Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 118 of 182
Found at i:36165925 original size:135 final size:135
Alignment explanation
Indices: 36165758--36166146 Score: 417
Period size: 142 Copynumber: 2.8 Consensus size: 135
36165748 ACTGCTAACA
* * * *
36165758 CCTAAACCTAAAACCCCAACCCTTAAACCATAA-CGCCTAAACCCCTATCCTCTATCCCCTAAAC
1 CCTAACCCTTAAACCACAACCCATAAACCATAATC-CCTAAACCCCTA-CCTCTATCCCCTAAAC
* *
36165822 ACTGAATCATAAAACATGAACTATAAACCCTAAACCCCTAACCCTTAA-CCTT-TAACACCTAAA
64 -CTGAATCATAAAACATAAATTATAAACCCTAAACCCCTAACCCTTAACCCTTCTAACACCTAAA
*
36165885 CCTCAATC
128 CCTCAAAC
* * *
36165893 CCTAACCCTTAAACCACAAACCATAAACCATAATCCCTAAACCTCTAACTCCTATCCCCTAAATC
1 CCTAACCCTTAAACCACAACCCATAAACCATAATCCCTAAACCCCTACCT-CTATCCCCTAAA-C
* * *
36165958 TTGAATCATAAAACATAAATTATAAACGCTAAACCCCTAACCCCTAACCCTTAACCCCTAACACC
64 CTGAATCATAAAACATAAATTATAAACCCTAAACCCCTAACCCTTAACCCTT-----CTAACACC
* *
36166023 TAAACTTTAAAC
124 TAAACCTCAAAC
* * * * * * **
36166035 CCCAACACTTAAAACATAACCCATAAACCATAATCCTTAAACCCTTAACC-CTTATCCTTTAAAC
1 CCTAACCCTTAAACCACAACCCATAAACCATAATCCCTAAACCCCT-ACCTC-TATCCCCTAAA-
*
36166099 CCTAAATCATAAAACATAAATTATAAACCCTAAACCCCTAACCCTTAA
63 CCTGAATCATAAAACATAAATTATAAACCCTAAACCCCTAACCCTTAA
36166147 ACCCCAACCC
Statistics
Matches: 211, Mismatches: 31, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
134 2 0.01
135 93 0.44
136 6 0.03
141 1 0.00
142 107 0.51
143 2 0.01
ACGTcount: A:0.41, C:0.35, G:0.01, T:0.22
Consensus pattern (135 bp):
CCTAACCCTTAAACCACAACCCATAAACCATAATCCCTAAACCCCTACCTCTATCCCCTAAACCT
GAATCATAAAACATAAATTATAAACCCTAAACCCCTAACCCTTAACCCTTCTAACACCTAAACCT
CAAAC
Found at i:36165999 original size:7 final size:7
Alignment explanation
Indices: 36165989--36166025 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
36165979 ATAAACGCTA
36165989 AACCCCT
1 AACCCCT
36165996 AACCCCT
1 AACCCCT
*
36166003 AACCCTT
1 AACCCCT
36166010 AACCCCT
1 AACCCCT
*
36166017 AACACCT
1 AACCCCT
36166024 AA
1 AA
36166026 ACTTTAAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.35, C:0.49, G:0.00, T:0.16
Consensus pattern (7 bp):
AACCCCT
Found at i:36166032 original size:21 final size:22
Alignment explanation
Indices: 36166010--36166100 Score: 55
Period size: 22 Copynumber: 4.2 Consensus size: 22
36166000 CCTAACCCTT
*
36166010 AACCCCTAACACCTAAACTTTA
1 AACCCCTAACACCTAAACCTTA
* * *
36166032 AACCCC-AACACTTAAAACAT-
1 AACCCCTAACACCTAAACCTTA
* *
36166052 AACCCATAA-ACCATAATCCTTA
1 AACCCCTAACACC-TAAACCTTA
* * *
36166074 AACCCTTAAC-CCTTATCCTTTA
1 AACCCCTAACACCTAAACC-TTA
36166096 AACCC
1 AACCC
36166101 TAAATCATAA
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
20 7 0.13
21 22 0.42
22 24 0.45
ACGTcount: A:0.41, C:0.36, G:0.00, T:0.23
Consensus pattern (22 bp):
AACCCCTAACACCTAAACCTTA
Found at i:36166111 original size:14 final size:14
Alignment explanation
Indices: 36166094--36166132 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
36166084 CCTTATCCTT
36166094 TAAACCCTAAATCA
1 TAAACCCTAAATCA
* * *
36166108 TAAAACATAAATTA
1 TAAACCCTAAATCA
36166122 TAAACCCTAAA
1 TAAACCCTAAA
36166133 CCCCTAACCC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.56, C:0.21, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAATCA
Found at i:36166141 original size:14 final size:14
Alignment explanation
Indices: 36166124--36166162 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
36166114 ATAAATTATA
36166124 AACCC-TAAACCCC
1 AACCCTTAAACCCC
36166137 TAACCCTTAAACCCC
1 -AACCCTTAAACCCC
36166152 AACCCTTAAAC
1 AACCCTTAAAC
36166163 AATAAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.15
Consensus pattern (14 bp):
AACCCTTAAACCCC
Found at i:36166196 original size:15 final size:15
Alignment explanation
Indices: 36166172--36166205 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
36166162 CAATAAATAA
*
36166172 TAAA-CCATAATCCT
1 TAAACCCATAATCCC
36166186 TAAACCCATAATCCC
1 TAAACCCATAATCCC
36166201 TAAAC
1 TAAAC
36166206 TACTAATACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAACCCATAATCCC
Found at i:36166843 original size:40 final size:38
Alignment explanation
Indices: 36166786--36166866 Score: 90
Period size: 39 Copynumber: 2.1 Consensus size: 38
36166776 TTTGTGGAGC
* * *
36166786 TTTTACAAAAGCGCCGCTAATGCTCGATCTATTGCGGTG
1 TTTTACAAAAGCACCGCTAATGCT-GACCTATTGCGGCG
* * *
36166825 TTTTAGAAAGAGCACCGCTATTGCTTACCTATTGCGGCG
1 TTTTACAAA-AGCACCGCTAATGCTGACCTATTGCGGCG
36166864 TTT
1 TTT
36166867 GTTTAAATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
39 22 0.63
40 13 0.37
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (38 bp):
TTTTACAAAAGCACCGCTAATGCTGACCTATTGCGGCG
Found at i:36175382 original size:19 final size:20
Alignment explanation
Indices: 36175351--36175394 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
36175341 TTCACAACCA
*
36175351 ATTTCACCATTTCATATTCT
1 ATTTCACCATTTCATATTCC
*
36175371 ATTTCA-CATTTCATTTTCC
1 ATTTCACCATTTCATATTCC
36175390 ATTTC
1 ATTTC
36175395 TCATCCTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.23, C:0.25, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTCACCATTTCATATTCC
Found at i:36195538 original size:26 final size:23
Alignment explanation
Indices: 36195505--36195551 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
36195495 TTCGAAAGTA
36195505 AAATGAAATTTGATTCGAGATTAATC
1 AAATGAAA-TTG-TTCGAG-TTAATC
36195531 AAATGAAATTGTTCGAGTTAA
1 AAATGAAATTGTTCGAGTTAA
36195552 ATTTAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 3 0.14
26 8 0.38
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (23 bp):
AAATGAAATTGTTCGAGTTAATC
Found at i:36195766 original size:23 final size:24
Alignment explanation
Indices: 36195732--36195780 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
36195722 TTAAGTCCCA
36195732 AAAATGATTATT-TTT-TTCTTTT
1 AAAATGATTATTCTTTATTCTTTT
* *
36195754 AAAATTATATATTCTTTATTTTTTT
1 AAAATGAT-TATTCTTTATTCTTTT
36195779 AA
1 AA
36195781 TATTTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 7 0.32
23 4 0.18
24 3 0.14
25 8 0.36
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (24 bp):
AAAATGATTATTCTTTATTCTTTT
Found at i:36195784 original size:11 final size:11
Alignment explanation
Indices: 36195770--36195807 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
36195760 ATATATTCTT
*
36195770 TATTTTTTTAA
1 TATTTTTATAA
36195781 TATTTTTATAA
1 TATTTTTATAA
*
36195792 T-TTTTTAAAA
1 TATTTTTATAA
36195802 TATTTT
1 TATTTT
36195808 GAATTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATTTTTATAA
Found at i:36195812 original size:19 final size:19
Alignment explanation
Indices: 36195768--36195834 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
36195758 TTATATATTC
* *
36195768 TTTATTTTTTTAATATT-T
1 TTTAATTTTTTAAAATTAT
36195786 TTATAATTTTTTAAAA-TAT
1 TT-TAATTTTTTAAAATTAT
*
36195805 TTTGAA-TTTTAAAAATTAT
1 TTT-AATTTTTTAAAATTAT
36195824 TTTAATTTTTT
1 TTTAATTTTTT
36195835 TTGTAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
18 14 0.35
19 26 0.65
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (19 bp):
TTTAATTTTTTAAAATTAT
Found at i:36204435 original size:3 final size:3
Alignment explanation
Indices: 36204427--36204457 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
36204417 AGTACATATT
36204427 ATC ATC ATC ATC ATC ATC ATC ATC AT- ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
36204458 TTAATCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:36235410 original size:30 final size:29
Alignment explanation
Indices: 36235376--36235439 Score: 101
Period size: 30 Copynumber: 2.2 Consensus size: 29
36235366 CAACTTAACA
36235376 AACAAATACCTCTAAAATAATAACAAAATT
1 AACAAATACCTCTAAAATAAT-ACAAAATT
* *
36235406 AACAAATGCCTTTAAAATAATACAAAATT
1 AACAAATACCTCTAAAATAATACAAAATT
36235435 AACAA
1 AACAA
36235440 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 13 0.41
30 19 0.59
ACGTcount: A:0.59, C:0.16, G:0.02, T:0.23
Consensus pattern (29 bp):
AACAAATACCTCTAAAATAATACAAAATT
Found at i:36246495 original size:18 final size:17
Alignment explanation
Indices: 36246464--36246497 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
36246454 CGTCATCCTT
36246464 TTTCTTCTCCTCTTTTA
1 TTTCTTCTCCTCTTTTA
*
36246481 TTTCATTCTCTTCTTTT
1 TTTC-TTCTCCTCTTTT
36246498 CTTCTCACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTCTTCTCCTCTTTTA
Found at i:36246645 original size:18 final size:18
Alignment explanation
Indices: 36246622--36246670 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
36246612 ACCGTAAATA
* *
36246622 CTTTTCATTTCTTTTTCT
1 CTTTTCTTTTCTTTTACT
36246640 CTTTTCTTTTACTTTTACT
1 CTTTTCTTTT-CTTTTACT
36246659 -TTTTCTTTTCTT
1 CTTTTCTTTTCTT
36246671 CCTTCTTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 3 0.11
18 18 0.64
19 7 0.25
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.73
Consensus pattern (18 bp):
CTTTTCTTTTCTTTTACT
Found at i:36246646 original size:7 final size:6
Alignment explanation
Indices: 36246629--36246667 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
36246619 ATACTTTTCA
* *
36246629 TTTCTT TTTCTCT TTTCTT TTACTT TTACTT TTTCTT TT
1 TTTCTT TTTCT-T TTTCTT TTTCTT TTTCTT TTTCTT TT
36246668 CTTCCTTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTCTT
Found at i:36247425 original size:39 final size:39
Alignment explanation
Indices: 36247382--36247456 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 39
36247372 TATTAAATAG
* * *
36247382 CATGCCACTGATTGTATCCTATATTGATTGCATGTATAA
1 CATGCCACTGACTGAAACCTATATTGATTGCATGTATAA
* * *
36247421 CATGCCATTGACTGAAACGTATATTGATTGCTTGTA
1 CATGCCACTGACTGAAACCTATATTGATTGCATGTA
36247457 CACATACAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 30 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.37
Consensus pattern (39 bp):
CATGCCACTGACTGAAACCTATATTGATTGCATGTATAA
Found at i:36247719 original size:24 final size:24
Alignment explanation
Indices: 36247692--36247763 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
36247682 TATTTGCATA
36247692 TCTGGTGGCTTGTCCACATATATT
1 TCTGGTGGCTTGTCCACATATATT
** *
36247716 TCTGGCAGCTTGAATGCA-AT-TA--
1 TCTGGTGGCTTG--TCCACATATATT
36247738 T-TGGTGGCTTGTCCACATATATT
1 TCTGGTGGCTTGTCCACATATATT
36247761 TCT
1 TCT
36247764 AGCAGCTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 3 0.09
20 2 0.06
21 10 0.29
22 1 0.03
23 1 0.03
24 13 0.37
25 2 0.06
26 3 0.09
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (24 bp):
TCTGGTGGCTTGTCCACATATATT
Found at i:36247771 original size:24 final size:23
Alignment explanation
Indices: 36247699--36247771 Score: 55
Period size: 24 Copynumber: 3.2 Consensus size: 23
36247689 ATATCTGGTG
36247699 GCTTGTCCACATATATTTCTGGCA
1 GCTTGTCCACATATATTTCT-GCA
* **
36247723 GCTTGAATGCA-AT-TATTGGTG--
1 GCTTG--TCCACATATATTTCTGCA
36247744 GCTTGTCCACATATATTTCTAGCA
1 GCTTGTCCACATATATTTCT-GCA
36247768 GCTT
1 GCTT
36247772 AACTTCAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 3 0.08
20 2 0.06
21 10 0.28
22 1 0.03
23 1 0.03
24 14 0.39
25 2 0.06
26 3 0.08
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (23 bp):
GCTTGTCCACATATATTTCTGCA
Found at i:36247781 original size:45 final size:45
Alignment explanation
Indices: 36247693--36247804 Score: 145
Period size: 45 Copynumber: 2.5 Consensus size: 45
36247683 ATTTGCATAT
*
36247693 CTGGTGGCTTGTCCACATATATTTCTGGCAGCTTGAATGCAATTA
1 CTGGTGGCTTGTCCACATATATTTCTAGCAGCTTGAATGCAATTA
* * *
36247738 TTGGTGGCTTGTCCACATATATTTCTAGCAGCTT-AACTTCAATTG
1 CTGGTGGCTTGTCCACATATATTTCTAGCAGCTTGAA-TGCAATTA
* *
36247783 CTAGTGACTTGTCCACAATATA
1 CTGGTGGCTTGTCCAC-ATATA
36247805 GTGTGTTTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
44 2 0.03
45 51 0.88
46 5 0.09
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.37
Consensus pattern (45 bp):
CTGGTGGCTTGTCCACATATATTTCTAGCAGCTTGAATGCAATTA
Found at i:36250976 original size:21 final size:21
Alignment explanation
Indices: 36250960--36251017 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
36250950 AGAACTGGGA
*
36250960 GTTCTATCGATACAACTCTGG
1 GTTCTACCGATACAACTCTGG
*
36250981 GTTCTACCAATACAACTCTGG
1 GTTCTACCGATACAACTCTGG
36251002 GTTCTACCGATACAAC
1 GTTCTACCGATACAAC
36251018 CCGGACTTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.29
Consensus pattern (21 bp):
GTTCTACCGATACAACTCTGG
Found at i:36252441 original size:12 final size:12
Alignment explanation
Indices: 36252424--36252451 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
36252414 CTTTTGATTT
36252424 CTTTAATTTTAA
1 CTTTAATTTTAA
36252436 CTTTAATTTTAA
1 CTTTAATTTTAA
36252448 CTTT
1 CTTT
36252452 TTAGTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.61
Consensus pattern (12 bp):
CTTTAATTTTAA
Found at i:36268309 original size:141 final size:141
Alignment explanation
Indices: 36267996--36268381 Score: 541
Period size: 141 Copynumber: 2.8 Consensus size: 141
36267986 GATTCCATTG
* * *
36267996 GCATTAGTTGTGGCATGTGAGAACTTTCTGTTGCCATTTTTGATTTCTTATGTGGTTCTTTTGCA
1 GCATTAGTTGTGGCATTTGAGAACTTTCTGTTGCCATTTTTGATTTCTTATGCGGTTCTGTTGCA
* * * *
36268061 AAAGACATCTGTGGTTCGAGCTTTTTGGTTCGTAGATC------TTCAGGTTGCTTAACTTCAAT
66 AAAGATATCTGTGGTTTGAGCTCTTTGGTTCGTAGTTCTTGAGGTTCAGGTTGCTTAACTTCAAT
36268120 GTGGACATTCT
131 GTGGACATTCT
* * * *
36268131 GCATTAGTTGTGGCATTTCAGAACTTCCTATTTCCATTTTTGATTTCTTATGCGGTTCTGTTGCA
1 GCATTAGTTGTGGCATTTGAGAACTTTCTGTTGCCATTTTTGATTTCTTATGCGGTTCTGTTGCA
* * *
36268196 AAAGATGTCTGCGGTTTGAGCTCTTTGGTTCGTAGTTCTTGAGGTTGAGGTTGCTTAACTTCAAT
66 AAAGATATCTGTGGTTTGAGCTCTTTGGTTCGTAGTTCTTGAGGTTCAGGTTGCTTAACTTCAAT
36268261 GTGGACATTCT
131 GTGGACATTCT
* * * * * *
36268272 GCGTTAGTTGTGGCATTTGAGAACTTTCTGTCGCCATTTTAGATTTCTTATGCTGCTCTGCTGCA
1 GCATTAGTTGTGGCATTTGAGAACTTTCTGTTGCCATTTTTGATTTCTTATGCGGTTCTGTTGCA
*
36268337 AAAGATATCTGTGGTTTGAGCTCTTTAGTTCGTAGTTCTTGAGGT
66 AAAGATATCTGTGGTTTGAGCTCTTTGGTTCGTAGTTCTTGAGGT
36268382 CTCTTAACTT
Statistics
Matches: 218, Mismatches: 27, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
135 90 0.41
141 128 0.59
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.42
Consensus pattern (141 bp):
GCATTAGTTGTGGCATTTGAGAACTTTCTGTTGCCATTTTTGATTTCTTATGCGGTTCTGTTGCA
AAAGATATCTGTGGTTTGAGCTCTTTGGTTCGTAGTTCTTGAGGTTCAGGTTGCTTAACTTCAAT
GTGGACATTCT
Found at i:36270915 original size:10 final size:9
Alignment explanation
Indices: 36270886--36270932 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
36270876 ATTAATTTTA
36270886 TTTTTAT-T
1 TTTTTATAT
*
36270894 TTTTTATGT
1 TTTTTATAT
36270903 TTTTTATAAT
1 TTTTTAT-AT
*
36270913 TTTTAATAT
1 TTTTTATAT
36270922 TTTTTA-AT
1 TTTTTATAT
36270930 TTT
1 TTT
36270933 AAAGTTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
8 12 0.35
9 15 0.44
10 7 0.21
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (9 bp):
TTTTTATAT
Found at i:36272088 original size:7 final size:7
Alignment explanation
Indices: 36272066--36272104 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
36272056 ACATACATTT
36272066 TAATATAC
1 TAAT-TAC
36272074 TAAATTAC
1 T-AATTAC
36272082 TAATTAC
1 TAATTAC
36272089 TAATTAC
1 TAATTAC
36272096 TAATTAC
1 TAATTAC
36272103 TA
1 TA
36272105 TTGATGTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 22 0.73
8 5 0.17
9 3 0.10
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (7 bp):
TAATTAC
Found at i:36275311 original size:16 final size:17
Alignment explanation
Indices: 36275271--36275319 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
36275261 TACTAATACA
*
36275271 ATTACTATTATTTTATT
1 ATTATTATTATTTTATT
36275288 ACTTTATTATTATTTTATT
1 A--TTATTATTATTTTATT
*
36275307 A-TATTATCATTTT
1 ATTATTATTATTTT
36275320 GTTTTTACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 11 0.39
17 1 0.04
19 16 0.57
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTATTATTATTTTATT
Found at i:36275313 original size:19 final size:20
Alignment explanation
Indices: 36275271--36275313 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
36275261 TACTAATACA
*
36275271 ATTACTATTATTTTATTACT
1 ATTATTATTATTTTATTACT
36275291 -TTATTATTATTTTATTA-T
1 ATTATTATTATTTTATTACT
36275309 ATTAT
1 ATTAT
36275314 CATTTTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTATTATTATTTTATTACT
Found at i:36282346 original size:94 final size:94
Alignment explanation
Indices: 36282177--36283223 Score: 1014
Period size: 94 Copynumber: 11.2 Consensus size: 94
36282167 AATTCTAGTC
* * * * * * * * *
36282177 CCCCTAAAGTTGCAGTGGGTTGGAATAAAACTATAGTGGCGAATCTTATCTCCTTAAAGATGCAA
1 CCCCTAAAGTTGCAGTAGGTCGGAATGAAACTACAATGGAGAATCTTATCTCCCTGAAGATGCAG
*
36282242 TGGAGCAAGATGAAACTACAAATCCTATA
66 TGGAGCAAGATGAAGCTACAAATCCTATA
* * * * ** * *
36282271 CCTCTAAAGTTGTAGTAGGTTGGAATAAAACTACAGCGGAGAATCTTATCTTCCTAAAGATGCAG
1 CCCCTAAAGTTGCAGTAGGTCGGAATGAAACTACAATGGAGAATCTTATCTCCCTGAAGATGCAG
*
36282336 TGGAGTAAGATGAAGCTACAAATCCTATA
66 TGGAGCAAGATGAAGCTACAAATCCTATA
* * * *
36282365 CCCC-AGAAGTTACAGTGGGTTGGAATGAAACTACAATGGCGAATCTTATCTCCCTGAAGATGCA
1 CCCCTA-AAGTTGCAGTAGGTCGGAATGAAACTACAATGGAGAATCTTATCTCCCTGAAGATGCA
36282429 GTGGAGCAAGATGAAGCTACAAATCCTATA
65 GTGGAGCAAGATGAAGCTACAAATCCTATA
* * * * *
36282459 TCCCTAAAGTTACAGT-GGAAT-GGATTGAAACTACAA-CGACGAATCTTATCTCCCTAAAGATG
1 CCCCTAAAGTTGCAGTAGG--TCGGAATGAAACTACAATGGA-GAATCTTATCTCCCTGAAGATG
* * *
36282521 CAGTAGAGCAAGATGAAGCTATAAGTCCTATA
63 CAGTGGAGCAAGATGAAGCTACAAATCCTATA
* * * * * * * *
36282553 CCCTTGAAGTTGCAGTAGGTCAGAATGAAATTACAATGGCA-AATATTATCTCCTTGAAGTTGTA
1 CCCCTAAAGTTGCAGTAGGTCGGAATGAAACTACAATGG-AGAATCTTATCTCCCTGAAGATGCA
* * *
36282617 ATGGAACAAGATGGAGCTACAAATCCTATA
65 GTGGAGCAAGATGAAGCTACAAATCCTATA
* * *
36282647 CCCCTAAAATTGCAGTGGGTCGGAATGAAACTACAATGGCGAATCTTATCTCCCTGAAG-T-CAT
1 CCCCTAAAGTTGCAGTAGGTCGGAATGAAACTACAATGGAGAATCTTATCTCCCTGAAGATGC--
*
36282710 AATGGAGCAAGATGAAGCTACAAATCCTATA
64 AGTGGAGCAAGATGAAGCTACAAATCCTATA
* * * * * ** * * *
36282741 CCTCTGAAGTTCCAATTGGTCAAAATGAAACTACAAT-TATAAATCTTATCTCCCTGAAGTTGCA
1 CCCCTAAAGTTGCAGTAGGTCGGAATGAAACTACAATGGA-GAATCTTATCTCCCTGAAGATGCA
36282805 GTGGAGCAAGATGAAGCTACAAATCCTATA
65 GTGGAGCAAGATGAAGCTACAAATCCTATA
* * * * * * *
36282835 CCCCTGAAGTTGTAGTAGGTCGAAATGAAACTACAACGGTGAATCTTATCTCCTTGAAG-TAGTA
1 CCCCTAAAGTTGCAGTAGGTCGGAATGAAACTACAATGGAGAATCTTATCTCCCTGAAGAT-GCA
*
36282899 GTGGAGCAAGATGGAGCTACAAATCCTATA
65 GTGGAGCAAGATGAAGCTACAAATCCTATA
* * *
36282929 CCCCTAAAGTTGCAGTAGGTCAGAATGAAACTACAATGGCGAATCTTATCTCCCTGAAGTTGCAG
1 CCCCTAAAGTTGCAGTAGGTCGGAATGAAACTACAATGGAGAATCTTATCTCCCTGAAGATGCAG
* * *
36282994 TCGAACAAGATGAAACTACAAATCCTATA
66 TGGAGCAAGATGAAGCTACAAATCCTATA
* * * * * *
36283023 CCCCTGAAGTTGTAGTGGGTC-GAATGAAACTACAATGGCA-AATCTTATCTCCATGTAGTTGCA
1 CCCCTAAAGTTGCAGTAGGTCGGAATGAAACTACAATGG-AGAATCTTATCTCCCTGAAGATGCA
* * *
36283086 ATAGAGCAAGATAAAGCTACAAATCCTATA
65 GTGGAGCAAGATGAAGCTACAAATCCTATA
* * * * * * * * *
36283116 CCTCTGAAGTTGTAGT-GGAACAGATTGAAACTACAA-CGACAAATCTCATCTCCCT-AAGGATG
1 CCCCTAAAGTTGCAGTAGG-TCGGAATGAAACTACAATGGA-GAATCTTATCTCCCTGAA-GATG
* *
36283178 CAGTGGAGCCAGATAAAG-T-CAAATCAC-AT-
63 CAGTGGAGCAAGATGAAGCTACAAATC-CTATA
*
36283207 CTTCCTAAAGTTGCAGT
1 C-CCCTAAAGTTGCAGT
36283224 GAAAGGGATA
Statistics
Matches: 803, Mismatches: 124, Indels: 54
0.82 0.13 0.06
Matches are distributed among these distances:
91 1 0.00
92 22 0.03
93 90 0.11
94 681 0.85
95 7 0.01
96 2 0.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Consensus pattern (94 bp):
CCCCTAAAGTTGCAGTAGGTCGGAATGAAACTACAATGGAGAATCTTATCTCCCTGAAGATGCAG
TGGAGCAAGATGAAGCTACAAATCCTATA
Found at i:36282819 original size:50 final size:46
Alignment explanation
Indices: 36282406--36283191 Score: 183
Period size: 44 Copynumber: 16.8 Consensus size: 46
36282396 TACAATGGCG
* *
36282406 AATCTTATCTCCCTGAAGATGCAGTGGAGCAAGATGAAGCTAC--A
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAACTACAAA
* * * * *
36282450 AATCCTATATCCCTAAAGTTACAGTGGA--ATGGATTGAAACTACAACGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCA-AGA-TGAAACTACAA--A
* * * * *
36282498 CGAATCTTATCTCCCTAAAGATGCAGTAGAGCAAGATGAAGCT--ATA
1 --AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAACTACAAA
* * * * *
36282544 AGTCCTATAC-CCTTGAAGTTGCAGTAGG-TC-AGAATGAAATTACAATGGCA
1 AATCTTAT-CTCCCTGAAGTTGCAGT-GGAGCAAG-ATGAAACTACAA----A
* * * * * * *
36282594 AATATTATCTCCTTGAAGTTGTAATGGAACAAGATGGAGCTAC--A
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAACTACAAA
* * * * *
36282638 AATCCTATAC-CCCTAAAATTGCAGTGG-GTC-GGAATGAAACTACAATGGCG
1 AATCTTAT-CTCCCTGAAGTTGCAGTGGAG-CAAG-ATGAAACTACAA----A
*** * *
36282688 AATCTTATCTCCCTGAAGTCATAATGGAGCAAGATGAAGCTAC--A
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAACTACAAA
* * * * * *
36282732 AATCCTATAC-CTCTGAAGTTCCAATTGG-TCAAAATGAAACTACAATTATA
1 AATCTTAT-CTCCCTGAAGTTGC-AGTGGAGCAAGATGAAACTAC-A--A-A
*
36282782 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTAC--A
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAACTACAAA
* * * *
36282826 AATCCTATAC-CCCTGAAGTTGTAGTAGG-TCGAA-ATGAAACTACAACGGTG
1 AATCTTAT-CTCCCTGAAGTTGCAGT-GGAGC-AAGATGAAACTACAA----A
* * * * *
36282876 AATCTTATCTCCTTGAAGTAGTAGTGGAGCAAGATGGAGCTAC--A
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAACTACAAA
* * * *
36282920 AATCCTATAC-CCCTAAAGTTGCAGTAGG-TC-AGAATGAAACTACAATGGCG
1 AATCTTAT-CTCCCTGAAGTTGCAGT-GGAGCAAG-ATGAAACTACAA----A
* *
36282970 AATCTTATCTCCCTGAAGTTGCAGTCGAACAAGATGAAACTAC--A
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAACTACAAA
* * *
36283014 AATCCTATAC-CCCTGAAGTTGTAGTGG-GTCGA-ATGAAACTACAATGGCA
1 AATCTTAT-CTCCCTGAAGTTGCAGTGGAG-CAAGATGAAACTACAA----A
* * * *
36283063 AATCTTATCTCCATGTAGTTGCAATAGAGCAAGAT-AAAGCTAC--A
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAA-CTACAAA
* * * *
36283107 AATCCTATAC-CTCTGAAGTTGTAGTGGAAC-AGATTGAAACTACAACGACA
1 AATCTTAT-CTCCCTGAAGTTGCAGTGGAGCAAGA-TGAAACTAC-A--A-A
* * *
36283157 AATCTCATCTCCCT-AAGGATGCAGTGGAGCCAGAT
1 AATCTTATCTCCCTGAA-GTTGCAGTGGAGCAAGAT
36283192 AAAGTCAAAT
Statistics
Matches: 526, Mismatches: 124, Indels: 178
0.64 0.15 0.21
Matches are distributed among these distances:
42 1 0.00
43 20 0.04
44 220 0.42
45 21 0.04
46 2 0.00
48 3 0.01
49 44 0.08
50 203 0.39
51 11 0.02
52 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (46 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAACTACAAA
Found at i:36285126 original size:8 final size:8
Alignment explanation
Indices: 36285109--36285149 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
36285099 ATACGATTAC
36285109 TATTATTT
1 TATTATTT
*
36285117 TATTACTT
1 TATTATTT
36285125 TATTATTT
1 TATTATTT
*
36285133 TATTATAT
1 TATTATTT
*
36285141 TATCATTT
1 TATTATTT
36285149 T
1 T
36285150 GTTTTTACCC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (8 bp):
TATTATTT
Found at i:36285962 original size:18 final size:17
Alignment explanation
Indices: 36285901--36285963 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 17
36285891 TAAAATATAT
*
36285901 AATTATAAATTT-TAAA
1 AATTAAAAATTTATAAA
36285917 AAGTCTAAATAATTTAT-AA
1 AA-T-TAAA-AATTTATAAA
36285936 AATTGAAAAATGTTATAAA
1 AATT-AAAAAT-TTATAAA
36285955 AATTAAAAA
1 AATTAAAAA
36285964 AAGTATTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
16 2 0.05
17 5 0.13
18 16 0.41
19 15 0.38
20 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.35
Consensus pattern (17 bp):
AATTAAAAATTTATAAA
Found at i:36286209 original size:19 final size:18
Alignment explanation
Indices: 36286159--36286241 Score: 60
Period size: 19 Copynumber: 4.2 Consensus size: 18
36286149 GTGAATTTTA
*
36286159 TTTTTATAATTTT-TATGT
1 TTTTTCTAATTTTATAT-T
36286177 TGTTTTCTAGATTTTATATT
1 T-TTTTCTA-ATTTTATATT
36286197 TTTTTCTGAATTTTTTTATATT
1 TTTTTCT-AA---TTTTATATT
* *
36286219 TATTTCCAATTATTATATT
1 TTTTTCTAATT-TTATATT
36286238 TTTT
1 TTTT
36286242 AATGTGCATA
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
18 3 0.06
19 23 0.43
20 8 0.15
21 5 0.09
22 14 0.26
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.69
Consensus pattern (18 bp):
TTTTTCTAATTTTATATT
Found at i:36286608 original size:34 final size:34
Alignment explanation
Indices: 36286566--36286630 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
36286556 GTATTAGTAA
36286566 TACTAATACATTATAATATATTATTATATTACCT
1 TACTAATACATTATAATATATTATTATATTACCT
*
36286600 TACTAATACATTATAATATATTGTTATATTA
1 TACTAATACATTATAATATATTATTATATTA
36286631 TGTGTTAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.48
Consensus pattern (34 bp):
TACTAATACATTATAATATATTATTATATTACCT
Found at i:36286811 original size:16 final size:17
Alignment explanation
Indices: 36286792--36286824 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
36286782 AATTTTATAG
36286792 ATTTTA-ATAATTATTA
1 ATTTTATATAATTATTA
*
36286808 ATTTTATATATTTATTA
1 ATTTTATATAATTATTA
36286825 TACATATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTATATAATTATTA
Found at i:36287027 original size:16 final size:16
Alignment explanation
Indices: 36287008--36287040 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
36286998 AAAATTATAT
36287008 TAATTATTAATGTCAA
1 TAATTATTAATGTCAA
36287024 TAATTATTAATGTCAA
1 TAATTATTAATGTCAA
36287040 T
1 T
36287041 TATGGTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATTATTAATGTCAA
Found at i:36293797 original size:39 final size:39
Alignment explanation
Indices: 36293742--36293827 Score: 154
Period size: 39 Copynumber: 2.2 Consensus size: 39
36293732 AATGGATAGA
*
36293742 AAATTAATATTTATTATCTTTACTGATATGACATACATGT
1 AAATT-ATATTTATTATCTTTACTGATATGACATACATAT
36293782 AAATTATATTTATTATCTTTACTGATATGACATACATAT
1 AAATTATATTTATTATCTTTACTGATATGACATACATAT
36293821 AAATTAT
1 AAATTAT
36293828 CACGTGGATG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 40 0.89
40 5 0.11
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (39 bp):
AAATTATATTTATTATCTTTACTGATATGACATACATAT
Found at i:36294944 original size:27 final size:27
Alignment explanation
Indices: 36294877--36294946 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
36294867 GTCGAGGGTT
* * *
36294877 TGCCACAGGCGGCACCAAATGTGTCAG
1 TGCCACAGGCGGCACCAAAGGTGCCAC
** * *
36294904 TAACAGAGGTGGCACCAAAGGTGCCAC
1 TGCCACAGGCGGCACCAAAGGTGCCAC
36294931 TGCCACAGGCGGCACC
1 TGCCACAGGCGGCACC
36294947 CCAGCCTTAT
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.27, C:0.31, G:0.30, T:0.11
Consensus pattern (27 bp):
TGCCACAGGCGGCACCAAAGGTGCCAC
Found at i:36295494 original size:37 final size:38
Alignment explanation
Indices: 36295447--36295533 Score: 108
Period size: 40 Copynumber: 2.3 Consensus size: 38
36295437 TAGTTTTTAC
*
36295447 ACTA-TATTATTGTTAG-T-TATTATTTCTAGTAAAAC
1 ACTATTATTATTGTTAGTTATATTATTTCTAGTAAAAA
* *
36295482 CCTAATTATTATTGTTAGTTAGTATTATTTTTAGTAAAAA
1 ACT-ATTATTATTGTTAGTTA-TATTATTTCTAGTAAAAA
36295522 ACTATTATTATT
1 ACTATTATTATT
36295534 ATTATTGTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
35 2 0.05
36 1 0.02
37 12 0.28
38 1 0.02
39 9 0.21
40 18 0.42
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51
Consensus pattern (38 bp):
ACTATTATTATTGTTAGTTATATTATTTCTAGTAAAAA
Found at i:36295531 original size:76 final size:78
Alignment explanation
Indices: 36295326--36295533 Score: 219
Period size: 76 Copynumber: 2.6 Consensus size: 78
36295316 GTTTAGTTAT
* * *
36295326 TAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAAATTAATATTATTATTATGGTTAGTTAT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGT-AAAAA--ACTATTATTA-T-TGGTTAGTTAT
36295391 TAGGATTAGTAAAAACCC
61 TAGGATTAGTAAAAACCC
* *** * *
36295409 TAATTATTATT-TTAGTTAGTATGATTGTTAGTTTTTACACTA-TATTATT-GTTAGTTATTA-T
1 TAATTATTATTGTTAGTTAGTATTATTGTTAG-TAAAAAACTATTATTATTGGTTAGTTATTAGG
*
36295470 TTCTAGT-AAAACCC
65 AT-TAGTAAAAACCC
*
36295484 TAATTATTATTGTTAGTTAGTATTATTTTTAGTAAAAAACTATTATTATT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAACTATTATTATT
36295534 ATTATTGTGT
Statistics
Matches: 105, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
75 25 0.24
76 40 0.38
77 1 0.01
78 1 0.01
79 5 0.05
80 3 0.03
82 19 0.18
83 11 0.10
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.50
Consensus pattern (78 bp):
TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAACTATTATTATTGGTTAGTTATTAGGA
TTAGTAAAAACCC
Found at i:36298175 original size:114 final size:114
Alignment explanation
Indices: 36297975--36298204 Score: 424
Period size: 114 Copynumber: 2.0 Consensus size: 114
36297965 CAGCTAATAG
36297975 AGGTAAGTACATGATATGAACCTTGTTATTGTTTGAACTGAGCATCAGTACTCCCCCTATAATAT
1 AGGTAAGTACATGATATGAACCTTGTTATTGTTTGAACTGAGCATCAGTACTCCCCCTATAATAT
*
36298040 GCATGATGTACGCTCGAGCAGCGCACATCAACTCACCTTCAGTGGCATT
66 GCATGATATACGCTCGAGCAGCGCACATCAACTCACCTTCAGTGGCATT
*
36298089 AGGTAAGTACATGATATGAACCTTGTTATTGTTTGAACTGGGCATCAGTACTCCCCCTATAATAT
1 AGGTAAGTACATGATATGAACCTTGTTATTGTTTGAACTGAGCATCAGTACTCCCCCTATAATAT
* *
36298154 GCATGATATACGCTCGAGCAGCGCACATCAACTCTCCTTCAGTTGCATT
66 GCATGATATACGCTCGAGCAGCGCACATCAACTCACCTTCAGTGGCATT
36298203 AG
1 AG
36298205 CTGATAAGTG
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 112 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (114 bp):
AGGTAAGTACATGATATGAACCTTGTTATTGTTTGAACTGAGCATCAGTACTCCCCCTATAATAT
GCATGATATACGCTCGAGCAGCGCACATCAACTCACCTTCAGTGGCATT
Found at i:36298833 original size:17 final size:17
Alignment explanation
Indices: 36298813--36298851 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
36298803 ATTTCAATGT
*
36298813 ATTTTTCTTATTTTCAG
1 ATTTTTCTTAATTTCAG
*
36298830 ATTTTTCTTAATTTCGG
1 ATTTTTCTTAATTTCAG
36298847 ATTTT
1 ATTTT
36298852 ATTACTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.10, G:0.08, T:0.64
Consensus pattern (17 bp):
ATTTTTCTTAATTTCAG
Found at i:36298890 original size:16 final size:15
Alignment explanation
Indices: 36298869--36298898 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
36298859 TCAAAAAATA
36298869 TATTATTTTCATATTT
1 TATTATTTT-ATATTT
36298885 TATTATTTTATATT
1 TATTATTTTATATT
36298899 GTTTTAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTTATATTT
Found at i:36299522 original size:158 final size:159
Alignment explanation
Indices: 36298830--36299685 Score: 1454
Period size: 159 Copynumber: 5.4 Consensus size: 159
36298820 TTATTTTCAG
* * *
36298830 ATTTTTCTTAATTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCATATTTTATTATTTTA
1 ATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTA
*
36298895 TATTGTTTTAGTACATAATA-TTTGAAATGTATTAATTTAGTGTGTTTTCTTATATAAATTTAGT
66 TATTATTTTAGTACATAA-AGTTTGAAATGTATTAATTTAGTGTGTTTTCTTATATAAATTTAGT
*
36298959 AAATAACCCTTATTTTGGCCATTTGTTCGT
130 AAATAACCCTTATTTTGGCCCTTTGTTCGT
* *
36298989 ATTTTTCTTATTTTCAGATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTATTTTA
1 ATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTA
36299054 TATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTCTTATATAAATTTAGTA
66 TATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTCTTATATAAATTTAGTA
*
36299119 AATAACCCTTATTTTGGCCCTTTATTCGT
131 AATAACCCTTATTTTGGCCCTTTGTTCGT
* * *
36299148 ATTTTTCTTATTTTCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTATATTATTATTCTA
1 ATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTA
36299213 TATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTCTTATATAAATTTAGTA
66 TATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTCTTATATAAATTTAGTA
36299278 AATAACCCTTATTTTGGCCC-TTGTTTCGT
131 AATAACCCTTATTTTGGCCCTTTG-TTCGT
36299307 ATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTA
1 ATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTA
*
36299372 TATTATTTTAGTACGTAAAGTTTGAAATGTATTAATTTAGTGTGTGTTT-TTATATAAATTTAGT
66 TATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGT-TTTCTTATATAAATTTAGT
36299436 AAA-AACCCTTATTTTGGCCCTTTGTTCGT
130 AAATAACCCTTATTTTGGCCCTTTGTTCGT
36299465 ATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTA
1 ATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTA
* * * *
36299530 TATTGTTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGTTTT-TTTTATAAATTTAGTA
66 TATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTCTTATATAAATTTAGTA
*
36299594 AA-AACCCCTTATTTTGGTCCTTTGTTCGT
131 AATAA-CCCTTATTTTGGCCCTTTGTTCGT
* * *
36299623 ATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTCGTTTTTTTTTATTT
1 ATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
36299686 CTTTTCGTAT
Statistics
Matches: 669, Mismatches: 23, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
157 22 0.03
158 214 0.32
159 430 0.64
160 3 0.00
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (159 bp):
ATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTA
TATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTCTTATATAAATTTAGTA
AATAACCCTTATTTTGGCCCTTTGTTCGT
Found at i:36299706 original size:20 final size:20
Alignment explanation
Indices: 36299667--36299706 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
36299657 AAATATACTA
*
36299667 TTTTCGTTTTTTTTTATTTC
1 TTTTCGTTTTTATTTATTTC
36299687 TTTTCGTATTTTATTT-TTTC
1 TTTTCGT-TTTTATTTATTTC
36299707 ATAAACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.07, C:0.10, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTTCGTTTTTATTTATTTC
Found at i:36299878 original size:12 final size:12
Alignment explanation
Indices: 36299861--36299893 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
36299851 TAGAATGTAC
36299861 ATAACATAAATA
1 ATAACATAAATA
36299873 ATAACATAAATA
1 ATAACATAAATA
*
36299885 ATAAAATAA
1 ATAACATAA
36299894 TAAGACATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAACATAAATA
Found at i:36300117 original size:3 final size:3
Alignment explanation
Indices: 36300111--36300230 Score: 53
Period size: 3 Copynumber: 42.7 Consensus size: 3
36300101 TTTTTTTCCT
* * * *
36300111 TTC TTC TTCC TTC -TC TCC CTC TTC TTC TTC TCC TTC -TC TTT TTC
1 TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* ** * **
36300155 TT- TT- TTC TT- TT- TTC TTC TTTC TAC GCC TCC TTC CCC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC
*
36300197 TCC TTC TTC -TC TTC -TC TTC TTC -TC TTC TT- TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
36300231 TCCTGCATCT
Statistics
Matches: 88, Mismatches: 19, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
2 20 0.23
3 62 0.70
4 6 0.07
ACGTcount: A:0.01, C:0.38, G:0.01, T:0.61
Consensus pattern (3 bp):
TTC
Found at i:36300217 original size:13 final size:13
Alignment explanation
Indices: 36300192--36300230 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
36300182 TCCTTCCCCT
36300192 TCTTCTCCTTCTTC
1 TCTTCT-CTTCTTC
36300206 TCTTCTCTTCTTC
1 TCTTCTCTTCTTC
*
36300219 TCTTCTTTTCTT
1 TCTTCTCTTCTT
36300231 TCCTGCATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (13 bp):
TCTTCTCTTCTTC
Found at i:36301115 original size:11 final size:11
Alignment explanation
Indices: 36301094--36301130 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
36301084 TTTATTTTTA
36301094 ATTTT-AAAAT
1 ATTTTAAAAAT
36301104 ATTTTAAAAAT
1 ATTTTAAAAAT
36301115 ATTTTAAAAAT
1 ATTTTAAAAAT
36301126 ATTTT
1 ATTTT
36301131 TATTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 5 0.19
11 21 0.81
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATTTTAAAAAT
Found at i:36301136 original size:6 final size:6
Alignment explanation
Indices: 36301125--36301156 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
36301115 ATTTTAAAAA
36301125 TATTTT TATTTT TATTTT TATTTT TATTTT TA
1 TATTTT TATTTT TATTTT TATTTT TATTTT TA
36301157 AAATATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:36305725 original size:28 final size:28
Alignment explanation
Indices: 36305686--36305746 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
36305676 ATGATGATGT
36305686 AAGCAATGATGGAAGCTA-CCA-TAACAC
1 AAGCAATGATGGAAGC-AGCCATTAACAC
*
36305713 AAGCAAGTGATGGAAGCAGCCATTAATAC
1 AAGCAA-TGATGGAAGCAGCCATTAACAC
36305742 AAGCA
1 AAGCA
36305747 TGCAACGTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 7 0.23
28 13 0.43
29 10 0.33
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (28 bp):
AAGCAATGATGGAAGCAGCCATTAACAC
Found at i:36307024 original size:27 final size:27
Alignment explanation
Indices: 36306943--36307028 Score: 79
Period size: 25 Copynumber: 3.3 Consensus size: 27
36306933 GAAACAATCT
36306943 GATGAAGAAAAAACTTCAACAGATCAG
1 GATGAAGAAAAAACTTCAACAGATCAG
* *** *** *
36306970 GA--AATAAAAAACAGAAATTTATC-T
1 GATGAAGAAAAAACTTCAACAGATCAG
36306994 GATGAAGAAAAAACTTCAACAGATCAG
1 GATGAAGAAAAAACTTCAACAGATCAG
36307021 GATGAAGA
1 GATGAAGA
36307029 CATAAAAGTC
Statistics
Matches: 40, Mismatches: 16, Indels: 6
0.65 0.26 0.10
Matches are distributed among these distances:
24 2 0.05
25 14 0.35
26 14 0.35
27 10 0.25
ACGTcount: A:0.53, C:0.12, G:0.17, T:0.17
Consensus pattern (27 bp):
GATGAAGAAAAAACTTCAACAGATCAG
Found at i:36308944 original size:21 final size:21
Alignment explanation
Indices: 36308906--36308950 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
36308896 AAGTGTAGGA
*
36308906 TTTGAAGTTTAGTGTTCAAAG
1 TTTGAAGTTTAGTATTCAAAG
*
36308927 TTTGAAGTTTTAG-ATTCAAGG
1 TTTGAAG-TTTAGTATTCAAAG
36308948 TTT
1 TTT
36308951 AAAACTTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.27, C:0.04, G:0.22, T:0.47
Consensus pattern (21 bp):
TTTGAAGTTTAGTATTCAAAG
Found at i:36318701 original size:2 final size:2
Alignment explanation
Indices: 36318694--36318723 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
36318684 ACATCTAAAA
*
36318694 AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
36318724 TGAAATCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:36325595 original size:20 final size:21
Alignment explanation
Indices: 36325570--36325610 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
36325560 ATATTCTTTT
*
36325570 AAAAATGTGAAAT-TATTAAA
1 AAAAATATGAAATATATTAAA
*
36325590 AAAAATATTAAATATATTAAA
1 AAAAATATGAAATATATTAAA
36325611 TATATAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (21 bp):
AAAAATATGAAATATATTAAA
Found at i:36325685 original size:11 final size:11
Alignment explanation
Indices: 36325669--36325756 Score: 56
Period size: 11 Copynumber: 7.8 Consensus size: 11
36325659 TCGCTTATAC
36325669 TTTCTTTTCTT
1 TTTCTTTTCTT
36325680 TTTCTTTTC-T
1 TTTCTTTTCTT
* *
36325690 CTTCCTTTCTT
1 TTTCTTTTCTT
* *
36325701 GTTCCTTTTATTT
1 -TTTCTTTT-CTT
36325714 TTTCCTCTTTC-T
1 TTT-CT-TTTCTT
*
36325726 TTACATTTTCTT
1 TTTC-TTTTCTT
*
36325738 CTT-TTTTCTT
1 TTTCTTTTCTT
36325748 TTTCTTTTC
1 TTTCTTTTC
36325757 GACAAAAACA
Statistics
Matches: 57, Mismatches: 12, Indels: 16
0.67 0.14 0.19
Matches are distributed among these distances:
10 17 0.30
11 20 0.35
12 13 0.23
13 4 0.07
14 3 0.05
ACGTcount: A:0.03, C:0.23, G:0.01, T:0.73
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:36325697 original size:26 final size:25
Alignment explanation
Indices: 36325668--36325746 Score: 68
Period size: 30 Copynumber: 2.8 Consensus size: 25
36325658 TTCGCTTATA
36325668 CTTTCTTTTCTTTTTCTTTTCTCTTC
1 CTTTCTTTTCTTTTT-TTTTCTCTTC
*
36325694 CTTTCTTGTTCCTTTTATTTTTTCCTCTTT
1 CTTTCTT-TT-C-TTT-TTTTTT-CTCTTC
*
36325724 CTTTACATTTTCTTCTTTTTTCT
1 CTTT-C-TTTTCTTTTTTTTTCT
36325747 TTTTCTTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
26 7 0.16
27 4 0.09
28 7 0.16
29 9 0.20
30 12 0.27
31 3 0.07
32 2 0.05
ACGTcount: A:0.04, C:0.24, G:0.01, T:0.71
Consensus pattern (25 bp):
CTTTCTTTTCTTTTTTTTTCTCTTC
Found at i:36325749 original size:15 final size:14
Alignment explanation
Indices: 36325678--36325755 Score: 54
Period size: 15 Copynumber: 5.2 Consensus size: 14
36325668 CTTTCTTTTC
36325678 TTTTTCTTTTCTCT
1 TTTTTCTTTTCTCT
*
36325692 TCCTTTCTTGTTC-CT
1 T-TTTTCTT-TTCTCT
36325707 TTTATT-TTTTCCTCT
1 TTT-TTCTTTT-CTCT
36325722 TTCTTTACATTTTCTTCT
1 TT-TTT-C-TTTTC-TCT
36325740 TTTTTCTTTT-TCT
1 TTTTTCTTTTCTCT
36325753 TTT
1 TTT
36325756 CGACAAAAAC
Statistics
Matches: 52, Mismatches: 2, Indels: 21
0.69 0.03 0.28
Matches are distributed among these distances:
13 8 0.15
14 5 0.10
15 21 0.40
16 5 0.10
17 4 0.08
18 9 0.17
ACGTcount: A:0.04, C:0.22, G:0.01, T:0.73
Consensus pattern (14 bp):
TTTTTCTTTTCTCT
Found at i:36327507 original size:19 final size:20
Alignment explanation
Indices: 36327483--36327521 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
36327473 TTTCAATCCA
36327483 TATAAAGCCTT-TTTT-AGTT
1 TATAAA-CCTTATTTTCAGTT
36327502 TATAAACCTTATTTTCAGTT
1 TATAAACCTTATTTTCAGTT
36327522 CTATGTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 10 0.56
20 4 0.22
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (20 bp):
TATAAACCTTATTTTCAGTT
Found at i:36331326 original size:16 final size:17
Alignment explanation
Indices: 36331305--36331339 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
36331295 CTCATTCTGT
*
36331305 AAAGG-CAACAAAATCA
1 AAAGGCCAACAAAACCA
36331321 AAAGGCCAACAAAACCA
1 AAAGGCCAACAAAACCA
36331338 AA
1 AA
36331340 TCTTCCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.63, C:0.23, G:0.11, T:0.03
Consensus pattern (17 bp):
AAAGGCCAACAAAACCA
Found at i:36339586 original size:69 final size:69
Alignment explanation
Indices: 36339424--36339916 Score: 334
Period size: 69 Copynumber: 7.2 Consensus size: 69
36339414 TAGCATTTTT
* * * * * * *
36339424 TGTCATATAAAGGC-T-CACAGACGAAGAACTGCAACCTCCAACACAGATAGTGAGAGCAAAACT
1 TGTCATATTAAGGCTTGCA-AG-CGAAGAGCCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCT
** *
36339487 CTTAGT
64 CCCAGC
* * * * * * ** * *
36339493 TGTTATATTAAGGCTCGTAGGCGAAGAGTCGCACCCTCCAACGTAGTTAGTGAGAGCAAAGCTCT
1 TGTCATATTAAGGCTTGCAAGCGAAGAGCCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCC
36339558 CAGC
66 CAGC
* * * * * * *
36339562 TGTTATATTAAGGCTTGCAAGCGAAGAGCCGTAGCCACCAATAAAGTTAGCGAGAGAAAAGTTCC
1 TGTCATATTAAGGCTTGCAAGCGAAGAGCCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCC
*
36339627 CAGT
66 CAGC
* * * * *
36339631 TGTCATATTAAGGCTTACAGGCGAATAGCCGCAGCCTTCAACACAATTAGCGAGAGCAGAA-CTC
1 TGTCATATTAAGGCTTGCAAGCGAAGAGCCGCAGCCTCCAACACAGTTAGCGAGAGCA-AAGCTC
*
36339695 CCAAC
65 CCAGC
* * * * * * *
36339700 TATTATATTAAGGCTCT-CAAGCAAACAGCCGCAGCCTCTAAGCA-A-TTAGCAAGATCAAAGCT
1 TGTCATATTAAGGCT-TGCAAGCGAAGAGCCGCAGCCTCCAA-CACAGTTAGCGAGAGCAAAGCT
36339762 CCCAGC
64 CCCAGC
* ** ** * ** *
36339768 TATCATATTAAGGCTCACAAATGAAGTGCTACAGCCTCCAACATAGTTAGCGAGAGCAAAGCTCC
1 TGTCATATTAAGGCTTGCAAGCGAAGAGCCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCC
*
36339833 CAAC
66 CAGC
* * * * * * * * *
36339837 TATCATGTTAAAGCTTGCAGGCGAAAAGTCGTAGCCTCCAACGCAGTTAGTGAGAAG-AAAGCTC
1 TGTCATATTAAGGCTTGCAAGCGAAGAGCCGCAGCCTCCAACACAGTTAGCGAG-AGCAAAGCTC
36339901 CCAGC
65 CCAGC
*
36339906 TGCCATATTAA
1 TGTCATATTAA
36339917 AGCTAGTAGG
Statistics
Matches: 327, Mismatches: 87, Indels: 20
0.75 0.20 0.05
Matches are distributed among these distances:
67 4 0.01
68 48 0.15
69 266 0.81
70 8 0.02
71 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (69 bp):
TGTCATATTAAGGCTTGCAAGCGAAGAGCCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCC
CAGC
Found at i:36340080 original size:56 final size:56
Alignment explanation
Indices: 36340004--36340166 Score: 222
Period size: 56 Copynumber: 2.9 Consensus size: 56
36339994 TTTTCTAAAT
* * * * *
36340004 ATAAAATAGCTCGTGGATTCACATTTCCAGCATATTATTTTAGAAAAATTTCAAGG
1 ATAAAATAGTTCGCGAATTCACATTCCCAGCTTATTATTTTAGAAAAATTTCAAGG
36340060 ATAAAATAGTTCGCGAATTCACATTCCCAGCTTATTATTTTAG-AAAATTTCCAAGG
1 ATAAAATAGTTCGCGAATTCACATTCCCAGCTTATTATTTTAGAAAAATTT-CAAGG
* * * *
36340116 ATAAAA-AGTTCACAAATCCACATTCCCAGCTTATTATTTTAGAAAATTTTC
1 ATAAAATAGTTCGCGAATTCACATTCCCAGCTTATTATTTTAGAAAAATTTC
36340167 CCAAGTACAA
Statistics
Matches: 96, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
55 41 0.43
56 55 0.57
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (56 bp):
ATAAAATAGTTCGCGAATTCACATTCCCAGCTTATTATTTTAGAAAAATTTCAAGG
Found at i:36340138 original size:55 final size:55
Alignment explanation
Indices: 36340023--36340164 Score: 214
Period size: 55 Copynumber: 2.6 Consensus size: 55
36340013 CTCGTGGATT
* * * * *
36340023 CACATTTCCAGCATATTATTTTAGAAAAATTTCAAGGATAAAATAGTTCGCGAATT
1 CACATTCCCAGCTTATTATTTTAG-AAAATTTCAAGGATAAAATAGTTCACAAATC
36340079 CACATTCCCAGCTTATTATTTTAGAAAATTTCCAAGGATAAAA-AGTTCACAAATC
1 CACATTCCCAGCTTATTATTTTAGAAAATTT-CAAGGATAAAATAGTTCACAAATC
36340134 CACATTCCCAGCTTATTATTTTAGAAAATTT
1 CACATTCCCAGCTTATTATTTTAGAAAATTT
36340165 TCCCAAGTAC
Statistics
Matches: 80, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
55 47 0.59
56 33 0.41
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.35
Consensus pattern (55 bp):
CACATTCCCAGCTTATTATTTTAGAAAATTTCAAGGATAAAATAGTTCACAAATC
Found at i:36343976 original size:82 final size:82
Alignment explanation
Indices: 36343873--36344035 Score: 238
Period size: 82 Copynumber: 2.0 Consensus size: 82
36343863 TTTTACTTCC
* * * *
36343873 CTTTAAATACCGTTCCATGCATGGGAACATCTCCTT-AATGCATGTTTCCTTTGCCATTAAGTAG
1 CTTTAAATACCGTTCCATGCATGGGAACAGCACCTTAAATGCATGTCTCCTTAGCCATTAAGTAG
*
36343937 CTGAATTTCAATGACCTT
66 CCGAA-TTCAATGACCTT
* * *
36343955 CTTTAAATGCCGTTCCTTGCATGGTAACAGCACCTTAAATGCATGTCTCCTTAGCCATTAAGTAG
1 CTTTAAATACCGTTCCATGCATGGGAACAGCACCTTAAATGCATGTCTCCTTAGCCATTAAGTAG
36344020 CCGAATTCAATGACCT
66 CCGAATTCAATGACCT
36344036 GCAGACACAA
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
82 42 0.58
83 30 0.42
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (82 bp):
CTTTAAATACCGTTCCATGCATGGGAACAGCACCTTAAATGCATGTCTCCTTAGCCATTAAGTAG
CCGAATTCAATGACCTT
Found at i:36347380 original size:82 final size:82
Alignment explanation
Indices: 36347277--36347439 Score: 238
Period size: 82 Copynumber: 2.0 Consensus size: 82
36347267 TTTTACTTCC
* * * *
36347277 CTTTAAATACCGTTCCATGCATGGGAACATCTCCTT-AATGCATGTTTCCTTTGCCATTAAGTAG
1 CTTTAAATACCGTTCCATGCATGGGAACAGCACCTTAAATGCATGTCTCCTTAGCCATTAAGTAG
36347341 CCGAATTTCAATGACCTT
66 CCGAA-TTCAATGACCTT
* * **
36347359 CTTTAAATGCCGTTCCTTGCATGTTAACAGCACCTTAAATGCATGTCTCCTTAGCCATTAAGTAG
1 CTTTAAATACCGTTCCATGCATGGGAACAGCACCTTAAATGCATGTCTCCTTAGCCATTAAGTAG
36347424 CCGAATTCAATGACCT
66 CCGAATTCAATGACCT
36347440 GCAGACACAA
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
82 41 0.57
83 31 0.43
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (82 bp):
CTTTAAATACCGTTCCATGCATGGGAACAGCACCTTAAATGCATGTCTCCTTAGCCATTAAGTAG
CCGAATTCAATGACCTT
Found at i:36349770 original size:7 final size:7
Alignment explanation
Indices: 36349754--36349784 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
36349744 AGGGAGAAAG
*
36349754 AAAAGGA
1 AAAAGAA
36349761 AAAAGAA
1 AAAAGAA
36349768 AAAAGAA
1 AAAAGAA
36349775 AAAAGAA
1 AAAAGAA
36349782 AAA
1 AAA
36349785 GGGGGAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:36351066 original size:67 final size:67
Alignment explanation
Indices: 36350957--36351088 Score: 210
Period size: 67 Copynumber: 2.0 Consensus size: 67
36350947 TTTCCAATTC
* *
36350957 AGAGAGCACACTCCCGCGAACCTCATTACTTACAGCGAGATTACCAGTCTAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTACTTACAACGAGATTACCAGTCCAGGCTAAATCCCCTG
36351022 CA
66 CA
* * * *
36351024 AGAGAGCACACTCCCGCGAACTTCATTTCTTACAACGGGATTATCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTACTTACAACGAGATTACCAGTCCAGGCTAAATCCCCTG
36351089 TAATATAAAC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (67 bp):
AGAGAGCACACTCCCGCGAACCTCATTACTTACAACGAGATTACCAGTCCAGGCTAAATCCCCTG
CA
Found at i:36351251 original size:57 final size:58
Alignment explanation
Indices: 36351176--36351296 Score: 165
Period size: 57 Copynumber: 2.1 Consensus size: 58
36351166 CCTAAATCCA
* *
36351176 TTTTCCACATATTATTCGGGAGGGCTATATCA-A-GATCACCCGTCCGAGCTAGATCT
1 TTTTCCACATATTATTCGGGAGGGCTATATCAGATGATCACCCGTCCAAACTAGATCT
*
36351232 TTTTCACACATATTCTTCGGGAGGGCTATATCAGGATTGGATCACCCGTCCAAACTAGATCT
1 TTTTC-CACATATTATTCGGGAGGGCTATATCA-GA-T-GATCACCCGTCCAAACTAGATCT
36351294 TTT
1 TTT
36351297 CTACCGTCAA
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
56 5 0.09
57 26 0.46
59 1 0.02
62 24 0.43
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (58 bp):
TTTTCCACATATTATTCGGGAGGGCTATATCAGATGATCACCCGTCCAAACTAGATCT
Found at i:36353807 original size:21 final size:22
Alignment explanation
Indices: 36353779--36353842 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 22
36353769 GCTTTGCCGA
36353779 TCAGGCACTATATGTGTCGTAT
1 TCAGGCACTATATGTGTCGTAT
* ** *
36353801 T-AGGCACCACGTGTGTC-TTT
1 TCAGGCACTATATGTGTCGTAT
* *
36353821 TCAGACACTTTATGTGTCGTAT
1 TCAGGCACTATATGTGTCGTAT
36353843 AGTGCTTCTG
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
20 3 0.10
21 24 0.80
22 3 0.10
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (22 bp):
TCAGGCACTATATGTGTCGTAT
Found at i:36357626 original size:17 final size:17
Alignment explanation
Indices: 36357604--36357641 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
36357594 AAATTGAAAC
*
36357604 AAAA-TTAAAAGTTTTAG
1 AAAATTTAAAAATTTT-G
36357621 AAAATTTAAAAATTTTG
1 AAAATTTAAAAATTTTG
36357638 AAAA
1 AAAA
36357642 CAGGGGTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (17 bp):
AAAATTTAAAAATTTTG
Found at i:36365330 original size:20 final size:20
Alignment explanation
Indices: 36365300--36365342 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
36365290 TTTCTCATAA
36365300 AAATGATTAAATAATAATTAT
1 AAATGATTAAATAA-AATTAT
*
36365321 AAAT-ATTAAATAAAATTTT
1 AAATGATTAAATAAAATTAT
36365340 AAA
1 AAA
36365343 ACTAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 9 0.43
21 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAATGATTAAATAAAATTAT
Found at i:36365401 original size:27 final size:26
Alignment explanation
Indices: 36365330--36365443 Score: 101
Period size: 28 Copynumber: 4.3 Consensus size: 26
36365320 TAAATATTAA
*
36365330 ATAAAATTT-TA-AAACTAAAAAAAT
1 ATAAAATTTATATAAACTTAAAAAAT
* * *
36365354 ATAAAAATAAT-TAAATATTAAAAAAT
1 ATAAAATTTATATAAA-CTTAAAAAAT
36365380 ATGAAAATTTATATAAACTTAAAAAATT
1 AT-AAAATTTATATAAACTTAAAAAA-T
*
36365408 ATAAAAATTCTA-ATAAATTATAAAAAAT
1 AT-AAAATT-TATATAAACT-TAAAAAAT
36365436 ATAAAATT
1 ATAAAATT
36365444 AATAAAAAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
24 7 0.10
25 4 0.05
26 10 0.14
27 21 0.29
28 22 0.30
29 9 0.12
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (26 bp):
ATAAAATTTATATAAACTTAAAAAAT
Found at i:36365510 original size:18 final size:18
Alignment explanation
Indices: 36365487--36365558 Score: 65
Period size: 19 Copynumber: 3.9 Consensus size: 18
36365477 TTAAAGTTAT
*
36365487 ATAAAAATCATAAAAATG
1 ATAAAAATCATAAAAATC
*
36365505 ATAAAAAT-ATTAAAATTC
1 ATAAAAATCA-TAAAAATC
* * *
36365523 ATATAAATTTATAAAAATT
1 ATA-AAAATCATAAAAATC
36365542 ATAAAAAATCATAAAAA
1 AT-AAAAATCATAAAAA
36365559 CTTGAACATG
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
17 1 0.02
18 17 0.40
19 23 0.53
20 2 0.05
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.29
Consensus pattern (18 bp):
ATAAAAATCATAAAAATC
Found at i:36365517 original size:37 final size:37
Alignment explanation
Indices: 36365469--36365548 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 37
36365459 TTTTTTTATA
*
36365469 AAAACATATTAAAGTT-ATATAAAAATCATAAAAATGAT
1 AAAA-ATATTAAAATTCATAT-AAAATCATAAAAATGAT
* * *
36365507 AAAAATATTAAAATTCATATAAATTTATAAAAATTAT
1 AAAAATATTAAAATTCATATAAAATCATAAAAATGAT
36365544 AAAAA
1 AAAAA
36365549 ATCATAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 29 0.78
38 8 0.22
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (37 bp):
AAAAATATTAAAATTCATATAAAATCATAAAAATGAT
Found at i:36365519 original size:8 final size:9
Alignment explanation
Indices: 36365487--36365558 Score: 65
Period size: 9 Copynumber: 7.8 Consensus size: 9
36365477 TTAAAGTTAT
36365487 ATAAAAATC
1 ATAAAAATC
*
36365496 ATAAAAATG
1 ATAAAAATC
36365505 ATAAAAAT-
1 ATAAAAATC
*
36365513 ATTAAAATTC
1 A-TAAAAATC
* *
36365523 ATATAAATTT
1 ATA-AAAATC
*
36365533 ATAAAAATT
1 ATAAAAATC
36365542 ATAAAAAATC
1 AT-AAAAATC
36365552 ATAAAAA
1 ATAAAAA
36365559 CTTGAACATG
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
8 1 0.02
9 36 0.67
10 17 0.31
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.29
Consensus pattern (9 bp):
ATAAAAATC
Found at i:36366051 original size:19 final size:21
Alignment explanation
Indices: 36366020--36366061 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
36366010 ATTTTTATTA
36366020 TTTTTTTATAATTCT-AATAT
1 TTTTTTTATAATTCTAAATAT
*
36366040 TTTTTTTA-AATTTTAAATAT
1 TTTTTTTATAATTCTAAATAT
36366060 TT
1 TT
36366062 CAAATAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTTTTATAATTCTAAATAT
Found at i:36366055 original size:47 final size:49
Alignment explanation
Indices: 36365964--36366061 Score: 112
Period size: 47 Copynumber: 2.0 Consensus size: 49
36365954 CAGTTTAAGG
* *
36365964 TTTTATGATTTTTTTTATAATTCTTATAAGTTTATATCAATTT-AATAT
1 TTTTATGATTTTTTTTATAATTCTAATAAGTTTATATAAATTTAAATAT
* * * *
36366012 TTTTATTA-TTTTTTTATAATTCTAAT-ATTTTTTTTAAATTTTAAATAT
1 TTTTATGATTTTTTTTATAATTCTAATAAGTTTATATAAA-TTTAAATAT
36366060 TT
1 TT
36366062 CAAATAAGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
46 8 0.19
47 20 0.48
48 14 0.33
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (49 bp):
TTTTATGATTTTTTTTATAATTCTAATAAGTTTATATAAATTTAAATAT
Found at i:36366102 original size:28 final size:27
Alignment explanation
Indices: 36366065--36366146 Score: 78
Period size: 28 Copynumber: 2.9 Consensus size: 27
36366055 AATATTTCAA
*
36366065 ATAAGTTTTATTAATTTCATAATTTTTTT
1 ATAA-TTTTATTAATTTCATAA-GTTTTT
*
36366094 ATAATTTTA-TAATATTTATAAGTTTTT
1 ATAATTTTATTAAT-TTCATAAGTTTTT
*
36366121 ATATATTTT-TTAATTTTAATAAGTTT
1 ATA-ATTTTATTAA-TTTCATAAGTTT
36366147 ATATCAATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
27 12 0.26
28 29 0.63
29 5 0.11
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (27 bp):
ATAATTTTATTAATTTCATAAGTTTTT
Found at i:36366185 original size:28 final size:28
Alignment explanation
Indices: 36366003--36366185 Score: 73
Period size: 28 Copynumber: 6.6 Consensus size: 28
36365993 GTTTATATCA
*
36366003 ATTTAATATTTTTATT-AT-TTTTTTAT
1 ATTTAATATTTTTATTAATATTTTTAAT
* *
36366029 AATTCTAATATTTTTTTTAA-ATTTTAAAT
1 -ATT-TAATATTTTTATTAATATTTTTAAT
* **
36366058 ATTTCAAATAAGTTTTATTAAT-TTCATAATT
1 ATTT--AAT-ATTTTTATTAATATTTTTAA-T
* * * *
36366089 TTTTTATAATTTTA-TAATATTTATAAGT
1 ATTTAATATTTTTATTAATATTTTTAA-T
*
36366117 -TTTTATATATTTT-TT-A-A-TTTTAAT
1 ATTTAATAT-TTTTATTAATATTTTTAAT
***
36366141 AAGTTT-ATATCAATATTAATATTTTTAAT
1 -A-TTTAATATTTTTATTAATATTTTTAAT
36366170 ATTTAATATTTTTATT
1 ATTTAATATTTTTATT
36366186 TTCTTTTATA
Statistics
Matches: 116, Mismatches: 21, Indels: 37
0.67 0.12 0.21
Matches are distributed among these distances:
24 1 0.01
25 6 0.05
26 7 0.06
27 23 0.20
28 43 0.37
29 19 0.16
30 13 0.11
31 4 0.03
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (28 bp):
ATTTAATATTTTTATTAATATTTTTAAT
Found at i:36367971 original size:16 final size:15
Alignment explanation
Indices: 36367950--36368001 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 15
36367940 TTCTATTTAG
36367950 TAATATAATAAATTAT
1 TAATATAAT-AATTAT
36367966 TAATATAAT--TTAT
1 TAATATAATAATTAT
*
36367979 TAATTTAATACATTATT
1 TAATATAATA-ATTA-T
36367996 TAATAT
1 TAATAT
36368002 TAATTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
13 12 0.40
16 12 0.40
17 6 0.20
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATATAATAATTAT
Found at i:36367976 original size:29 final size:31
Alignment explanation
Indices: 36367944--36368007 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
36367934 AATTATTTCT
36367944 ATTTAGTAATATAATAAATTA-TTAATA-TA
1 ATTTAGTAATATAATAAATTATTTAATATTA
* * *
36367973 ATTTATTAATTTAATACATTATTTAATATTA
1 ATTTAGTAATATAATAAATTATTTAATATTA
36368004 ATTT
1 ATTT
36368008 TTTTTGTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 18 0.60
30 6 0.20
31 6 0.20
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (31 bp):
ATTTAGTAATATAATAAATTATTTAATATTA
Found at i:36368040 original size:15 final size:16
Alignment explanation
Indices: 36368015--36368045 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
36368005 TTTTTTTTGT
36368015 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
36368031 AATAAT-AATTTTAAA
1 AATAATAAATTTTAAA
36368046 GTTTTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:36368115 original size:17 final size:17
Alignment explanation
Indices: 36368093--36368143 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
36368083 TTATATATTA
36368093 ATATATTAATAATAAAT
1 ATATATTAATAATAAAT
*
36368110 ATATATTACA-ATTATAA-
1 ATATATTA-ATAATA-AAT
36368127 ATATATTAATAATAAAT
1 ATATATTAATAATAAAT
36368144 GTTTTATAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 3 0.11
17 22 0.79
18 3 0.11
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATATTAATAATAAAT
Found at i:36368310 original size:20 final size:20
Alignment explanation
Indices: 36368285--36368326 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
36368275 ATTAACATTG
*
36368285 TTAATTTTGTTGATGTGTAA
1 TTAATTTGGTTGATGTGTAA
36368305 TTAATTTGGTTGATGTGTAA
1 TTAATTTGGTTGATGTGTAA
36368325 TT
1 TT
36368327 TTTAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (20 bp):
TTAATTTGGTTGATGTGTAA
Found at i:36368559 original size:27 final size:23
Alignment explanation
Indices: 36368527--36368588 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 23
36368517 GTATAGGGAC
36368527 ATATGACATATTTTAATCTAGTATAAA
1 ATATGA-ATATTTTAAT-TA-TAT-AA
*
36368554 ATATGAATGTTTTAATTATATAA
1 ATATGAATATTTTAATTATATAA
*
36368577 ATATGAGTATTT
1 ATATGAATATTT
36368589 GTTTAAATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 12 0.38
24 3 0.09
25 2 0.06
26 9 0.28
27 6 0.19
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (23 bp):
ATATGAATATTTTAATTATATAA
Found at i:36368568 original size:26 final size:24
Alignment explanation
Indices: 36368527--36368582 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 24
36368517 GTATAGGGAC
36368527 ATATGACATATTTTAATCTAGTATAAA
1 ATATGACATATTTTAAT-TA-TAT-AA
*
36368554 ATATGA-ATGTTTTAATTATATAA
1 ATATGACATATTTTAATTATATAA
36368577 ATATGA
1 ATATGA
36368583 GTATTTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 8 0.29
24 3 0.11
25 2 0.07
26 9 0.32
27 6 0.21
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.43
Consensus pattern (24 bp):
ATATGACATATTTTAATTATATAA
Found at i:36369026 original size:21 final size:22
Alignment explanation
Indices: 36369002--36369044 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
36368992 GTAGCTTAAG
36369002 AACAC-TAAAATAGAA-AAGAAA
1 AACACATAAAAT-GAATAAGAAA
36369023 AACACATTAAAATGAATAAGAA
1 AACACA-TAAAATGAATAAGAA
36369045 TTGGCAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.14
Consensus pattern (22 bp):
AACACATAAAATGAATAAGAAA
Found at i:36369227 original size:17 final size:17
Alignment explanation
Indices: 36369205--36369245 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
36369195 CATATGTGTT
36369205 AATAATACACATACGAA
1 AATAATACACATACGAA
*
36369222 AATAATACACATATGAA
1 AATAATACACATACGAA
36369239 AATAATA
1 AATAATA
36369246 TATTAACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.61, C:0.12, G:0.05, T:0.22
Consensus pattern (17 bp):
AATAATACACATACGAA
Found at i:36373465 original size:96 final size:96
Alignment explanation
Indices: 36373301--36373491 Score: 310
Period size: 96 Copynumber: 2.0 Consensus size: 96
36373291 TTAACATGAC
* *
36373301 ATTCCGAGACTAAAGAATCAGAGTAATCAGACGCATTTAAATCCCTTAGCCGAGGAAGCCCAATA
1 ATTCCGAGACTAAAGAATCAGAGTAATCAGACACATTTAAATCCCCTAGCCGAGGAAGCCCAATA
* * *
36373366 CACATATTAGACCTAGTATACACCCGAGCAG
66 CACACATCAGACCCAGTATACACCCGAGCAG
* *
36373397 ATTCCGAGACTGAAGAATCAGAGTAATCAGACATATTTAAATCCCCTAGCCGAGGAAGCCCAATA
1 ATTCCGAGACTAAAGAATCAGAGTAATCAGACACATTTAAATCCCCTAGCCGAGGAAGCCCAATA
*
36373462 CACACATCAGACCCAGTATACACCTGAGCA
66 CACACATCAGACCCAGTATACACCCGAGCA
36373492 CGCGGTTTGG
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 87 1.00
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (96 bp):
ATTCCGAGACTAAAGAATCAGAGTAATCAGACACATTTAAATCCCCTAGCCGAGGAAGCCCAATA
CACACATCAGACCCAGTATACACCCGAGCAG
Found at i:36377126 original size:13 final size:13
Alignment explanation
Indices: 36377108--36377137 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
36377098 CAAATCTGTT
36377108 TACAAATATCCAA
1 TACAAATATCCAA
36377121 TACAAATATCCAA
1 TACAAATATCCAA
36377134 TACA
1 TACA
36377138 GGAACCACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (13 bp):
TACAAATATCCAA
Found at i:36387197 original size:29 final size:30
Alignment explanation
Indices: 36387164--36387228 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
36387154 CTTGCAACAA
*
36387164 TAAAAAGAAAGCAAAAT-AAAATAAAAAGG
1 TAAAAAGAAAACAAAATAAAAATAAAAAGG
* * *
36387193 TAAAAATAAAATAAAATAAAAATAAAAATG
1 TAAAAAGAAAACAAAATAAAAATAAAAAGG
36387223 -AAAAAG
1 TAAAAAG
36387229 GATCTAGTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.14
Consensus pattern (30 bp):
TAAAAAGAAAACAAAATAAAAATAAAAAGG
Found at i:36387226 original size:7 final size:6
Alignment explanation
Indices: 36387176--36387227 Score: 56
Period size: 6 Copynumber: 8.7 Consensus size: 6
36387166 AAAAGAAAGC
36387176 AAAAT- AAAATA AAAAGGTA AAAAT- AAAAT- AAAATA AAAATA AAAATGA
1 AAAATA AAAATA AAAA--TA AAAATA AAAATA AAAATA AAAATA AAAAT-A
36387224 AAAA
1 AAAA
36387228 GGATCTAGTG
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
5 15 0.36
6 16 0.38
7 5 0.12
8 6 0.14
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:36387227 original size:24 final size:23
Alignment explanation
Indices: 36387176--36387226 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
36387166 AAAAGAAAGC
36387176 AAAATAAAATAAAAAGGTAAAAAT
1 AAAATAAAATAAAAA-GTAAAAAT
36387200 AAAATAAAATAAAAA-TAAAAAT
1 AAAATAAAATAAAAAGTAAAAAT
36387222 GAAAA
1 -AAAA
36387227 AGGATCTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 7 0.27
23 4 0.15
24 15 0.58
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (23 bp):
AAAATAAAATAAAAAGTAAAAAT
Found at i:36399769 original size:48 final size:47
Alignment explanation
Indices: 36399716--36399811 Score: 117
Period size: 48 Copynumber: 2.0 Consensus size: 47
36399706 CGTCTTCCAC
36399716 TTTATTTGTTA-AAATTTCCATT-TCTTATTTATTTATC-ATTTATTTATT
1 TTTATTTGTTACAAATTT-C-TTCTCTTATTT-TTT-TCAATTTATTTATT
*
36399764 TTTATTTGTTATCAAATTTCTTCTTTTATTTTTTTCAATTTATTTATT
1 TTTATTTGTTA-CAAATTTCTTCTCTTATTTTTTTCAATTTATTTATT
36399812 ACTAAATTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
47 2 0.05
48 27 0.63
49 8 0.19
50 6 0.14
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (47 bp):
TTTATTTGTTACAAATTTCTTCTCTTATTTTTTTCAATTTATTTATT
Found at i:36402267 original size:7 final size:7
Alignment explanation
Indices: 36402239--36402280 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
36402229 TTTAATTTCC
*
36402239 ATTTCTT
1 ATTTATT
36402246 ATTTATT
1 ATTTATT
*
36402253 -TATGATT
1 AT-TTATT
36402260 ATTTATT
1 ATTTATT
36402267 ATTTATT
1 ATTTATT
36402274 ATTTATT
1 ATTTATT
36402281 TGTTCTTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 1 0.03
7 28 0.93
8 1 0.03
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (7 bp):
ATTTATT
Found at i:36406248 original size:42 final size:42
Alignment explanation
Indices: 36406193--36406529 Score: 340
Period size: 42 Copynumber: 8.0 Consensus size: 42
36406183 GCGCTTACAT
36406193 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* * *
36406235 AAAAAAATGCCGCTAAAGATCATGTTCTTTAGCGGCGGTTAT
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
** * * *
36406277 AAAAATGCGCCGTTAAAGATCATGTTCTTTAGTGGCGCTTAC
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* * ** *
36406319 AAATAAACGCCGCTAAAGAACATAATCTTTAGCGGCACTTAG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* * *
36406361 AAATAAACGCCGCTAAATATCATGTTCTTTAGCGGTGCTTAGG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA-G
* * *
36406404 AAAAAAACGCCGCTAAAGTTCATGTTTTTTAGCGGCGCTTTTG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTAG
** * * * * *
36406447 AGGAAAACGCCTCTAAA-AGTAATATTCTATAGCGGTGCTT-G
1 AAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTAG
**
36406488 TTCAAAAACGCCGCTAAA-AGT-AGTGTTCTTTAGCGGCGCTTA
1 -AAAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTTA
36406530 TTTCACAAAT
Statistics
Matches: 241, Mismatches: 48, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
41 2 0.01
42 174 0.72
43 63 0.26
44 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
Found at i:36406993 original size:10 final size:12
Alignment explanation
Indices: 36406949--36407000 Score: 86
Period size: 12 Copynumber: 4.3 Consensus size: 12
36406939 TTTTGAACCT
* *
36406949 CTGCTTCTATTG
1 CTGCTTCTCTCG
36406961 CTGCTTCTCTCG
1 CTGCTTCTCTCG
36406973 CTGCTTCTCTCG
1 CTGCTTCTCTCG
36406985 CTGCTTCTCTCG
1 CTGCTTCTCTCG
36406997 CTGC
1 CTGC
36407001 GGCCTCTACT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.02, C:0.38, G:0.17, T:0.42
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:36411986 original size:9 final size:9
Alignment explanation
Indices: 36411972--36412068 Score: 122
Period size: 9 Copynumber: 10.8 Consensus size: 9
36411962 GTATTATGTA
36411972 ATGTAAGTT
1 ATGTAAGTT
*
36411981 ATGTAATTT
1 ATGTAAGTT
* *
36411990 ATTTAATTT
1 ATGTAAGTT
36411999 ATGTAAGTT
1 ATGTAAGTT
36412008 ATGTAAGTT
1 ATGTAAGTT
* *
36412017 ATTTAATTT
1 ATGTAAGTT
*
36412026 ATGTAAATT
1 ATGTAAGTT
36412035 ATGTAAGTT
1 ATGTAAGTT
* *
36412044 ATTTAATTT
1 ATGTAAGTT
36412053 ATGTAAGTT
1 ATGTAAGTT
36412062 ATGTAAG
1 ATGTAAG
36412069 NNNNNNNNNN
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 75 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:36412003 original size:27 final size:27
Alignment explanation
Indices: 36411972--36412068 Score: 176
Period size: 27 Copynumber: 3.6 Consensus size: 27
36411962 GTATTATGTA
*
36411972 ATGTAAGTTATGTAATTTATTTAATTT
1 ATGTAAGTTATGTAAGTTATTTAATTT
36411999 ATGTAAGTTATGTAAGTTATTTAATTT
1 ATGTAAGTTATGTAAGTTATTTAATTT
*
36412026 ATGTAAATTATGTAAGTTATTTAATTT
1 ATGTAAGTTATGTAAGTTATTTAATTT
36412053 ATGTAAGTTATGTAAG
1 ATGTAAGTTATGTAAG
36412069 NNNNNNNNNN
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (27 bp):
ATGTAAGTTATGTAAGTTATTTAATTT
Found at i:36412370 original size:24 final size:26
Alignment explanation
Indices: 36412327--36412381 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
36412317 TTATGTACGG
* *
36412327 TATGTGTTATTATGTAAGTTCTTTAT
1 TATGTGTTATTATGTAAGTTATGTAT
*
36412353 TATGT-TTGTTATGT-AGTTATGTAT
1 TATGTGTTATTATGTAAGTTATGTAT
36412377 TATGT
1 TATGT
36412382 AAGATATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 13 0.50
25 8 0.31
26 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.18, T:0.58
Consensus pattern (26 bp):
TATGTGTTATTATGTAAGTTATGTAT
Found at i:36412575 original size:15 final size:15
Alignment explanation
Indices: 36412555--36412587 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
36412545 AGAATTTTTT
*
36412555 ATAAATTTAATAGTA
1 ATAAATTTAATACTA
36412570 ATAAATTTAATACTA
1 ATAAATTTAATACTA
36412585 ATA
1 ATA
36412588 TAGAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (15 bp):
ATAAATTTAATACTA
Found at i:36413960 original size:181 final size:181
Alignment explanation
Indices: 36413616--36413969 Score: 683
Period size: 180 Copynumber: 2.0 Consensus size: 181
36413606 TACGGAATAA
36413616 TGGGCTTTAATCCGAAGAAATATAACCTTAACCGAATAGAAGAAACACTGAATAGAAGAAGTAGA
1 TGGGCTTTAATCCGAAGAAATATAACCTTAACCGAATAGAAGAAACACTGAATAGAAGAAGTAGA
*
36413681 CGACTGCAAATGCAGGTTATAGAGCGACCGCCGGAGTGGAGCCGACTGCAACGACAGGGGGATTT
66 CGACTGCAAATGCAGGTTATAGAGCGACCGCCGGAGTGGAGCCAACTGCAACGACAGGGGGATTT
36413746 GGGAATTTGGGGATTTAGGGAAACTGGGGGAATAGGAATTGGGAGAAAATG
131 GGGAATTTGGGGATTTAGGGAAACTGGGGGAATAGGAATTGGGAGAAAATG
36413797 TGGGC-TTAATCCGAAGAAATATAACCTTAACCGAATAGAAGAAACACTGAATAGAAGAAGTAGA
1 TGGGCTTTAATCCGAAGAAATATAACCTTAACCGAATAGAAGAAACACTGAATAGAAGAAGTAGA
36413861 CGACTGCAAATGCAGGTTATAGAGCGACCGCCGGAGTGGAGCCAACTGCAACGACAGGGGGGATT
66 CGACTGCAAATGCAGGTTATAGAGCGACCGCCGGAGTGGAGCCAACTGCAACGACA-GGGGGATT
36413926 TGGGAATTTGGGGATTTAGGGAAACTGGGGGAATAGGAATTGGG
130 TGGGAATTTGGGGATTTAGGGAAACTGGGGGAATAGGAATTGGG
36413970 GGGAAATGAA
Statistics
Matches: 171, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
180 114 0.67
181 57 0.33
ACGTcount: A:0.35, C:0.14, G:0.32, T:0.19
Consensus pattern (181 bp):
TGGGCTTTAATCCGAAGAAATATAACCTTAACCGAATAGAAGAAACACTGAATAGAAGAAGTAGA
CGACTGCAAATGCAGGTTATAGAGCGACCGCCGGAGTGGAGCCAACTGCAACGACAGGGGGATTT
GGGAATTTGGGGATTTAGGGAAACTGGGGGAATAGGAATTGGGAGAAAATG
Found at i:36413990 original size:24 final size:24
Alignment explanation
Indices: 36413961--36414014 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
36413951 TGGGGGAATA
36413961 GGAATTGGGGGGAA-ATGAAATCGG
1 GGAATTGGGGGGAATATGAAAT-GG
36413985 GGAATTGGGGGGAATATGAAATGG
1 GGAATTGGGGGGAATATGAAATGG
*
36414009 GAAATT
1 GGAATT
36414015 AGGGAATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 21 0.75
25 7 0.25
ACGTcount: A:0.35, C:0.02, G:0.43, T:0.20
Consensus pattern (24 bp):
GGAATTGGGGGGAATATGAAATGG
Found at i:36418249 original size:189 final size:189
Alignment explanation
Indices: 36417936--36418328 Score: 596
Period size: 189 Copynumber: 2.1 Consensus size: 189
36417926 GCGTTTGAAC
*
36417936 GTAAGCGCCACTAATTAAAGTATACATCGAGACCAAAACGGTGCGTTTTGGTTCAGATATTTTGC
1 GTAAGCGCCACTAATTAAAGTATACATCGAGACCAAAACGGTGCGTTTTGGTTCAGATAGTTTGC
*
36418001 GGCGTTTTCATATAAGCGCCACTAAATGTAACATAGCTTAAAACAAACCACTACGTTTTGTT-AA
66 GGCGTTTTCATATAAGCGCCACTAAATGTAACATAACTTAAAACAAACCACTACGTTTTGTTAAA
* *
36418065 GATACGTTGCGGCGCTTTACCCAAAGCGCCGCTAAAT-ATATTCTTTAACGGCGTTTTCTA
131 G-TACGTTGCGGCGCTTCACCCAAAGCGCCGCT-AATGATATTCTATAACGGCGTTTTCTA
* *
36418125 GTAAGCGCCACTAATTGAAGTATACATCGAGACCAAAATGGTGCGTTTTGGTTCAGATAGTTTGC
1 GTAAGCGCCACTAATTAAAGTATACATCGAGACCAAAACGGTGCGTTTTGGTTCAGATAGTTTGC
* * *
36418190 GGCGTTTTGC-TATAAGCGCCACTAAATGTAACATAACTTCAGACGAAA-CACTGCGTTTTGTTA
66 GGCGTTTT-CATATAAGCGCCACTAAATGTAACATAACTTAAAAC-AAACCACTACGTTTTGTTA
* ** * *
36418253 AAGTACTTTGCGGCGCTTCGGCTAAAGCGCCGCTAATGCTATTCTATAACGGCGTTTTCTA
129 AAGTACGTTGCGGCGCTTCACCCAAAGCGCCGCTAATGATATTCTATAACGGCGTTTTCTA
36418314 GTAAGCGCCACTAAT
1 GTAAGCGCCACTAAT
36418329 ATAATCAAAA
Statistics
Matches: 186, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
188 3 0.02
189 176 0.95
190 7 0.04
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (189 bp):
GTAAGCGCCACTAATTAAAGTATACATCGAGACCAAAACGGTGCGTTTTGGTTCAGATAGTTTGC
GGCGTTTTCATATAAGCGCCACTAAATGTAACATAACTTAAAACAAACCACTACGTTTTGTTAAA
GTACGTTGCGGCGCTTCACCCAAAGCGCCGCTAATGATATTCTATAACGGCGTTTTCTA
Found at i:36429933 original size:21 final size:20
Alignment explanation
Indices: 36429909--36429960 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
36429899 ATGAACAATT
*
36429909 AAGAAAAAGAAAAATACAAAA
1 AAGAAATAGAAAAAT-CAAAA
*
36429930 AAG-AATAGATCAAATCAAAA
1 AAGAAATAGA-AAAATCAAAA
36429950 AAGAAATAGAA
1 AAGAAATAGAA
36429961 TCAATGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.73, C:0.06, G:0.12, T:0.10
Consensus pattern (20 bp):
AAGAAATAGAAAAATCAAAA
Found at i:36429950 original size:20 final size:23
Alignment explanation
Indices: 36429920--36429964 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
36429910 AGAAAAAGAA
36429920 AAATACAAAAAAG-AATAG-ATC
1 AAATACAAAAAAGAAATAGAATC
36429941 AAAT-CAAAAAAGAAATAGAATC
1 AAATACAAAAAAGAAATAGAATC
36429963 AA
1 AA
36429965 TGATTTGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.13
Consensus pattern (23 bp):
AAATACAAAAAAGAAATAGAATC
Found at i:36432852 original size:35 final size:34
Alignment explanation
Indices: 36432775--36433038 Score: 324
Period size: 35 Copynumber: 7.8 Consensus size: 34
36432765 AAATAATACA
* *
36432775 TGAACAGGAGAGATTCCCTGCAA-GAAATGAT-G
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGG
36432807 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATG-G
* *
36432842 TGAACAGGAGAGATTCCCTGCAA-GAAATGAT-G
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGG
*
36432874 TGAACAGGAAAGATTCCCTGCAACAAAATAATGTG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATG-G
*
36432909 TGAACAGGAGAGATTCCCTGCAACAAAATAATGTA
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATG-G
* * *
36432944 TGAACAGGAGAGATTCCATGCAA-GAAATTAT-G
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGG
* *
36432976 TGAACAGGAAAGATTCCCTGCAACAGAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATG-G
* * *
36433011 TGAACAGGAAATATTCCCTGCAAGAAAA
1 TGAACAGGAGAGATTCCCTGCAACAAAA
36433039 GACAAGTGAA
Statistics
Matches: 202, Mismatches: 21, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
32 67 0.33
33 17 0.08
34 12 0.06
35 106 0.52
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (34 bp):
TGAACAGGAGAGATTCCCTGCAACAAAATAATGG
Found at i:36432873 original size:67 final size:67
Alignment explanation
Indices: 36432765--36433038 Score: 338
Period size: 67 Copynumber: 4.0 Consensus size: 67
36432755 GTCCAAAAAG
* * * *
36432765 AAATAATACATGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATAATGTGAACAGGAAAGATTCCCTGCAA
36432830 CA
66 CA
*
36432832 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATAATGTGAACAGGAAAGATTCCCTGCAA
36432897 CA
66 CA
* * * *
36432899 AAATAATGTGTGAACAGGAGAGATTCCCTGCAACAAAATAATGTATGAACAGGAGAGATTCCATG
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAA-GAAATAATG--TGAACAGGAAAGATTCCCTG
*
36432964 CAA-G
63 CAACA
* * * *
36432968 AAATTAT--GTGAACAGGAAAGATTCCCTGCAACAGAATAATGCGTGAACAGGAAATATTCCCTG
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGA-AATAAT--GTGAACAGGAAAGATTCCCTG
*
36433031 CAAGA
63 CAACA
36433036 AAA
1 AAA
36433039 GACAAGTGAA
Statistics
Matches: 184, Mismatches: 16, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
66 1 0.01
67 145 0.79
68 10 0.05
69 7 0.04
70 21 0.11
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (67 bp):
AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATAATGTGAACAGGAAAGATTCCCTGCAA
CA
Found at i:36432948 original size:102 final size:102
Alignment explanation
Indices: 36432775--36433038 Score: 399
Period size: 102 Copynumber: 2.6 Consensus size: 102
36432765 AAATAATACA
* * *
36432775 TGAACAGGAGAGATTCCCTGCAA-GAAATGA--TGTGAACAGGAGAGATTCCCTGCAACAAAATA
1 TGAACAGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTGCAACAAAATA
* *
36432837 ATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATG
66 ATGCATGAACAGGAGAGATTCCATGCAAGAAATGATG
36432874 TGAACAGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTGCAACAAAATA
1 TGAACAGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTGCAACAAAATA
* *
36432939 ATGTATGAACAGGAGAGATTCCATGCAAGAAATTATG
66 ATGCATGAACAGGAGAGATTCCATGCAAGAAATGATG
* * * * *
36432976 TGAACAGGAAAGATTCCCTGCAACAGAATAATGCGTGAACAGGAAATATTCCCTGCAAGAAAA
1 TGAACAGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTGCAACAAAA
36433039 GACAAGTGAA
Statistics
Matches: 150, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
99 22 0.15
100 5 0.03
102 123 0.82
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (102 bp):
TGAACAGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTGCAACAAAATA
ATGCATGAACAGGAGAGATTCCATGCAAGAAATGATG
Found at i:36433289 original size:29 final size:29
Alignment explanation
Indices: 36433257--36433329 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 29
36433247 TTCTCAAGAC
* *
36433257 ATTTAAGTTTTCAAAAATTTAGTTTTTAA
1 ATTTAAGTTTTCAAAAATTAAGTTTTCAA
*
36433286 ATTTCCAAATTTTC--AAATTAAGTTTTCAA
1 ATTT--AAGTTTTCAAAAATTAAGTTTTCAA
* *
36433315 ACTTAAGCTTTCAAA
1 ATTTAAGTTTTCAAA
36433330 TTACAAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
27 6 0.18
29 21 0.62
31 7 0.21
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.45
Consensus pattern (29 bp):
ATTTAAGTTTTCAAAAATTAAGTTTTCAA
Found at i:36433313 original size:13 final size:13
Alignment explanation
Indices: 36433295--36433332 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
36433285 AATTTCCAAA
36433295 TTTTCAAATTAAG
1 TTTTCAAATTAAG
36433308 TTTTCAAACTTAAG
1 TTTTCAAA-TTAAG
*
36433322 CTTTCAAATTA
1 TTTTCAAATTA
36433333 CAAATATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (13 bp):
TTTTCAAATTAAG
Found at i:36433453 original size:10 final size:10
Alignment explanation
Indices: 36433440--36433472 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
36433430 AATTTATTCT
36433440 GAAATCATAA
1 GAAATCATAA
36433450 GAAATCAT-A
1 GAAATCATAA
*
36433459 GATATCATAA
1 GAAATCATAA
36433469 GAAA
1 GAAA
36433473 ATTAATTCGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (10 bp):
GAAATCATAA
Found at i:36434001 original size:23 final size:24
Alignment explanation
Indices: 36433958--36434003 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
36433948 ATATTATGTC
*
36433958 ATTTATATCACATCAAAATTAAAT
1 ATTTATATAACATCAAAATTAAAT
36433982 ATTT-TATAACAT-AAATATTAAA
1 ATTTATATAACATCAAA-ATTAAA
36434004 AAAACAAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 13 0.65
24 4 0.20
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (24 bp):
ATTTATATAACATCAAAATTAAAT
Found at i:36434688 original size:20 final size:22
Alignment explanation
Indices: 36434663--36434703 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
36434653 ATTCCTAACC
36434663 CCATCCG-CT-ACACACCATCT
1 CCATCCGTCTAACACACCATCT
36434683 CCATCCGTCTCAACACACCAT
1 CCATCCGTCT-AACACACCAT
36434704 ATAGGACATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
23 9 0.50
ACGTcount: A:0.27, C:0.49, G:0.05, T:0.20
Consensus pattern (22 bp):
CCATCCGTCTAACACACCATCT
Found at i:36435319 original size:63 final size:63
Alignment explanation
Indices: 36435218--36435423 Score: 216
Period size: 63 Copynumber: 3.3 Consensus size: 63
36435208 TCCTAATGTA
* * ** * * * * *
36435218 CAAACAGTATGTTACACTGCCTAGACACACGCCTGTGTCTCTGGCTCGTATGATTTATAGTGG
1 CAAACAGTAAGTCACACAACCTGGACACACGCCCGTGTCTCTGGCTCATGTGATCTATAGTGG
* * * * *
36435281 CCAACAGTGAA-TCATACAACCTGGACACACGCCCGTGTCTTTGGCCCATGTGATCAATAGTGG
1 CAAACAGT-AAGTCACACAACCTGGACACACGCCCGTGTCTCTGGCTCATGTGATCTATAGTGG
* * *
36435344 CAAACCGTAAGTCACACGACCTGGACACACGCCCGTGTCTCTAGCTCATGTGATCTATAGTGG
1 CAAACAGTAAGTCACACAACCTGGACACACGCCCGTGTCTCTGGCTCATGTGATCTATAGTGG
* * *
36435407 CAAGCAATGAGTCACAC
1 CAAACAGTAAGTCACAC
36435424 GGTCGTGTAA
Statistics
Matches: 115, Mismatches: 26, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
62 2 0.02
63 112 0.97
64 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (63 bp):
CAAACAGTAAGTCACACAACCTGGACACACGCCCGTGTCTCTGGCTCATGTGATCTATAGTGG
Found at i:36438607 original size:28 final size:28
Alignment explanation
Indices: 36438576--36438632 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
36438566 AAATTAATTA
36438576 ATTAAATGACGCTTTTGACAATAGATGT
1 ATTAAATGACGCTTTTGACAATAGATGT
*
36438604 ATTAAATGACTCTTTTGACAATAGATGT
1 ATTAAATGACGCTTTTGACAATAGATGT
36438632 A
1 A
36438633 AGCGAATATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (28 bp):
ATTAAATGACGCTTTTGACAATAGATGT
Found at i:36457322 original size:27 final size:27
Alignment explanation
Indices: 36457284--36457351 Score: 136
Period size: 27 Copynumber: 2.5 Consensus size: 27
36457274 CAATGAAGGT
36457284 GACCCCGATCATTCTCTTCTTGTAAAA
1 GACCCCGATCATTCTCTTCTTGTAAAA
36457311 GACCCCGATCATTCTCTTCTTGTAAAA
1 GACCCCGATCATTCTCTTCTTGTAAAA
36457338 GACCCCGATCATTC
1 GACCCCGATCATTC
36457352 AATTTCTTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.25, C:0.32, G:0.12, T:0.31
Consensus pattern (27 bp):
GACCCCGATCATTCTCTTCTTGTAAAA
Found at i:36457601 original size:26 final size:27
Alignment explanation
Indices: 36457554--36457604 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
36457544 TAATAATGGT
** *
36457554 TATTTATATTAATTATATAAAATTAAA
1 TATTTATATTAAAAATAAAAAATTAAA
36457581 TATTT-TATTAAAAATAAAAAATTA
1 TATTTATATTAAAAATAAAAAATTA
36457605 TGTCTATATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TATTTATATTAAAAATAAAAAATTAAA
Found at i:36457742 original size:128 final size:127
Alignment explanation
Indices: 36457495--36457750 Score: 369
Period size: 127 Copynumber: 2.0 Consensus size: 127
36457485 TTTGTTTCAA
* * * * *
36457495 AAAACACTAATGAATATTTTAAAATATATTATATATTTTACTTATCTCCTAATAATGGTTATTTA
1 AAAACACTAAAGAATATTTTAAAATATATTATACATTTTACATATCTACTAATAATGATTATTTA
*
36457560 TATTAATTATATAAAATTAAATATTTTATTAAAAATAAAAAATTATGTCTATATGATATGATAT
66 TATTAATTATATAAAATTAAATATTTTATT--AAATAAAAAATCATGTCTATATGATATGATAT
*
36457624 AAAA-ACTAAAGAATATTTTAAAATATTTTATACA-TTTACATATCTACTAATAATGATTATTTA
1 AAAACACTAAAGAATATTTTAAAATATATTATACATTTTACATATCTACTAATAATGATTATTTA
* *
36457687 TATTAATTATATAAAATTAAAATATTTTATT-AA-AAAAAGTCATGTC-ACATGATATGATAT
66 TATTAATTATATAAAATT-AAATATTTTATTAAATAAAAAATCATGTCTATATGATATGATAT
36457747 AAAA
1 AAAA
36457751 TAGTAATGCA
Statistics
Matches: 117, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
123 17 0.15
124 11 0.09
125 2 0.02
127 44 0.38
128 39 0.33
129 4 0.03
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.42
Consensus pattern (127 bp):
AAAACACTAAAGAATATTTTAAAATATATTATACATTTTACATATCTACTAATAATGATTATTTA
TATTAATTATATAAAATTAAATATTTTATTAAATAAAAAATCATGTCTATATGATATGATAT
Found at i:36458366 original size:6 final size:6
Alignment explanation
Indices: 36458355--36458390 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
36458345 ACCAAAGCTC
36458355 CCATCA CCATCA CCATCA CCATCA CCATCA CCATCA
1 CCATCA CCATCA CCATCA CCATCA CCATCA CCATCA
36458391 TCTGAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.50, G:0.00, T:0.17
Consensus pattern (6 bp):
CCATCA
Done.