found at i:553081 original size:35 final size:35
Alignment explanation
Indices: 553042--553122 Score: 135
Period size: 35 Copynumber: 2.3 Consensus size: 35
553032 TAGGTAAAAC
* *
553042 ATTCATTGAAACAAAAATAAGAAAATCATTTGACT
1 ATTCATTCAAACAAAAATAAGAAAATCATTCGACT
*
553077 ATTCATTCAAACAAAAATAAGCAAATCATTCGACT
1 ATTCATTCAAACAAAAATAAGAAAATCATTCGACT
553112 ATTCATTCAAA
1 ATTCATTCAAA
553123 TTCAAATAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.49, C:0.16, G:0.06, T:0.28
Consensus pattern (35 bp):
ATTCATTCAAACAAAAATAAGAAAATCATTCGACT
Found at i:553130 original size:35 final size:34
Alignment explanation
Indices: 553042--553136 Score: 127
Period size: 35 Copynumber: 2.7 Consensus size: 34
553032 TAGGTAAAAC
* *
553042 ATTCATTGAAACAAAAATAAGAAAATCATTTGACT
1 ATTCATTCAAACAAAAATAAG-AAATCATTCGACT
553077 ATTCATTCAAACAAAAATAAGCAAATCATTCGACT
1 ATTCATTCAAACAAAAATAAG-AAATCATTCGACT
***
553112 ATTCATTCAAATTCAAATAAGAAAT
1 ATTCATTCAAACAAAAATAAGAAAT
553137 AATTTAAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
34 4 0.07
35 50 0.93
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (34 bp):
ATTCATTCAAACAAAAATAAGAAATCATTCGACT
Found at i:561385 original size:19 final size:20
Alignment explanation
Indices: 561361--561400 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
561351 TATCATTTCT
561361 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
561380 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
561400 T
1 T
561401 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:561403 original size:19 final size:18
Alignment explanation
Indices: 561357--561403 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
561347 TCTCTATCAT
561357 TTCTT-TATTTCATTTCA
1 TTCTTATATTTCATTTCA
*
561374 TTCTTATTATTTCTTTTCA
1 TTCTTA-TATTTCATTTCA
561393 TTACTTATATT
1 TT-CTTATATT
561404 ATTATTCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
19 17 0.65
20 4 0.15
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.66
Consensus pattern (18 bp):
TTCTTATATTTCATTTCA
Found at i:561657 original size:19 final size:18
Alignment explanation
Indices: 561630--561690 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
561620 AAAGAAGTTC
* *
561630 AAAAACAAAAGAAGAGAA
1 AAAAACAAAAAAAAAGAA
561648 AAAAATCAAAAAAAAAGAAA
1 AAAAA-CAAAAAAAAAG-AA
*
561668 AGAAAAGAAAAGAAAAAGAA
1 A-AAAACAAAA-AAAAAGAA
561688 AAA
1 AAA
561691 TTCAAAAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 5 0.14
19 11 0.31
20 10 0.28
21 10 0.28
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.02
Consensus pattern (18 bp):
AAAAACAAAAAAAAAGAA
Found at i:561690 original size:6 final size:5
Alignment explanation
Indices: 561631--561689 Score: 57
Period size: 5 Copynumber: 11.8 Consensus size: 5
561621 AAGAAGTTCA
* * ** *
561631 AAAAC AAAAG AAGAG AAAA- AAATC AAAAA AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
561680 AAAAAG AAAA
1 -AAAAG AAAA
561690 ATTCAAAAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
4 3 0.07
5 37 0.82
6 5 0.11
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:568844 original size:17 final size:17
Alignment explanation
Indices: 568805--568863 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
568795 AAGTATGTTG
* * *
568805 TTCATTAAAGCATGCAT
1 TTCATTTAAGCACGTAT
*
568822 TGCATTTAAGCACGTAT
1 TTCATTTAAGCACGTAT
* *
568839 TTCATTTAGGCACGTAG
1 TTCATTTAAGCACGTAT
568856 TTCATTTA
1 TTCATTTA
568864 TGAATCTAGT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (17 bp):
TTCATTTAAGCACGTAT
Found at i:576262 original size:14 final size:14
Alignment explanation
Indices: 576243--576273 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
576233 TTACAAACAT
*
576243 AAAAATAAGTTGAC
1 AAAAATAAGTTCAC
576257 AAAAATAAGTTCAC
1 AAAAATAAGTTCAC
576271 AAA
1 AAA
576274 TGGGGAGCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.19
Consensus pattern (14 bp):
AAAAATAAGTTCAC
Found at i:578068 original size:23 final size:23
Alignment explanation
Indices: 578042--578129 Score: 70
Period size: 23 Copynumber: 3.8 Consensus size: 23
578032 TATTCTTTCA
* *
578042 TTTAACGATT-GTGAACGTGTTCG
1 TTTAACG-TTCGTGAACATATTCG
*
578065 TTTAATGTTCGTGAACATATTCG
1 TTTAACGTTCGTGAACATATTCG
* ** * *
578088 TTTAGATGTTCAAGAACATGTTTG
1 TTTA-ACGTTCGTGAACATATTCG
*
578112 TTTAGCGTTCGTGAACAT
1 TTTAACGTTCGTGAACAT
578130 GTTCATTTGG
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
22 2 0.04
23 31 0.60
24 19 0.37
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (23 bp):
TTTAACGTTCGTGAACATATTCG
Found at i:578104 original size:24 final size:24
Alignment explanation
Indices: 578061--578116 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
578051 TGTGAACGTG
**
578061 TTCGTTTA-ATGTTCGTGAACATA
1 TTCGTTTAGATGTTCAAGAACATA
*
578084 TTCGTTTAGATGTTCAAGAACATG
1 TTCGTTTAGATGTTCAAGAACATA
*
578108 TTTGTTTAG
1 TTCGTTTAG
578117 CGTTCGTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 8 0.29
24 20 0.71
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.45
Consensus pattern (24 bp):
TTCGTTTAGATGTTCAAGAACATA
Found at i:578130 original size:23 final size:23
Alignment explanation
Indices: 578052--578143 Score: 94
Period size: 23 Copynumber: 4.0 Consensus size: 23
578042 TTTAACGATT
* *
578052 GTGAACGTGTTCGTTTAATGTTC
1 GTGAACATGTTCGTTTAGTGTTC
*
578075 GTGAACATATTCGTTTAGATGTTC
1 GTGAACATGTTCGTTTAG-TGTTC
** * *
578099 AAGAACATGTTTGTTTAGCGTTC
1 GTGAACATGTTCGTTTAGTGTTC
* *
578122 GTGAACATGTTCATTTGGTGTT
1 GTGAACATGTTCGTTTAGTGTT
578144 TTAAACATGT
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
23 35 0.65
24 19 0.35
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.42
Consensus pattern (23 bp):
GTGAACATGTTCGTTTAGTGTTC
Found at i:579625 original size:19 final size:20
Alignment explanation
Indices: 579601--579640 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
579591 TATCCTTTCT
579601 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
579620 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
579640 T
1 T
579641 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:579945 original size:18 final size:18
Alignment explanation
Indices: 579924--579968 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
579914 GAAAAAGACA
579924 AAAAGAAGAGAAAATTAG
1 AAAAGAAGAGAAAATTAG
579942 AAAAGAAGAGAAAATTAG
1 AAAAGAAGAGAAAATTAG
579960 AAAAGAAGA
1 AAAAGAAGA
579969 AAAGAAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.09
Consensus pattern (18 bp):
AAAAGAAGAGAAAATTAG
Found at i:579979 original size:18 final size:18
Alignment explanation
Indices: 579906--579981 Score: 68
Period size: 18 Copynumber: 4.2 Consensus size: 18
579896 TTGGAGTGCA
579906 AAAAGAA-AGAAAAAGACA-
1 AAAAGAAGAGAAAAA-A-AG
**
579924 AAAAGAAGAGAAAATTAG
1 AAAAGAAGAGAAAAAAAG
**
579942 AAAAGAAGAGAAAATTAG
1 AAAAGAAGAGAAAAAAAG
579960 AAAAGAAGA-AAAGAAAAG
1 AAAAGAAGAGAAA-AAAAG
579978 AAAA
1 AAAA
579982 AGAAAAATTC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
17 4 0.08
18 41 0.80
19 6 0.12
ACGTcount: A:0.74, C:0.01, G:0.20, T:0.05
Consensus pattern (18 bp):
AAAAGAAGAGAAAAAAAG
Found at i:584880 original size:19 final size:20
Alignment explanation
Indices: 584856--584895 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
584846 TATCCTTTCT
584856 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
584875 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
584895 T
1 T
584896 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:589671 original size:17 final size:17
Alignment explanation
Indices: 589630--589680 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
589620 ACCTAAAAAT
*
589630 AATCTTTTTTTAA-AAA
1 AATCATTTTTTAAGAAA
*
589646 AA-CA-ATTTTAAGAAA
1 AATCATTTTTTAAGAAA
589661 AATCATTTTTTAAGACAA
1 AATCATTTTTTAAGA-AA
589679 AA
1 AA
589681 GTTGCTCTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 6 0.21
15 6 0.21
16 4 0.14
17 8 0.29
18 4 0.14
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (17 bp):
AATCATTTTTTAAGAAA
Found at i:591436 original size:132 final size:132
Alignment explanation
Indices: 591198--591473 Score: 462
Period size: 132 Copynumber: 2.1 Consensus size: 132
591188 GGTGATATTT
* * *
591198 ATCCAACTCCATATACGATGGTTTTGAGTGAAATGAAAACATCGATCCACCTCCTTATGTGATGG
1 ATCCAACTCCTTATACGATGGATTTGAGCGAAATGAAAACATCGATCCACCTCCTTATGTGATGG
591263 AATCGAACAAGATGTCGATGATGATCTATCTCTTTCAGTGATAGAATCAAGCAAAAAGTTGATGT
66 AATCGAACAAGATGTCGATGATGATCTATCTCTTTCAGTGATAGAATCAAGCAAAAAGTTGATGT
591328 TG
131 TG
* * *
591330 ATCCAACTCCTTTTGCGATGGATTTGAGCGAAATGAAAACATCGATCCACCTCCTTTTGTGATGG
1 ATCCAACTCCTTATACGATGGATTTGAGCGAAATGAAAACATCGATCCACCTCCTTATGTGATGG
* ** *
591395 TATCGAACGGGATGTCGATGATGATCTATCTCTTTCTGTGATAGAATCAAGCAAAAAGTTGATGT
66 AATCGAACAAGATGTCGATGATGATCTATCTCTTTCAGTGATAGAATCAAGCAAAAAGTTGATGT
591460 TG
131 TG
591462 ATCCAACTCCTT
1 ATCCAACTCCTT
591474 CTCTTTTTGT
Statistics
Matches: 134, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 134 1.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (132 bp):
ATCCAACTCCTTATACGATGGATTTGAGCGAAATGAAAACATCGATCCACCTCCTTATGTGATGG
AATCGAACAAGATGTCGATGATGATCTATCTCTTTCAGTGATAGAATCAAGCAAAAAGTTGATGT
TG
Found at i:591485 original size:50 final size:50
Alignment explanation
Indices: 591423--591525 Score: 152
Period size: 50 Copynumber: 2.1 Consensus size: 50
591413 TGATGATCTA
* * *
591423 TCTCTTTCTGTGATAGAATCAAGCAAAAAGTTGATGTTGATCCAACTCCT
1 TCTCTTTCTGTGATAGAATCAAGCAAAAAGTTAACGCTGATCCAACTCCT
* * *
591473 TCTCTTTTTGTGATAGAATCGAGCTAAAAGTTAACGCTGATCCAACTCCT
1 TCTCTTTCTGTGATAGAATCAAGCAAAAAGTTAACGCTGATCCAACTCCT
591523 TCT
1 TCT
591526 ACGATGGATT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (50 bp):
TCTCTTTCTGTGATAGAATCAAGCAAAAAGTTAACGCTGATCCAACTCCT
Found at i:591757 original size:44 final size:44
Alignment explanation
Indices: 591691--591777 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 44
591681 ATATCGATTC
* * * *
591691 ACCTCCTTCTATGATGGAATCGAACGAAATGTTGGTGCTGATCT
1 ACCTCATTCTATGATAGAATCGAACGAAAAGTTGGCGCTGATCT
* * *
591735 ACCTCATTCTTTGATAGAATCGAGCTAAAAGTTGGCGCTGATC
1 ACCTCATTCTATGATAGAATCGAACGAAAAGTTGGCGCTGATC
591778 CAACTCCTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (44 bp):
ACCTCATTCTATGATAGAATCGAACGAAAAGTTGGCGCTGATCT
Found at i:591881 original size:130 final size:131
Alignment explanation
Indices: 591481--591971 Score: 673
Period size: 130 Copynumber: 3.7 Consensus size: 131
591471 CTTCTCTTTT
* *
591481 TGTGATAGAATCGAGCTAAAAGTTAACGCTGATCCAACTCCTTCTACGATGGATTTGAGCGAAAT
1 TGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTACGATGGATTTGAGCGAAAA
* * * * * *
591546 AAAATGTCGATCCATCTCCTTCTGTGATGATGGATTTGAACGAGATATCGGTTTTGATCTACCTC
66 AAAATGTCGATCCACCTCCTTC--T-ATGATGGAATCGAACGAGATGTTGGTGTTGATCTACCTC
* *
591611 TTTT
128 ATTC
*
591615 TGTGATAGAATTGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTACGATGGATTTGAGC--AAA
1 TGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTACGATGGATTTGAGCGAAAA
* * * *
591678 AAAATATCGATTCACCTCCTTCTATGATGGAATCGAACGAAATGTTGGTGCTGATCTACCTCATT
66 AAAATGTCGATCCACCTCCTTCTATGATGGAATCGAACGAGATGTTGGTGTTGATCTACCTCATT
591743 C
131 C
* * * * *
591744 TTTGATAGAATCGAGCTAAAAGTTGGCGCTGATCCAACTCCTTCTGCGATGGATTTAAAC-AAAA
1 TGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTACGATGGATTTGAGCGAAAA
* * *
591808 AAAATGTCGATCCACCTCCTTCTATGATGGAATCGAATGAGATGTTGGTGTTGATTTACCTCCTT
66 AAAATGTCGATCCACCTCCTTCTATGATGGAATCGAACGAGATGTTGGTGTTGATCTACCTCATT
591873 C
131 C
* **
591874 TGTGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTGTGATGGATTTGAGCGAAAA
1 TGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTACGATGGATTTGAGCG-AAA
*
591939 TAAAAATGTCGATCCACCTCCTTCTGTGATGGA
65 -AAAAATGTCGATCCACCTCCTTCTATGATGGA
591972 TTTGAACCAA
Statistics
Matches: 318, Mismatches: 35, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
129 88 0.28
130 117 0.37
132 24 0.08
133 31 0.10
134 58 0.18
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (131 bp):
TGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTACGATGGATTTGAGCGAAAA
AAAATGTCGATCCACCTCCTTCTATGATGGAATCGAACGAGATGTTGGTGTTGATCTACCTCATT
C
Found at i:592566 original size:68 final size:70
Alignment explanation
Indices: 592474--592603 Score: 212
Period size: 68 Copynumber: 1.9 Consensus size: 70
592464 GACGAAATTT
592474 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA-TT-TGTTTCAAGGGAAACTATCTCAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAACTTCTGTTTCAAGGGAAACTATCTCAAAGTT
592537 TTTTA
66 TTTTA
*
592542 TGTTTCAAGGGAAA-TCGTCTCAAGGGAGACAAAATCTTCTGTTTCGAGGGAAACTATCTCAA
1 TGTTTCAAGGGAAACT-GTCTCAAGGGAGACAAAA-CTTCTGTTTCAAGGGAAACTATCTCAA
592604 GGGAGATAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
67 1 0.02
68 32 0.56
70 2 0.04
71 22 0.39
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (70 bp):
TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAACTTCTGTTTCAAGGGAAACTATCTCAAAGTT
TTTTA
Found at i:592602 original size:39 final size:39
Alignment explanation
Indices: 592542--592776 Score: 337
Period size: 39 Copynumber: 6.0 Consensus size: 39
592532 AAGTTTTTTA
* * * *
592542 TGTTTCAAGGGAAA-TCGTCTCAAGGGAGACAAAATCTTC
1 TGTTTCGAGGGAAACT-ATCTCAAGCGAGATAAAATCTTC
*
592581 TGTTTCGAGGGAAACTATCTCAAGGGAGATAAAATCTTC
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* *
592620 TGTTCCGAGGGAAACTATCTCAAGCGAGATAAAATCTTA
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * * *
592659 AGTTTCAAAGGAAACTATCTCAAGCGAGACAAAATCTTC
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
*
592698 TGTTTCGAGGGAAACTATCTCAAGCAAGATAAAATCTTC
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
*
592737 TGTTTCGAGGGCAACTATCTCAAGCGAGATAAAATCTTC
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
592776 T
1 T
592777 TTTAAGAAAA
Statistics
Matches: 176, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
39 175 0.99
40 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (39 bp):
TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
Found at i:592716 original size:117 final size:117
Alignment explanation
Indices: 592438--592774 Score: 439
Period size: 117 Copynumber: 3.0 Consensus size: 117
592428 AAAATTTCTT
* * *
592438 GTTTCAAGGGAAACTGTCTCAAGCGAGACGAAAT-TT-TGTTTCAAGGGAAACTGTCTCAAGGGA
1 GTTTCAAGGGAAACTGTCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGGGA
* * * * *
592501 GACAAAA--TT-TGTTTCAAGGGAAACTATCTCAA---AG-T---TTTTTAT
66 GATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTAA
*
592543 GTTTCAAGGGAAA-TCGTCTCAAGGGAGACAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGGG
1 GTTTCAAGGGAAACT-GTCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGGG
*
592607 AGATAAAATCTTCTGTTCCGAGGGAAACTATCTCAAGCGAGATAAAATCTTAA
65 AGATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTAA
* * **
592660 GTTTCAAAGGAAACTATCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCAA
1 GTTTCAAGGGAAACTGTCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGGGA
*
592725 GATAAAATCTTCTGTTTCGAGGGCAACTATCTCAAGCGAGATAAAATCTT
66 GATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTT
592775 CTTTTAAGAA
Statistics
Matches: 201, Mismatches: 17, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
104 1 0.00
105 30 0.15
106 2 0.01
107 31 0.15
109 2 0.01
110 21 0.10
113 2 0.01
114 1 0.00
117 110 0.55
118 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.28
Consensus pattern (117 bp):
GTTTCAAGGGAAACTGTCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGGGA
GATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTAA
Found at i:594308 original size:24 final size:25
Alignment explanation
Indices: 594276--594322 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
594266 TTTTTATTAT
*
594276 TTTTCTTTCATTTTTC-TCTTTTCC
1 TTTTATTTCATTTTTCTTCTTTTCC
*
594300 TTTTATTTCTTTTTTCTTCTTTT
1 TTTTATTTCATTTTTCTTCTTTT
594323 TTTTCTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTATTTCATTTTTCTTCTTTTCC
Found at i:594314 original size:17 final size:18
Alignment explanation
Indices: 594288--594329 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
594278 TTCTTTCATT
*
594288 TTTCTCTTTTC-CTTTTA
1 TTTCTTTTTTCTCTTTTA
*
594305 TTTCTTTTTTCTTCTTTTT
1 TTTCTTTTTTC-TCTTTTA
594324 TTTCTT
1 TTTCTT
594330 CTTGCTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 10 0.48
19 11 0.52
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTCTTTTTTCTCTTTTA
Found at i:594325 original size:35 final size:34
Alignment explanation
Indices: 594248--594329 Score: 82
Period size: 33 Copynumber: 2.4 Consensus size: 34
594238 TCGATTCTCG
*
594248 TTCTTTTTTTCT-TTTTCGTTTTTATTATTTTTC
1 TTCTTTTTTTCTCTTTTCCTTTTTATTATTTTTC
* *
594281 TT-TCATTTTTCTCTTTTCC-TTTTATTTCTTTTTTC
1 TTCT-TTTTTTCTCTTTTCCTTTTTA-TT-ATTTTTC
594316 TTCTTTTTTT-TCTT
1 TTCTTTTTTTCTCTT
594330 CTTGCTATTG
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
32 1 0.03
33 14 0.35
34 11 0.28
35 13 0.32
36 1 0.03
ACGTcount: A:0.05, C:0.16, G:0.01, T:0.78
Consensus pattern (34 bp):
TTCTTTTTTTCTCTTTTCCTTTTTATTATTTTTC
Found at i:599479 original size:11 final size:10
Alignment explanation
Indices: 599463--599541 Score: 63
Period size: 10 Copynumber: 7.5 Consensus size: 10
599453 TTGATTTATT
599463 TTTTTATTCTA
1 TTTTTATT-TA
599474 TTTTTATTTA
1 TTTTTATTTA
**
599484 TTTTCCTTTAA
1 TTTTTATTT-A
599495 CTTTTT-TTTCA
1 -TTTTTATTT-A
*
599506 TTTTT-CTTA
1 TTTTTATTTA
599515 TTATTTATTTCA
1 TT-TTTATTT-A
599527 TTTTTATTTA
1 TTTTTATTTA
599537 TTTTT
1 TTTTT
599542 TTTTCCTTTC
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
9 3 0.05
10 25 0.44
11 22 0.39
12 7 0.12
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:599482 original size:23 final size:22
Alignment explanation
Indices: 599426--599487 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 22
599416 TTTTTAAAAC
* *
599426 ATTTTTAATTATTTTTTTTTGT
1 ATTTTTATTTATTTTTTTTTCT
*
599448 GTTCTTTGATTTATTTTTTTATTCT
1 ATT-TTT-ATTTATTTTTTT-TTCT
599473 ATTTTTATTTATTTT
1 ATTTTTATTTATTTT
599488 CCTTTAACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 14 0.42
25 5 0.15
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (22 bp):
ATTTTTATTTATTTTTTTTTCT
Found at i:599546 original size:21 final size:21
Alignment explanation
Indices: 599463--599546 Score: 75
Period size: 21 Copynumber: 4.0 Consensus size: 21
599453 TTGATTTATT
599463 TTTTTATTCTATTTTTATTT-A
1 TTTTTATT-TATTTTTATTTCA
**
599484 TTTTCCTTTAACTTTTT-TTTCA
1 TTTTTATTT-A-TTTTTATTTCA
*
599506 TTTTT-CTTATTATTTATTTCA
1 TTTTTATTTATT-TTTATTTCA
*
599527 TTTTTATTTATTTTTTTTTC
1 TTTTTATTTATTTTTATTTC
599547 CTTTCTTTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
19 2 0.04
20 5 0.10
21 29 0.57
22 15 0.29
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTATTTATTTTTATTTCA
Found at i:604625 original size:79 final size:75
Alignment explanation
Indices: 604424--605143 Score: 438
Period size: 71 Copynumber: 9.5 Consensus size: 75
604414 TTTAAGACAA
* * * * *
604424 CATTTACAGCAAAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGAGTACG
1 CATTTACAGCATAACT-AAGTC-AGAAGGGTTATCT---ACCAAAGACC-CCGAGTTCGA-TACA
* * *
604489 CTCAACTCTAAGACACAT
59 CTCAGCTC-GAGGCACAT
* * *
604507 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTACCAAAGACCACCGAGTTCGATTACATTC
1 CATTTACAGCATAAC-TAAGTC-AGAAGGGTTATCTACCAAAGACC-CCGAGTTCGA-TACACTC
604572 AGCCTCGAGGGCACAT
62 AG-CTCGA-GGCACAT
* * * *
604588 TATTTACTGCATAACTCAAGT-AGAAGGGTTATCTACCAAAGACCTTCGAG-TCGATACGCTCAG
1 CATTTACAGCATAACT-AAGTCAGAAGGGTTATCTACCAAAGACC-CCGAGTTCGATACACTCAG
*
604651 CT-TAGG--CA-
64 CTCGAGGCACAT
* * * *
604659 CATTTGCAGCATAGCTAAGTCAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCTC
1 CATTTACAGCATAACTAAGTCAGAAGGGTTATCT--ACCAAAGACC-CCGAGTTCGA-TACACTC
*
604724 AGCTCCAAGG--CAT
62 AGCT-CGAGGCACAT
* * *
604737 CATTTGCAGCATAGCTAAGTCAGAAGGG-TATCTGCCAAAGA-CCCGAGTTCGATACACTCAGCT
1 CATTTACAGCATAACTAAGTCAGAAGGGTTATCTACCAAAGACCCCGAGTTCGATACACTCAGCT
604800 CGATGGCACAT
66 CGA-GGCACAT
* *
604811 CATTATA-A-CATAACTCAAGT-AGAAGGG-TATCTGCCAAAGA-CCCGAGTTCGATACGCTCAG
1 CATT-TACAGCATAACT-AAGTCAGAAGGGTTATCTACCAAAGACCCCGAGTTCGATACACTCAG
**
604871 CTTAAGGCACAT
64 CTCGAGGCACAT
*
604883 CA-TT--AGC----CTAAGTCGAGAAGGGTTATCTGCACCAAAGACCTTC-AGTTCGATACACTC
1 CATTTACAGCATAACTAAGTC-AGAAGGGTTATCT--ACCAAAGACC-CCGAGTTCGATACACTC
*
604940 AGCTCCAGG--CAT
62 AGCTCGAGGCACAT
* * * * * *
604952 CATTTGCAGC-T-TC-AAGT-AGAAGGGTTATCTGCAACAAAGACCTTC-AGTTTGACTACGCTC
1 CATTTACAGCATAACTAAGTCAGAAGGGTTATCT--ACCAAAGACC-CCGAGTTCGA-TACACTC
* *
605012 AGCTCAAAGGGACAT
62 AGCTC-GAGGCACAT
* * *
605027 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTACACTC
1 CATTTACAGCATAAC-TAAGTC-AGAAGGGTTATCTACCAAAGACCC-CGAGTTCGA-TACACTC
**
605092 AGCTTCGAGGGTGCAT
62 AGC-TCGA-GGCACAT
* ** *
605108 CATGTACAATATAACTCAAGGCTAGAAGGGTTATCT
1 CATTTACAGCATAACT-AAGTC-AGAAGGGTTATCT
605144 GTCAACAAAA
Statistics
Matches: 529, Mismatches: 63, Indels: 92
0.77 0.09 0.13
Matches are distributed among these distances:
65 4 0.01
66 2 0.00
67 7 0.01
68 5 0.01
69 6 0.01
70 15 0.03
71 82 0.16
72 38 0.07
73 80 0.15
74 20 0.04
75 33 0.06
76 3 0.01
77 18 0.03
78 32 0.06
79 40 0.08
80 43 0.08
81 71 0.13
83 29 0.05
84 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (75 bp):
CATTTACAGCATAACTAAGTCAGAAGGGTTATCTACCAAAGACCCCGAGTTCGATACACTCAGCT
CGAGGCACAT
Found at i:604699 original size:152 final size:151
Alignment explanation
Indices: 604419--605095 Score: 564
Period size: 152 Copynumber: 4.5 Consensus size: 151
604409 CATTTTTTAA
* * *
604419 GACAACATTTACAGCAAAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGA
1 GACATCATTTACAGCATAACTCAA-G-TAGAAGGGTTATCT---ACCAAAGACCTTCGAGTTCGA
* * *
604484 GTACGCTCAACTCTAAGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCT-ACCAA
61 -TACACTCAGCTCT-AG--GCATCATTTGCAGCATAGC-TAAGT--AGAAGGGTTATCTGACCAA
* * ** * *
604548 AGACCACCGAGTTCGATTACATTCAGCCTCGAGG
119 AGACCTCCGAGTTCGACTACGCTCAG-CTCAAAG
* * *
604582 GCACATTATTTACTGCATAACTCAAGTAGAAGGGTTATCTACCAAAGACCTTCGAG-TCGATACG
1 G-ACATCATTTACAGCATAACTCAAGTAGAAGGGTTATCTACCAAAGACCTTCGAGTTCGATACA
*
604646 CTCAGCT-TAGGCA-CATTTGCAGCATAGCTAAGTCAGAAGGGTTATCTGCACCAAAGACCTTCG
65 CTCAGCTCTAGGCATCATTTGCAGCATAGCTAAGT-AGAAGGGTTATCTG-ACCAAAGACCTCCG
*
604709 AGTTCGACTACGCTCAGCTCCAAG
128 AGTTCGACTACGCTCAGCTCAAAG
* * *
604733 G-CATCATTTGCAGCATAGCT-AAGTCAGAAGGG-TATCTGCCAAAGACC--CGAGTTCGATACA
1 GACATCATTTACAGCATAACTCAAGT-AGAAGGGTTATCTACCAAAGACCTTCGAGTTCGATACA
* * *
604793 CTCAGCTCGATGGCACATCATTAT--AACATAACTCAAGTAGAAGGG-TATCTG-CCAAAGA-C-
65 CTCAGCTCTA-GG--CATCATT-TGCAGCATAGCT-AAGTAGAAGGGTTATCTGACCAAAGACCT
*
604852 CCGAGTTCGA-TACGCTCAGCT-TAAG
125 CCGAGTTCGACTACGCTCAGCTCAAAG
* *
604877 GCACATCA-TT--AGCCTAAGTC--G-AGAAGGGTTATCTGCACCAAAGACCTTC-AGTTCGATA
1 G-ACATCATTTACAGCATAACTCAAGTAGAAGGGTTATCT--ACCAAAGACCTTCGAGTTCGATA
* * * *
604935 CACTCAGCTCCAGGCATCATTTGCAGC-T-TC-AAGTAGAAGGGTTATCTGCAACAAAGACCTTC
63 CACTCAGCTCTAGGCATCATTTGCAGCATAGCTAAGTAGAAGGGTTATCTG-ACCAAAGACCTCC
*
604997 -AGTTTGACTACGCTCAGCTCAAAGG
127 GAGTTCGACTACGCTCAGCTCAAA-G
* * * * *
605022 GACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTA
1 GACATCATTTACAGCATAACTCAAGT--AGAAGGGTTATCTACCAAAGACCTTCGAGTTCGA-TA
605087 CACTCAGCT
63 CACTCAGCT
605096 TCGAGGGTGC
Statistics
Matches: 431, Mismatches: 43, Indels: 91
0.76 0.08 0.16
Matches are distributed among these distances:
138 11 0.03
139 6 0.01
140 9 0.02
141 19 0.04
142 10 0.02
143 29 0.07
144 32 0.07
145 18 0.04
146 18 0.04
147 21 0.05
148 26 0.06
149 25 0.06
150 30 0.07
151 34 0.08
152 73 0.17
153 3 0.01
155 2 0.00
156 1 0.00
157 10 0.02
158 4 0.01
159 15 0.03
162 14 0.03
163 2 0.00
164 19 0.04
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (151 bp):
GACATCATTTACAGCATAACTCAAGTAGAAGGGTTATCTACCAAAGACCTTCGAGTTCGATACAC
TCAGCTCTAGGCATCATTTGCAGCATAGCTAAGTAGAAGGGTTATCTGACCAAAGACCTCCGAGT
TCGACTACGCTCAGCTCAAAG
Found at i:604843 original size:73 final size:75
Alignment explanation
Indices: 604431--605144 Score: 464
Period size: 73 Copynumber: 9.4 Consensus size: 75
604421 CAACATTTAC
* * * *
604431 AGCAAAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGAGTACGCTCAACT
1 AGCATAACTCAA-G-TAGAAGGGTTATCTG-C--CAAAGACC-TCGAGTTCGACTACACTCAGCT
* *
604496 CTAAGACACATCATTT
60 CGAAGGCACATCATTT
* * * * * *
604512 GCAGCATAGCTTAAGTCGAGAAGGGTTATCTACCAAAGACCACCGAGTTCGATTACATTCAGCCT
1 --AGCATAACTCAAGT--AGAAGGGTTATCTGCCAAAGACC-TCGAGTTCGACTACACTCAG-CT
* *
604577 CGAGGGCACATTATTT
60 CGAAGGCACATCATTT
* * *
604593 ACTGCATAACTCAAGTAGAAGGGTTATCTACCAAAGACCTTCGAG-TCGA-TACGCTCAGCT--T
1 A--GCATAACTCAAGTAGAAGGGTTATCTGCCAAAGACC-TCGAGTTCGACTACACTCAGCTCGA
*
604654 AGGCACAT--TTGC
63 AGGCACATCATT-T
* * *
604666 AGCATAGCT-AAGTCAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCC
1 AGCATAACTCAAGT-AGAAGGGTTATCTG--CCAAAGACC-TCGAGTTCGACTACACTCAGCTCG
604730 AAGG--CATCATTT
62 AAGGCACATCATTT
*
604742 GCAGCATAGCT-AAGTCAGAAGGG-TATCTGCCAAAGACC-CGAGTTCGA-TACACTCAGCTCGA
1 --AGCATAACTCAAGT-AGAAGGGTTATCTGCCAAAGACCTCGAGTTCGACTACACTCAGCTCGA
*
604803 TGGCACATCATTAT
63 AGGCACATCATT-T
* * *
604817 AACATAACTCAAGTAGAAGGG-TATCTGCCAAAGACC-CGAGTTCGA-TACGCTCAGCT-TAAGG
1 AGCATAACTCAAGTAGAAGGGTTATCTGCCAAAGACCTCGAGTTCGACTACACTCAGCTCGAAGG
604878 CACATCA-TT
66 CACATCATTT
* * *
604887 AGCCTAAGTC--G-AGAAGGGTTATCTGCACCAAAGACCTTC-AGTTCGA-TACACTCAGCTC-C
1 AGCATAACTCAAGTAGAAGGGTTATCTG--CCAAAGACC-TCGAGTTCGACTACACTCAGCTCGA
604946 AGG--CATCATTT
63 AGGCACATCATTT
* * * *
604957 -GC--AGCTTCAAGTAGAAGGGTTATCTGCAACAAAGACCTTC-AGTTTGACTACGCTCAGCTCA
1 AGCATAAC-TCAAGTAGAAGGGTTATCTGC--CAAAGACC-TCGAGTTCGACTACACTCAGCTCG
*
605018 AAGGGACATCATTT
62 AAGGCACATCATTT
* * *
605032 GCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTT
1 --AGCATAACTCAAGT--AGAAGGGTTATCTGCCAAAGA-CCTCGAGTTCGACTACACTCAGC-T
* ** *
605097 CGAGGGTGCATCATGT
60 CGAAGGCACATCATTT
605113 A-CAATATAACTCAAGGCTAGAAGGGTTATCTG
1 AGC---ATAACTCAA-G-TAGAAGGGTTATCTG
605145 TCAACAAAAA
Statistics
Matches: 522, Mismatches: 56, Indels: 108
0.76 0.08 0.16
Matches are distributed among these distances:
67 8 0.02
68 9 0.02
69 8 0.02
70 24 0.05
71 72 0.14
72 38 0.07
73 76 0.15
74 22 0.04
75 32 0.06
76 2 0.00
77 18 0.03
78 28 0.05
79 42 0.08
80 43 0.08
81 74 0.14
82 3 0.01
83 23 0.04
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (75 bp):
AGCATAACTCAAGTAGAAGGGTTATCTGCCAAAGACCTCGAGTTCGACTACACTCAGCTCGAAGG
CACATCATTT
Found at i:605197 original size:21 final size:20
Alignment explanation
Indices: 605172--605233 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
605162 GATTATTTCC
605172 CTTGAAACAAATTTTGTCTCT
1 CTTGAAAC-AATTTTGTCTCT
* *
605193 CTTGAGAC-A----GTTTCT
1 CTTGAAACAATTTTGTCTCT
605208 CTTGAAACTAATTTTGTCTCT
1 CTTGAAAC-AATTTTGTCTCT
605229 CTTGA
1 CTTGA
605234 GACAGTTTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 12
0.66 0.09 0.26
Matches are distributed among these distances:
15 12 0.39
17 1 0.03
19 1 0.03
21 17 0.55
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (20 bp):
CTTGAAACAATTTTGTCTCT
Found at i:605269 original size:37 final size:36
Alignment explanation
Indices: 605167--605289 Score: 192
Period size: 36 Copynumber: 3.4 Consensus size: 36
605157 TTTGAGATTA
605167 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
605203 TTTCTCTTGAAACTAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
605239 TTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
**
605276 TTTTTCTTGAAACA
1 TTTCCCTTGAAACA
605290 CTAATCTTCG
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
36 47 0.60
37 31 0.40
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:605386 original size:35 final size:36
Alignment explanation
Indices: 605344--605452 Score: 121
Period size: 43 Copynumber: 2.9 Consensus size: 36
605334 TGAGACTATT
605344 TCTCTTGAAACAC-AAAAACAACCTTTGAAATTGTG
1 TCTCTTGAAACACAAAAAACAACCTTTGAAATTGTG
* *
605379 TCTCTTGAAACACAAAAAAAACAAAAAAATCTTTGAAATTGTT
1 TCTCTTGAAACAC--AAAAAAC-----AACCTTTGAAATTGTG
*
605422 TCTCTTGAAACACAAAAAAAAACCTTTGAAA
1 TCTCTTGAAACACAAAAAACAACCTTTGAAA
605453 ATGCTTCTAT
Statistics
Matches: 62, Mismatches: 4, Indels: 15
0.77 0.05 0.19
Matches are distributed among these distances:
35 13 0.21
36 10 0.16
38 6 0.10
41 6 0.10
43 27 0.44
ACGTcount: A:0.48, C:0.17, G:0.08, T:0.27
Consensus pattern (36 bp):
TCTCTTGAAACACAAAAAACAACCTTTGAAATTGTG
Found at i:605418 original size:43 final size:44
Alignment explanation
Indices: 605355--605442 Score: 151
Period size: 43 Copynumber: 2.0 Consensus size: 44
605345 CTCTTGAAAC
605355 ACAAAAACAACCTTTGAAATTGTGTCTCTTGAAACACAAAAAAA
1 ACAAAAACAACCTTTGAAATTGTGTCTCTTGAAACACAAAAAAA
* *
605399 ACAAAAA-AATCTTTGAAATTGTTTCTCTTGAAACACAAAAAAA
1 ACAAAAACAACCTTTGAAATTGTGTCTCTTGAAACACAAAAAAA
605442 A
1 A
605443 ACCTTTGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
43 35 0.83
44 7 0.17
ACGTcount: A:0.51, C:0.16, G:0.08, T:0.25
Consensus pattern (44 bp):
ACAAAAACAACCTTTGAAATTGTGTCTCTTGAAACACAAAAAAA
Found at i:607532 original size:11 final size:10
Alignment explanation
Indices: 607516--607668 Score: 60
Period size: 10 Copynumber: 15.4 Consensus size: 10
607506 TTGATTTATT
607516 TTTTTATTCTA
1 TTTTTATT-TA
607527 TTTTTATTTA
1 TTTTTATTTA
**
607537 TTTTCCTTTAA
1 TTTTTATTT-A
607548 CTTTTT-TTTCA
1 -TTTTTATTT-A
607559 TTTTTCATTT-
1 TTTTT-ATTTA
*
607569 TATTTATTTCA
1 TTTTTATTT-A
607580 TTTTTATTTA
1 TTTTTATTTA
607590 --TTTA---A
1 TTTTTATTTA
607595 TTTTTATTTA
1 TTTTTATTTA
*
607605 TTTTTCTTT-
1 TTTTTATTTA
*
607614 TCTTTTCTTT-
1 T-TTTTATTTA
*
607624 TCCTCTTGATTTA
1 T--T-TTTATTTA
607637 TTATTTATTTA
1 TT-TTTATTTA
607648 -TTTTA--TA
1 TTTTTATTTA
*
607655 TATTTATTTA
1 TTTTTATTTA
607665 TTTT
1 TTTT
607669 AACATTTATT
Statistics
Matches: 111, Mismatches: 13, Indels: 37
0.69 0.08 0.23
Matches are distributed among these distances:
5 1 0.01
7 6 0.05
8 8 0.07
9 9 0.08
10 43 0.39
11 31 0.28
12 12 0.11
13 1 0.01
ACGTcount: A:0.18, C:0.08, G:0.01, T:0.73
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:607535 original size:23 final size:22
Alignment explanation
Indices: 607479--607616 Score: 70
Period size: 24 Copynumber: 6.0 Consensus size: 22
607469 TTTTTAAAAC
* *
607479 ATTTTTAATTATTTTTTTTTGT
1 ATTTTTATTTATTTTTTTTTCT
*
607501 GTTCTTTGATTTATTTTTTTATTCT
1 ATT-TTT-ATTTATTTTTTT-TTCT
**
607526 ATTTTTATTTATTTTCCTTTAACT
1 ATTTTTATTTATTTT--TTTTTCT
* *
607550 -TTTTT-TTCATTTTTCATTT-T
1 ATTTTTATTTATTTTT-TTTTCT
*
607570 A--TTTATTTCATTTTTATTTATTT
1 ATTTTTATTT-ATTTTT-TTT-TCT
607593 AATTTTTATTTATTTTTCTTTTCT
1 -ATTTTTATTTATTTTT-TTTTCT
607617 TTTCTTTTCC
Statistics
Matches: 87, Mismatches: 15, Indels: 26
0.68 0.12 0.20
Matches are distributed among these distances:
19 3 0.03
20 4 0.05
21 9 0.10
22 10 0.11
23 18 0.21
24 19 0.22
25 17 0.20
26 7 0.08
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (22 bp):
ATTTTTATTTATTTTTTTTTCT
Found at i:607569 original size:15 final size:15
Alignment explanation
Indices: 607561--607607 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
607551 TTTTTTCATT
607561 TTTCA-TTTTATTTA
1 TTTCATTTTTATTTA
607575 TTTCATTTTTATTTA
1 TTTCATTTTTATTTA
*
607590 TTTAATTTTTATTTA
1 TTTCATTTTTATTTA
607605 TTT
1 TTT
607608 TTCTTTTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 5 0.16
15 26 0.84
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTCATTTTTATTTA
Found at i:607577 original size:16 final size:16
Alignment explanation
Indices: 607558--607683 Score: 53
Period size: 15 Copynumber: 8.2 Consensus size: 16
607548 CTTTTTTTTC
607558 ATTTTTCATTTTATTT
1 ATTTTTCATTTTATTT
607574 A--TTTCATTTTTATTT
1 ATTTTTCA-TTTTATTT
*
607589 A--TTTAATTTTTATTT
1 ATTTTTCA-TTTTATTT
*
607604 ATTTTTC-TTTTCTTT
1 ATTTTTCATTTTATTT
* *
607619 -TCTTTTCCTCTTGATTT
1 AT-TTTTCAT-TTTATTT
607636 A---TT-A-TTTATTT
1 ATTTTTCATTTTATTT
607647 ATTTTAT-ATATTTATTT
1 ATTTT-TCAT-TTTATTT
*
607664 ATTTTAACA-TTTATTT
1 ATTTT-TCATTTTATTT
607680 ATTT
1 ATTT
607684 CTTTTTTATC
Statistics
Matches: 88, Mismatches: 8, Indels: 28
0.71 0.06 0.23
Matches are distributed among these distances:
11 7 0.08
14 9 0.10
15 37 0.42
16 13 0.15
17 21 0.24
18 1 0.01
ACGTcount: A:0.21, C:0.07, G:0.01, T:0.71
Consensus pattern (16 bp):
ATTTTTCATTTTATTT
Found at i:607579 original size:21 final size:19
Alignment explanation
Indices: 607554--607692 Score: 63
Period size: 19 Copynumber: 7.6 Consensus size: 19
607544 TTAACTTTTT
607554 TTTCATTTTTCATTTTATTTA
1 TTTCATTTTT-A-TTTATTTA
607575 TTTCATTTTTATTTATTTA
1 TTTCATTTTTATTTATTTA
607594 ----ATTTTTATTTA-TT-
1 TTTCATTTTTATTTATTTA
*
607607 TTTC-TTTTCT-TTTCTTT-
1 TTTCATTTT-TATTTATTTA
*
607624 TCCTC-TTGATTTA-TTATTTA
1 T-TTCATT--TTTATTTATTTA
*
607644 TTT-A-TTTTATATATTTA
1 TTTCATTTTTATTTATTTA
*
607661 TTT-ATTTTAACATTTATTTA
1 TTTCATTTT--TATTTATTTA
*
607681 TTTCTTTTTTAT
1 TTTCATTTTTAT
607693 CTAACATTTT
Statistics
Matches: 92, Mismatches: 9, Indels: 36
0.67 0.07 0.26
Matches are distributed among these distances:
14 2 0.02
15 11 0.12
16 11 0.12
17 14 0.15
18 8 0.09
19 17 0.18
20 15 0.16
21 14 0.15
ACGTcount: A:0.19, C:0.08, G:0.01, T:0.72
Consensus pattern (19 bp):
TTTCATTTTTATTTATTTA
Found at i:618196 original size:20 final size:21
Alignment explanation
Indices: 618171--618222 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
618161 TTTTCCTAAT
*
618171 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
618191 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
618212 TCGCAATGCGA
1 TCGCAATGCGA
618223 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:618236 original size:20 final size:20
Alignment explanation
Indices: 618211--618304 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
618201 AATTGGGAAA
618211 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
618231 ATCGCAATACGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
618251 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
618272 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
618292 TTCGCAACGCGAT
1 ATCGCAATGCGAT
618305 TTACATAGCG
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.03
20 43 0.72
21 13 0.22
22 2 0.03
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:618877 original size:19 final size:19
Alignment explanation
Indices: 618853--618897 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
618843 GCAACGAGAG
*
618853 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
618872 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
618891 AATCGCA
1 AATCGCA
618898 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:618915 original size:19 final size:19
Alignment explanation
Indices: 618893--619076 Score: 172
Period size: 19 Copynumber: 10.1 Consensus size: 19
618883 GAAACCAAAA
*
618893 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
618912 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
618931 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
618950 TCACGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
618969 TCGCGGTGCGATTCTC--T
1 TCGCGTTGCGATTTTCATT
* **
618986 T---GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
619002 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
619016 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
619035 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
619055 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
619075 TC
1 TC
619077 AACCAAAAGA
Statistics
Matches: 135, Mismatches: 18, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
14 18 0.13
16 4 0.03
17 4 0.03
19 77 0.57
20 31 0.23
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:619001 original size:33 final size:33
Alignment explanation
Indices: 618964--619051 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
618954 GTTGCGATTT
* *
618964 TCATTTCGCGGTGCGATTCTCTTGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
618997 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
619030 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
619052 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.26, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:621225 original size:42 final size:42
Alignment explanation
Indices: 621165--621371 Score: 218
Period size: 42 Copynumber: 4.9 Consensus size: 42
621155 GCCCGACTCG
* * *
621165 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
621207 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * * * *
621249 ACTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
621291 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
621333 ACTGTCATCGTTGAAGAAGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAG-AGTCCACTCCCACCGTTCAAGAG
621372 CCCGATTCAC
Statistics
Matches: 134, Mismatches: 30, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
42 129 0.96
43 5 0.04
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:621245 original size:21 final size:21
Alignment explanation
Indices: 621221--621371 Score: 58
Period size: 21 Copynumber: 7.2 Consensus size: 21
621211 TCATTCCTCG
621221 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** *
621242 AGAGGCCACTGTCATCC-CTCA
1 AGAGTCCCCTCCCA-CCGTTCA
* * * *
621263 AGAGTCCACTCCTATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
* ** *
621284 AGAGGCCCCTATCATTCC--TCG
1 AGAGTCCCCTCCCA--CCGTTCA
621305 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
621326 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
621347 AGAAGT-CCCTCCCACCATTCA
1 AG-AGTCCCCTCCCACCGTTCA
621368 AGAG
1 AGAG
621372 CCCGATTCAC
Statistics
Matches: 86, Mismatches: 37, Indels: 15
0.62 0.27 0.11
Matches are distributed among these distances:
19 2 0.02
20 3 0.03
21 76 0.88
22 4 0.05
23 1 0.01
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Done.