Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003164.1 Hibiscus syriacus cultivar Beakdansim tig00006658_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: 105912
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:5319 original size:26 final size:27
Alignment explanation
Indices: 5276--5329 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
5266 GAAAATATCT
*
5276 AAAATATATGAAGCAAAATCAACATGA
1 AAAATATATGAAGAAAAATCAACATGA
*
5303 AAAATAT-TGCAGAAAAATCAACATGA
1 AAAATATATGAAGAAAAATCAACATGA
5329 A
1 A
5330 GCTCAAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.19
Consensus pattern (27 bp):
AAAATATATGAAGAAAAATCAACATGA
Found at i:10667 original size:7 final size:7
Alignment explanation
Indices: 10655--10679 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
10645 TAGAGCTTGA
10655 AATCATG
1 AATCATG
10662 AATCATG
1 AATCATG
10669 AATCATG
1 AATCATG
10676 AATC
1 AATC
10680 GTGTATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (7 bp):
AATCATG
Found at i:13825 original size:4 final size:4
Alignment explanation
Indices: 13816--13853 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
13806 ATTTGGTCAT
13816 ATTA ATTA ATTA ATTA ATTA ATTA ATT- ATTA A-TA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA
13854 TAAAAATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 6 0.19
4 26 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:15890 original size:16 final size:16
Alignment explanation
Indices: 15869--15903 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
15859 ATTATTTGTG
* *
15869 AAAACAGAAAAGAATT
1 AAAACAAAAAAGAAAT
15885 AAAACAAAAAAGAAAT
1 AAAACAAAAAAGAAAT
15901 AAA
1 AAA
15904 GGAATGCATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.77, C:0.06, G:0.09, T:0.09
Consensus pattern (16 bp):
AAAACAAAAAAGAAAT
Found at i:24122 original size:44 final size:44
Alignment explanation
Indices: 24064--24200 Score: 217
Period size: 44 Copynumber: 3.2 Consensus size: 44
24054 AATAAACCCG
24064 TGCCAAC-T-AATTTTCAAGAGATGACAACTTTTATGTCTCATA
1 TGCCAACATGAATTTTCAAGAGATGACAACTTTTATGTCTCATA
* *
24106 TGTCAACATGATTTTTCAAGAGATGACAACTTTTATGTCTCATA
1 TGCCAACATGAATTTTCAAGAGATGACAACTTTTATGTCTCATA
*
24150 TGCCAAACATGAATTTTCAAGAGAT-ACAACTTTTATGTCTCGTA
1 TGCC-AACATGAATTTTCAAGAGATGACAACTTTTATGTCTCATA
24194 TGCCAAC
1 TGCCAAC
24201 TTACAATCAT
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
42 6 0.07
43 4 0.05
44 58 0.67
45 19 0.22
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (44 bp):
TGCCAACATGAATTTTCAAGAGATGACAACTTTTATGTCTCATA
Found at i:24339 original size:63 final size:63
Alignment explanation
Indices: 24192--24377 Score: 175
Period size: 63 Copynumber: 3.0 Consensus size: 63
24182 TTATGTCTCG
* * * ** * ***
24192 TATGCCAACTTACAATCATC-CGAGATAACAGAGTGGTG-TTGTTTTTTCACAACACTATCT-C
1 TATGCCAACTTACAGTCA-CACGAGAGAAAAGAGTGGTGACAGTTTTTTTACAACACCGGCTCC
* * ** *
24253 -ATGCCAACTTACAGTCACCCGAGAGAATAGAGTGGTGATTGTTTTTTTACAATACCGGCTCC
1 TATGCCAACTTACAGTCACACGAGAGAAAAGAGTGGTGACAGTTTTTTTACAACACCGGCTCC
* *
24315 TATGCCAACTTATAGTTC-CACGAGAGAAAATAGTGGTGACAGTTTTTTTACAACACCGGCTCC
1 TATGCCAACTTACAG-TCACACGAGAGAAAAGAGTGGTGACAGTTTTTTTACAACACCGGCTCC
24378 CATTCTTACT
Statistics
Matches: 105, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
59 1 0.01
60 32 0.30
61 17 0.16
62 1 0.01
63 52 0.50
64 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (63 bp):
TATGCCAACTTACAGTCACACGAGAGAAAAGAGTGGTGACAGTTTTTTTACAACACCGGCTCC
Found at i:24667 original size:69 final size:69
Alignment explanation
Indices: 24586--24725 Score: 262
Period size: 69 Copynumber: 2.0 Consensus size: 69
24576 AAGTAAGATA
*
24586 AATTTTATATTACTATGATAAATTATATAAAATATGAGATGAAATAAAATAAATATAAAAAAGAA
1 AATTTTATATTACTATGATAAATTATATAAAATATGAGATGAAATAAAATAAATACAAAAAAGAA
24651 ATTT
66 ATTT
*
24655 AATTTTATATTACTATGATAAATTATATAAAATATGAGATGAAATAAAATAAATACAAAAAATAA
1 AATTTTATATTACTATGATAAATTATATAAAATATGAGATGAAATAAAATAAATACAAAAAAGAA
24720 ATTT
66 ATTT
24724 AA
1 AA
24726 ACGTGATTTT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.34
Consensus pattern (69 bp):
AATTTTATATTACTATGATAAATTATATAAAATATGAGATGAAATAAAATAAATACAAAAAAGAA
ATTT
Found at i:28644 original size:29 final size:29
Alignment explanation
Indices: 28598--28676 Score: 113
Period size: 29 Copynumber: 2.7 Consensus size: 29
28588 GGATATGTCA
*
28598 CCAGGGCATCCCAGCGACATTGTAGGACG
1 CCAGGGCATCCCAGCGACATGGTAGGACG
* *
28627 CCATGGCATCCCAGCGACATGGTAGGTCG
1 CCAGGGCATCCCAGCGACATGGTAGGACG
* *
28656 CCAGGGCATCCGAGTGACATG
1 CCAGGGCATCCCAGCGACATG
28677 CATGCTTTGC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.23, C:0.30, G:0.32, T:0.15
Consensus pattern (29 bp):
CCAGGGCATCCCAGCGACATGGTAGGACG
Found at i:28852 original size:23 final size:24
Alignment explanation
Indices: 28797--28855 Score: 86
Period size: 23 Copynumber: 2.5 Consensus size: 24
28787 TGAATTCAGC
*
28797 TGCATTATTACAGCACTTATTGCT
1 TGCATTATTGCAGCACTTATTGCT
*
28821 T-CATTATTGCAGCCCTTATTG-T
1 TGCATTATTGCAGCACTTATTGCT
28843 TGCATTATTGCAG
1 TGCATTATTGCAG
28856 TCGTTCAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 2 0.06
23 29 0.91
24 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.42
Consensus pattern (24 bp):
TGCATTATTGCAGCACTTATTGCT
Found at i:29113 original size:39 final size:39
Alignment explanation
Indices: 29070--29154 Score: 161
Period size: 39 Copynumber: 2.2 Consensus size: 39
29060 TTAGTTTATG
29070 GTTTAAGGTAAAACAAAATTTTAGTTAATTAGTTAGTTA
1 GTTTAAGGTAAAACAAAATTTTAGTTAATTAGTTAGTTA
*
29109 GTTTAAGGTAAAACAAAATTTTAGTTAATTAGTTTGTTA
1 GTTTAAGGTAAAACAAAATTTTAGTTAATTAGTTAGTTA
29148 GTTTAAG
1 GTTTAAG
29155 TTATATTATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.42
Consensus pattern (39 bp):
GTTTAAGGTAAAACAAAATTTTAGTTAATTAGTTAGTTA
Found at i:29268 original size:28 final size:27
Alignment explanation
Indices: 29237--29289 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
29227 ATATTAAAAA
29237 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
29265 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
29290 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:29270 original size:39 final size:40
Alignment explanation
Indices: 29195--29270 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 40
29185 ACATAAATAT
* * *
29195 AAAATTATCTAATTAGTTTGTTTGATAGTTATATATTAAA
1 AAAATAATCTAATTAGTGTGTTAGATAGTTATATATTAAA
*
29235 AAAATAAT-TAATTAGTGTGTTAGTTAGTCTA-ATATT
1 AAAATAATCTAATTAGTGTGTTAGATAGT-TATATATT
29271 TAATTAGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
39 22 0.71
40 9 0.29
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.46
Consensus pattern (40 bp):
AAAATAATCTAATTAGTGTGTTAGATAGTTATATATTAAA
Found at i:29295 original size:27 final size:29
Alignment explanation
Indices: 29236--29300 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
29226 TATATTAAAA
29236 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
29265 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
29291 AAATAGTTAA
1 AAATAATTAA
29301 GTTATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:29459 original size:29 final size:30
Alignment explanation
Indices: 29418--29477 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
29408 TAAAAGAATA
*
29418 ATTATTTATATTAGTTTATTATTATAAATT
1 ATTAGTTATATTAGTTTATTATTATAAATT
29448 ATTAGTTA-ATTAGTTTATTATTATAAATT
1 ATTAGTTATATTAGTTTATTATTATAAATT
29477 A
1 A
29478 GGGTAAAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (30 bp):
ATTAGTTATATTAGTTTATTATTATAAATT
Found at i:29502 original size:44 final size:44
Alignment explanation
Indices: 29448--29547 Score: 191
Period size: 44 Copynumber: 2.3 Consensus size: 44
29438 ATTATAAATT
29448 ATTAGTTAATTAGTTTATTATTATAAATTAGGGTAAAACAAAAA
1 ATTAGTTAATTAGTTTATTATTATAAATTAGGGTAAAACAAAAA
*
29492 ATTAGTTAATTAGTTTATTATTATAAATTATGGTAAAACAAAAA
1 ATTAGTTAATTAGTTTATTATTATAAATTAGGGTAAAACAAAAA
29536 ATTAGTTAATTA
1 ATTAGTTAATTA
29548 CTTTGTTAGT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (44 bp):
ATTAGTTAATTAGTTTATTATTATAAATTAGGGTAAAACAAAAA
Found at i:29575 original size:21 final size:21
Alignment explanation
Indices: 29550--29589 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
29540 GTTAATTACT
29550 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
29571 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
29590 CATATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:32038 original size:21 final size:22
Alignment explanation
Indices: 32008--32052 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
31998 TATTCATTAG
*
32008 TAAATCATTAGT-ATCAAATAAT
1 TAAATCATTAATAAT-AAATAAT
32030 TAAAT-ATTAATAATAAATAAT
1 TAAATCATTAATAATAAATAAT
32051 TA
1 TA
32053 TTAATAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (22 bp):
TAAATCATTAATAATAAATAAT
Found at i:32054 original size:17 final size:17
Alignment explanation
Indices: 32024--32062 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
32014 ATTAGTATCA
*
32024 AATAATTAAATATTAAT
1 AATAAATAAATATTAAT
*
32041 AATAAATAATTATTAAT
1 AATAAATAAATATTAAT
32058 AATAA
1 AATAA
32063 TTACCAAATC
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAAATAAATATTAAT
Found at i:32111 original size:26 final size:26
Alignment explanation
Indices: 32062--32151 Score: 125
Period size: 26 Copynumber: 3.6 Consensus size: 26
32052 ATTAATAATA
* *
32062 ATTACCAAATCATTA-T-T-ATCATT
1 ATTATCAAATCATTATTATAATGATT
32085 ATTATCAAATCATTATTATAATGATT
1 ATTATCAAATCATTATTATAATGATT
32111 ATTA-CTAAATCATTATTATAATGATT
1 ATTATC-AAATCATTATTATAATGATT
32137 ATTATCAAATCATTA
1 ATTATCAAATCATTA
32152 CTAAATCATC
Statistics
Matches: 60, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
23 14 0.23
24 1 0.02
25 2 0.03
26 42 0.70
27 1 0.02
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.44
Consensus pattern (26 bp):
ATTATCAAATCATTATTATAATGATT
Found at i:32220 original size:49 final size:51
Alignment explanation
Indices: 32068--32221 Score: 169
Period size: 49 Copynumber: 3.1 Consensus size: 51
32058 AATAATTACC
* * *
32068 AAATCATTAT-T-ATCATTATTATCAAATCATTATTATAATGAT-TATTACT
1 AAATCATTATATAATCATTATTATCAAATCATTACTA-AATCATATATTATT
* *
32117 AAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAGTA-CATT
1 AAATCATTA-TATAATCATTATTATCAAATCATTACTAAATCAT-A-TATTATT
32170 AAAT-ATTA-A-AATCATTATTATCAAATCATTACTAAATCATATAATTATT
1 AAATCATTATATAATCATTATTATCAAATCATTACTAAATCATAT-ATTATT
32219 AAA
1 AAA
32222 AAACCCATGT
Statistics
Matches: 90, Mismatches: 7, Indels: 16
0.80 0.06 0.14
Matches are distributed among these distances:
47 1 0.01
48 2 0.02
49 45 0.50
50 2 0.02
51 6 0.07
52 26 0.29
53 6 0.07
54 2 0.02
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (51 bp):
AAATCATTATATAATCATTATTATCAAATCATTACTAAATCATATATTATT
Found at i:32749 original size:49 final size:50
Alignment explanation
Indices: 32680--32872 Score: 255
Period size: 49 Copynumber: 3.7 Consensus size: 50
32670 ATTACTAATA
*
32680 ATTACTAAATCATTAGTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
*
32730 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTTATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAAT-A----A-T-TT-C--ATT
32789 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
*
32839 ATTACT-AACCATTACTATCAAATCATTAAATATT
1 ATTACTAAATCATTACTATCAAATCATTAAATATT
32873 GGTTGACTCA
Statistics
Matches: 128, Mismatches: 4, Indels: 23
0.83 0.03 0.15
Matches are distributed among these distances:
49 60 0.47
50 15 0.12
52 1 0.01
53 2 0.02
54 2 0.02
55 2 0.02
56 2 0.02
57 1 0.01
59 9 0.07
60 34 0.27
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (50 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
Found at i:32764 original size:21 final size:20
Alignment explanation
Indices: 32740--32824 Score: 52
Period size: 21 Copynumber: 4.2 Consensus size: 20
32730 ATTACTAATC
32740 ATTACTATCAAATCATTAAAT
1 ATTACTATC-AATCATTAAAT
* * *
32761 ATTA--AT-AATAATTTTATT
1 ATTACTATCAATCA-TTAAAT
* *
32779 ATTACTAATC-ATTACTAAAT
1 ATTACT-ATCAATCATTAAAT
32799 CATTACTATCAAATCATTAAAT
1 -ATTACTATC-AATCATTAAAT
32821 ATTA
1 ATTA
32825 ATAATAATTT
Statistics
Matches: 47, Mismatches: 9, Indels: 16
0.65 0.12 0.22
Matches are distributed among these distances:
17 4 0.09
18 8 0.17
19 2 0.04
20 6 0.13
21 19 0.40
22 8 0.17
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTACTATCAATCATTAAAT
Found at i:32866 original size:63 final size:60
Alignment explanation
Indices: 32730--32855 Score: 227
Period size: 60 Copynumber: 2.1 Consensus size: 60
32720 TAATTTCATT
* *
32730 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTTATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAACC
32789 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAACC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAACC
32849 ATTACTA
1 ATTACTA
32856 TCAAATCATT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
59 6 0.09
60 58 0.91
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.42
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAACC
Found at i:32888 original size:109 final size:108
Alignment explanation
Indices: 32670--32872 Score: 361
Period size: 109 Copynumber: 1.9 Consensus size: 108
32660 TAATTTAATG
*
32670 ATTACTAATAATTACTAAATCATTAGTATCAAATCATTAAATATTAATAATAATTTCATTATTAC
1 ATTACTAATAATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTAC
* *
32735 TAATCATTACTATCAAATCATTAAATATTAATAATAATTTTATT
66 TAACCATTACTATCAAATCATTAAATATTAAT-ATAATATTATT
*
32779 ATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTAC
1 ATTACTAATAATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTAC
32844 TAACCATTACTATCAAATCATTAAATATT
66 TAACCATTACTATCAAATCATTAAATATT
32873 GGTTGACTCA
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 91 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (108 bp):
ATTACTAATAATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTAC
TAACCATTACTATCAAATCATTAAATATTAATATAATATTATT
Found at i:36142 original size:14 final size:14
Alignment explanation
Indices: 36125--36151 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
36115 ACAAATGCAC
36125 AACAACAAAAAATG
1 AACAACAAAAAATG
36139 AACAACAAAAAAT
1 AACAACAAAAAAT
36152 AATTAATTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (14 bp):
AACAACAAAAAATG
Found at i:36143 original size:17 final size:16
Alignment explanation
Indices: 36117--36150 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
36107 ACTAATTTAC
*
36117 AAATGCACAACAACAAA
1 AAATGAACAACAA-AAA
36134 AAATGAACAACAAAAA
1 AAATGAACAACAAAAA
36150 A
1 A
36151 TAATTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.71, C:0.18, G:0.06, T:0.06
Consensus pattern (16 bp):
AAATGAACAACAAAAA
Found at i:36620 original size:21 final size:21
Alignment explanation
Indices: 36587--36635 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
36577 CTAATATAAT
*
36587 ATAACTTAAACTAACAAATTA
1 ATAACTTAAACTAACAAACTA
* *
36608 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
36629 ATTAACT
1 A-TAACT
36636 AAATTTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:37732 original size:21 final size:21
Alignment explanation
Indices: 37679--37718 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
37669 TGCATGTATC
37679 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
37700 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
37719 ACTAATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:37749 original size:39 final size:39
Alignment explanation
Indices: 37706--37790 Score: 152
Period size: 39 Copynumber: 2.2 Consensus size: 39
37696 AATAATATAA
*
37706 CTTAAACTAACAAACTAATTAATTAAAATTTTGTTTTAC
1 CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
*
37745 CTTAAACTAACTAACTAATTAACTAAAATTTTGTTTTAC
1 CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
37784 CTTAAAC
1 CTTAAAC
37791 CATAAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.42, C:0.15, G:0.02, T:0.40
Consensus pattern (39 bp):
CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
Found at i:37814 original size:39 final size:38
Alignment explanation
Indices: 37706--37814 Score: 112
Period size: 39 Copynumber: 2.8 Consensus size: 38
37696 AATAATATAA
* ** *
37706 CTTAAACTAACAAACTAATTAATTAAAATTTTGTTTTAC
1 CTTAAACCAAC-AACTAACAAACTAAAATTTTGTTTTAC
* **
37745 CTTAAACTAACTAACTAATTAACTAAAATTTTGTTTTAC
1 CTTAAACCAAC-AACTAACAAACTAAAATTTTGTTTTAC
37784 CTTAAACCATA-AACTAACAAACTAATAATTT
1 CTTAAACCA-ACAACTAACAAACTAA-AATTT
37815 AAAATAATAA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
38 12 0.19
39 50 0.79
40 1 0.02
ACGTcount: A:0.45, C:0.16, G:0.02, T:0.38
Consensus pattern (38 bp):
CTTAAACCAACAACTAACAAACTAAAATTTTGTTTTAC
Found at i:38056 original size:23 final size:23
Alignment explanation
Indices: 38026--38085 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
38016 AGCTGAACGA
38026 CTGCAATAATGCAGCAATAAGGG
1 CTGCAATAATGCAGCAATAAGGG
* *
38049 CTGCAATAATGCAACAATAAGTG
1 CTGCAATAATGCAGCAATAAGGG
*
38072 ATGCAATAATGCAG
1 CTGCAATAATGCAG
38086 TTGAATTCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.20
Consensus pattern (23 bp):
CTGCAATAATGCAGCAATAAGGG
Found at i:38237 original size:29 final size:29
Alignment explanation
Indices: 38205--38283 Score: 113
Period size: 29 Copynumber: 2.7 Consensus size: 29
38195 GCAAAGCATG
*
38205 CATGTCGCTCGGATGCCCTGGCAACCTAC
1 CATGTCGCTGGGATGCCCTGGCAACCTAC
* *
38234 CATGTCGCTGGGATGCCATGGCATCCTAC
1 CATGTCGCTGGGATGCCCTGGCAACCTAC
* *
38263 AATGTCGTTGGGATGCCCTGG
1 CATGTCGCTGGGATGCCCTGG
38284 TGACCTATCC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.16, C:0.30, G:0.29, T:0.24
Consensus pattern (29 bp):
CATGTCGCTGGGATGCCCTGGCAACCTAC
Found at i:38603 original size:30 final size:30
Alignment explanation
Indices: 38532--38603 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 30
38522 AATTCAACTG
*
38532 CCCCTGACGCTG-TGCATGCTTCCCCGCTGC
1 CCCCTGACGC-GCTACATGCTTCCCCGCTGC
*
38562 CCCCT-ACGCGCTACA-GCTTTCCCGCTGCC
1 CCCCTGACGCGCTACATGCTTCCCCGCTG-C
38591 CCCCTGACGCGCT
1 CCCCTGACGCGCT
38604 GCTGTGCCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
28 12 0.32
29 13 0.35
30 12 0.32
ACGTcount: A:0.08, C:0.50, G:0.21, T:0.21
Consensus pattern (30 bp):
CCCCTGACGCGCTACATGCTTCCCCGCTGC
Found at i:39417 original size:24 final size:24
Alignment explanation
Indices: 39380--39466 Score: 142
Period size: 24 Copynumber: 3.7 Consensus size: 24
39370 TTTGCGAATG
*
39380 TGTTCGTTT-AATGTTCGCAAACA
1 TGTTCATTTAAATGTTCGCAAACA
*
39403 TGCTCATTTAAATGTTCGCAAACA
1 TGTTCATTTAAATGTTCGCAAACA
39427 TGTTCATTTAAATGTTCGCAAACA
1 TGTTCATTTAAATGTTCGCAAACA
39451 TGTTCATTT-AATGTTC
1 TGTTCATTTAAATGTTC
39467 ATGAATAAGT
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
23 14 0.23
24 46 0.77
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (24 bp):
TGTTCATTTAAATGTTCGCAAACA
Found at i:44350 original size:18 final size:18
Alignment explanation
Indices: 44283--44357 Score: 59
Period size: 18 Copynumber: 4.3 Consensus size: 18
44273 GATGAATTCT
*
44283 AAATG-TTTACAATTATC
1 AAATGTTTTACAGTTATC
* * *
44300 AGATATTATACAGTTATC
1 AAATGTTTTACAGTTATC
*
44318 ATACT-TTTT--AGTTATC
1 A-AATGTTTTACAGTTATC
44334 AAATGTTTTACAGTTATC
1 AAATGTTTTACAGTTATC
*
44352 AGATGT
1 AAATGT
44358 AGATTAATAA
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
15 2 0.05
16 12 0.27
17 3 0.07
18 26 0.59
19 1 0.02
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.44
Consensus pattern (18 bp):
AAATGTTTTACAGTTATC
Found at i:44518 original size:20 final size:20
Alignment explanation
Indices: 44493--44671 Score: 125
Period size: 20 Copynumber: 8.8 Consensus size: 20
44483 ATGCGAAACA
*
44493 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* * *
44513 AAAATCGCAATGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
44533 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
44553 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
*
44574 AAGAATCGCAATGCGATTCAA-
1 AA-AATCGCAACGCGATT-AAG
* *
44595 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTAAG
*
44615 AAAATCGCAACGCGATTCCAG
1 AAAATCGCAACGCGATT-AAG
* * *
44636 -GAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTAAG
44655 AAAATCGCAACGCGATT
1 AAAATCGCAACGCGATT
44672 CCAAGAATCG
Statistics
Matches: 125, Mismatches: 23, Indels: 22
0.74 0.14 0.13
Matches are distributed among these distances:
18 1 0.01
19 3 0.02
20 98 0.78
21 9 0.07
22 14 0.11
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:44631 original size:40 final size:40
Alignment explanation
Indices: 44577--44684 Score: 180
Period size: 40 Copynumber: 2.7 Consensus size: 40
44567 ATCTTCCAAG
* *
44577 AATCGCAATGCGATTCAAAGAATCGCAACGCGATTGAGAA
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAA
* *
44617 AATCGCAACGCGATTCCAGGAATCGCAATGCGATTGAGAA
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAA
44657 AATCGCAACGCGATTCCAAGAATCGCAA
1 AATCGCAACGCGATTCCAAGAATCGCAA
44685 AACGGCAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (40 bp):
AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAA
Found at i:44663 original size:60 final size:61
Alignment explanation
Indices: 44551--44671 Score: 192
Period size: 60 Copynumber: 2.0 Consensus size: 61
44541 AACGGTCAAA
44551 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTG
1 AGAAAATCGCAACGCGA-CTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTG
* *
44613 AGAAAATCGCAACGCGA-TTCCAGGAATCGCAATGCGATTGAGAA-AATCGCAACGCGATT
1 AGAAAATCGCAACGCGACTTCCAAGAATCGCAATGCGATTCA-AAGAATCGCAACGCGATT
44672 CCAAGAATCG
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
60 37 0.66
61 2 0.04
62 17 0.30
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.17
Consensus pattern (61 bp):
AGAAAATCGCAACGCGACTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTG
Found at i:44680 original size:20 final size:20
Alignment explanation
Indices: 44555--44684 Score: 138
Period size: 20 Copynumber: 6.4 Consensus size: 20
44545 GTCAAAAGAA
44555 AATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGA--TTCCAAG
* *
44577 AATCGCAATGCGATTCAAAG
1 AATCGCAACGCGATTCCAAG
* *
44597 AATCGCAACGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
*
44617 AATCGCAACGCGATTCCAGG
1 AATCGCAACGCGATTCCAAG
* * *
44637 AATCGCAATGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
44657 AATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAG
44677 AATCGCAA
1 AATCGCAA
44685 AACGGCAAAA
Statistics
Matches: 89, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
19 2 0.02
20 73 0.82
21 2 0.02
22 12 0.13
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGATTCCAAG
Found at i:44806 original size:6 final size:6
Alignment explanation
Indices: 44795--44845 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
44785 GACACGTATT
44795 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
44843 ACC
1 ACC
44846 CGAGACGAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:45165 original size:6 final size:6
Alignment explanation
Indices: 45154--45216 Score: 126
Period size: 6 Copynumber: 10.5 Consensus size: 6
45144 TCTCGTCTCG
45154 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
45202 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
45217 AATACGTGTC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:45355 original size:20 final size:20
Alignment explanation
Indices: 45329--45464 Score: 236
Period size: 20 Copynumber: 6.7 Consensus size: 20
45319 TTGTCGTTCA
45329 ATCGCATTGCGATTCTTTGG
1 ATCGCATTGCGATTCTTTGG
*
45349 CTCGCATTGCGATTCTTTGG
1 ATCGCATTGCGATTCTTTGG
45369 ATCGCATTGCGATTCTTTGG
1 ATCGCATTGCGATTCTTTGG
45389 ATCGCATTGCGATTCTTTGG
1 ATCGCATTGCGATTCTTTGG
45409 ATCGCATTGCGATTCTTTGG
1 ATCGCATTGCGATTCTTTGG
45429 ATCGCATTGCGATTCTTTGAAG
1 ATCGCATTGCGATTCTTTG--G
*
45451 ATCGCGTTGCGATT
1 ATCGCATTGCGATT
45465 TTCTTTTGAC
Statistics
Matches: 111, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
20 97 0.87
22 14 0.13
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.39
Consensus pattern (20 bp):
ATCGCATTGCGATTCTTTGG
Found at i:45480 original size:20 final size:20
Alignment explanation
Indices: 45455--45508 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
45445 TTGAAGATCG
* *
45455 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTCAA
45475 CGTTGCGATTTTCTTTTCAA
1 CGTTGCGATTTTCTTTTCAA
45495 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
45509 AAATCGCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.20, G:0.19, T:0.50
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTCAA
Found at i:45535 original size:19 final size:19
Alignment explanation
Indices: 45495--45546 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
45485 TTCTTTTCAA
*
45495 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTT-GAAATCG
*
45515 CGTTGCGATTTTGATATCG
1 CGTTGCGATTTTGAAATCG
45534 CGTTGCGATTTTG
1 CGTTGCGATTTTG
45547 TTGGTCATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTGAAATCG
Found at i:48039 original size:2 final size:2
Alignment explanation
Indices: 48032--48064 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
48022 ATAGAATGTA
48032 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
48065 AGTAATAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49806 original size:29 final size:31
Alignment explanation
Indices: 49739--49811 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
49729 TATGAAAATA
*
49739 TAAATAAATTTTATTATATATTGTATTAGTT
1 TAAAAAAATTTTATTATATATTGTATTAGTT
*
49770 TATAAAAACTTTTATTAT-TATT-T-TT-GTAT
1 TA-AAAAAATTTTATTATATATTGTATTAGT-T
49799 TAAAAAAATTTTA
1 TAAAAAAATTTTA
49812 AAATTAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 12 0.32
29 5 0.14
30 1 0.03
31 6 0.16
32 13 0.35
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (31 bp):
TAAAAAAATTTTATTATATATTGTATTAGTT
Found at i:50394 original size:23 final size:23
Alignment explanation
Indices: 50368--50415 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
50358 ATAAAGTACA
* *
50368 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
**
50391 ATAATGTAATAGATAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
50414 AT
1 AT
50416 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGATAGCGCTTAT
Found at i:50823 original size:21 final size:22
Alignment explanation
Indices: 50798--50849 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
50788 ACACTTTACA
*
50798 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
50821 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
50844 ATATAA
1 ATATAA
50850 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:50834 original size:23 final size:23
Alignment explanation
Indices: 50808--50870 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
50798 ATATAACCAC
50808 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
50831 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
50854 TACCTATTACATCATAT
1 TACCTATTACATTATAT
50871 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:51717 original size:17 final size:18
Alignment explanation
Indices: 51695--51737 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
51685 ATATATCCGG
51695 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
51712 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
51732 TATCAT
1 TATCAT
51738 ATTTTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:52377 original size:229 final size:228
Alignment explanation
Indices: 51976--52424 Score: 781
Period size: 229 Copynumber: 2.0 Consensus size: 228
51966 TTAAAACTGC
51976 TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
**
52041 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
* *
52106 TTAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAA
131 TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTC-ACAGTGAAATAA
*
52171 GTATGAACACTTTTATAAAAATGATATATACTTT
195 GTATGAACACTTTTATAAAAAGGATATATACTTT
* *
52205 TTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTTATGTTTTCCACCTACAATA
1 TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
*
52270 TTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
* * *
52335 TTATATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTCACAGTGAAATAAG
131 TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAAG
*
52400 TATGGACACTTTTATAAAAAGGATA
196 TATGAACACTTTTATAAAAAGGATA
52425 GATAATTTAC
Statistics
Matches: 208, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
228 36 0.17
229 172 0.83
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (228 bp):
TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAAG
TATGAACACTTTTATAAAAAGGATATATACTTT
Found at i:53350 original size:3 final size:3
Alignment explanation
Indices: 53328--53379 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
53318 AGCAATCTAT
* * *
53328 GCA GCA ACA GCA GCA ACA GCA GCA GCA GCA GCA ACA GCA GCA GCA GCA
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
53376 GCA G
1 GCA G
53380 AACCAAAATC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.38, C:0.33, G:0.29, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:63145 original size:18 final size:17
Alignment explanation
Indices: 63117--63152 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
63107 TTATCATAAA
63117 TATTTTTTTTTTTATTT
1 TATTTTTTTTTTTATTT
63134 TATTTTTATTTTTTATTT
1 TATTTTT-TTTTTTATTT
63152 T
1 T
63153 TTTCTACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (17 bp):
TATTTTTTTTTTTATTT
Found at i:63698 original size:17 final size:16
Alignment explanation
Indices: 63655--63700 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 16
63645 CAATCTAAAC
63655 TATAATAAAAAATATA
1 TATAATAAAAAATATA
*
63671 TATAA-AGAAAATATAA
1 TATAATAAAAAATAT-A
63687 TTATAATAAAAAAT
1 -TATAATAAAAAAT
63701 TATTTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 8 0.32
16 6 0.24
17 5 0.20
18 6 0.24
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (16 bp):
TATAATAAAAAATATA
Found at i:65721 original size:3 final size:3
Alignment explanation
Indices: 65713--65757 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
65703 ATTTTTAAAC
** *
65713 TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
65758 AATAATAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:65725 original size:15 final size:15
Alignment explanation
Indices: 65701--65759 Score: 73
Period size: 15 Copynumber: 3.7 Consensus size: 15
65691 TTTTTTCATT
* *
65701 TTATTTTTAAACTTA
1 TTATTATTAAAATTA
65716 TTATTATTAAAATTA
1 TTATTATTAAAATTA
65731 TTATTATTATTAATATTA
1 TTATTATTA--AA-ATTA
65749 TTATTATTAAA
1 TTATTATTAAA
65760 TAATAATTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
15 22 0.56
16 2 0.05
17 2 0.05
18 13 0.33
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATTATTAAAATTA
Found at i:65732 original size:9 final size:9
Alignment explanation
Indices: 65717--65780 Score: 56
Period size: 9 Copynumber: 6.9 Consensus size: 9
65707 TTAAACTTAT
65717 TATTATTAA
1 TATTATTAA
* *
65726 AATTATTAT
1 TATTATTAA
65735 TATTATTAA
1 TATTATTAA
*
65744 TATTATTAT
1 TATTATTAA
*
65753 TATTAAATAA
1 TATT-ATTAA
**
65763 TAATTACAAA
1 T-ATTATTAA
65773 TATTATTA
1 TATTATTA
65781 CAGGCCCAGT
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
9 31 0.74
10 8 0.19
11 3 0.07
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (9 bp):
TATTATTAA
Found at i:65734 original size:18 final size:18
Alignment explanation
Indices: 65713--65757 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
65703 ATTTTTAAAC
65713 TTATTATTATTAAAATTA
1 TTATTATTATTAAAATTA
*
65731 TTATTATTATTAATATTA
1 TTATTATTATTAAAATTA
65749 TTATTATTA
1 TTATTATTA
65758 AATAATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTATTATTAAAATTA
Found at i:67008 original size:25 final size:25
Alignment explanation
Indices: 66962--67011 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
66952 AAAAGCATGT
*
66962 TTTTATTTATTTTTTGGAATTTATA
1 TTTTATTTATTTTTAGGAATTTATA
* **
66987 TTTTATTTCTTTTTAGTCATTTATA
1 TTTTATTTATTTTTAGGAATTTATA
67012 CATGTATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.68
Consensus pattern (25 bp):
TTTTATTTATTTTTAGGAATTTATA
Found at i:67749 original size:2 final size:2
Alignment explanation
Indices: 67742--67772 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
67732 AAAACCCTAA
67742 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
67773 TTTTTCTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:68808 original size:46 final size:46
Alignment explanation
Indices: 68742--68829 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
68732 TGATTTCATT
68742 TTTTTCTAAACAAAGCATGGAACTAGAAATCATGCA-GTTAGGTTAA
1 TTTTTCTAAACAAAGCATGGAACTAGAAATCATG-AGGTTAGGTTAA
* *
68788 TTTTTCTAAATAAAGCATGGAATTAGAAATCATGAGGTTAGG
1 TTTTTCTAAACAAAGCATGGAACTAGAAATCATGAGGTTAGG
68830 ATTTATACCT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 1 0.03
46 38 0.97
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (46 bp):
TTTTTCTAAACAAAGCATGGAACTAGAAATCATGAGGTTAGGTTAA
Found at i:69757 original size:3 final size:3
Alignment explanation
Indices: 69749--69780 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
69739 GGATACTATC
69749 ATT ATT ATT ATT ATT A-T ATT ATT -TT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
69781 ATAATAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:70472 original size:20 final size:20
Alignment explanation
Indices: 70449--70503 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
70439 GCACTAACTC
70449 TATTATACT-GCCACCACTAA
1 TATT-TACTGGCCACCACTAA
*
70469 TATTTGCTGGCCACCACTAA
1 TATTTACTGGCCACCACTAA
*
70489 TATTTGCTGGCCACC
1 TATTTACTGGCCACC
70504 CATGTTTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.25, C:0.31, G:0.13, T:0.31
Consensus pattern (20 bp):
TATTTACTGGCCACCACTAA
Found at i:71105 original size:146 final size:146
Alignment explanation
Indices: 70835--71109 Score: 354
Period size: 146 Copynumber: 1.9 Consensus size: 146
70825 TCTCGCCGGA
* *
70835 GATCGGGATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATA
1 GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCAACACGAACAACATA
* ** * ** *
70900 TTGAAAATTCAAGACGATCGGACGGTGGACGGTGACGGATCGGAGAAAACATATCCGGACGGTTT
66 TTGAAAAATCAAGACGATCGGACGGTGGACGACGACAGATCAAAGAAAACACATCCGGACGGTTT
70965 TTAGCCTCTTGCTGGT
131 TTAGCCTCTTGCTGGT
* * * * * *
70981 GATCGGAATCTTCGATCAATATTCCGAACGGTGAAAAGTTGTGTG-ATGCCAACACGAACAACCT
1 GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCG-GAAGGCCAACACGAACAACAT
* * * * *
71045 ATTGAAAAATCAGGACGATCGGACGGTGGATGACGGCAGATCAAAGAAAATACATTCGGACGGTT
65 ATTGAAAAATCAAGACGATCGGACGGTGGACGACGACAGATCAAAGAAAACACATCCGGACGGTT
71110 ATCTTTGTAT
Statistics
Matches: 108, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
146 107 0.99
147 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (146 bp):
GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCAACACGAACAACATA
TTGAAAAATCAAGACGATCGGACGGTGGACGACGACAGATCAAAGAAAACACATCCGGACGGTTT
TTAGCCTCTTGCTGGT
Found at i:77279 original size:3 final size:3
Alignment explanation
Indices: 77271--77302 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
77261 CTTTAGTATT
77271 GAA GAA GAA GAA GAA GAA GAA GAA GATA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA G
77303 GCCTTGGTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:78446 original size:8 final size:8
Alignment explanation
Indices: 78427--78503 Score: 74
Period size: 9 Copynumber: 9.8 Consensus size: 8
78417 TTAAAGATAA
78427 AAAAAATG
1 AAAAAATG
78435 -AAAAATG
1 AAAAAATG
78442 AAAAAAATG
1 -AAAAAATG
78451 AAAAAAATG
1 -AAAAAATG
78460 AAAAAATG
1 AAAAAATG
*
78468 -AAATA-G
1 AAAAAATG
78474 -AAAAATAG
1 AAAAAAT-G
78482 AAAAAATGG
1 AAAAAAT-G
78491 AAAAAAT-
1 AAAAAATG
78498 AAAAAA
1 AAAAAA
78504 AAAGAAGAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
6 5 0.08
7 17 0.28
8 9 0.15
9 30 0.49
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:78447 original size:9 final size:9
Alignment explanation
Indices: 78426--78515 Score: 71
Period size: 9 Copynumber: 9.8 Consensus size: 9
78416 CTTAAAGATA
78426 AAAAAAATG
1 AAAAAAATG
78435 --AAAAATG
1 AAAAAAATG
78442 AAAAAAATG
1 AAAAAAATG
78451 AAAAAAATG
1 AAAAAAATG
78460 -AAAAAATG
1 AAAAAAATG
78468 AAATAGAAAAAT-
1 --A-A-AAAAATG
78480 AGAAAAAATG
1 A-AAAAAATG
* *
78490 GAAAAAATA
1 AAAAAAATG
*
78499 AAAAAAAAG
1 AAAAAAATG
78508 AAGAAAAA
1 AA-AAAAA
78516 AAGAAGAAGA
Statistics
Matches: 66, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
7 7 0.11
8 8 0.12
9 37 0.56
10 7 0.11
12 1 0.02
13 6 0.09
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (9 bp):
AAAAAAATG
Found at i:78471 original size:22 final size:22
Alignment explanation
Indices: 78446--78489 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
78436 AAAATGAAAA
78446 AAATGAAAAAAAT-GAAAAAATG
1 AAAT-AAAAAAATAGAAAAAATG
*
78468 AAATAGAAAAATAGAAAAAATG
1 AAATAAAAAAATAGAAAAAATG
78490 GAAAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (22 bp):
AAATAAAAAAATAGAAAAAATG
Found at i:78478 original size:39 final size:38
Alignment explanation
Indices: 78430--78504 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 38
78420 AAGATAAAAA
*
78430 AAATGAAAAAT-GAAAAAAATGAAAAAAATGAAAAAATG
1 AAATGAAAAATAG-AAAAAATGAAAAAAATAAAAAAATG
*
78468 AAATAGAAAAATAGAAAAAATGGAAAAAATAAAAAAA
1 AAAT-GAAAAATAGAAAAAATGAAAAAAATAAAAAAA
78505 AAGAAGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 4 0.12
39 28 0.85
40 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (38 bp):
AAATGAAAAATAGAAAAAATGAAAAAAATAAAAAAATG
Found at i:78504 original size:8 final size:8
Alignment explanation
Indices: 78426--78545 Score: 52
Period size: 9 Copynumber: 14.5 Consensus size: 8
78416 CTTAAAGATA
78426 AAAAAAAT
1 AAAAAAAT
*
78434 -GAAAAAT
1 AAAAAAAT
78441 GAAAAAAAT
1 -AAAAAAAT
78450 GAAAAAAAT
1 -AAAAAAAT
*
78459 GAAAAAAT
1 AAAAAAAT
*
78467 ---GAAAT
1 AAAAAAAT
*
78472 AGAAAAAT
1 AAAAAAAT
78480 AGAAAAAAT
1 A-AAAAAAT
*
78489 GGAAAAAAT
1 -AAAAAAAT
78498 AAAAAAA-
1 AAAAAAAT
*
78505 AAGAAGAAAA
1 AA-AA-AAAT
*
78515 AAAGAAGAAGA
1 AAA-AA-AA-T
*
78526 AAAAAAAC
1 AAAAAAAT
78534 AAAAAAAT
1 AAAAAAAT
78542 AAAA
1 AAAA
78546 GGGGGGTTCA
Statistics
Matches: 89, Mismatches: 10, Indels: 26
0.71 0.08 0.21
Matches are distributed among these distances:
5 4 0.04
7 8 0.09
8 31 0.35
9 35 0.39
10 7 0.08
11 4 0.04
ACGTcount: A:0.79, C:0.01, G:0.12, T:0.08
Consensus pattern (8 bp):
AAAAAAAT
Found at i:78515 original size:14 final size:14
Alignment explanation
Indices: 78498--78532 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
78488 TGGAAAAAAT
78498 AAAAAAAAAGAAGA
1 AAAAAAAAAGAAGA
*
78512 AAAAAAGAAGAAGA
1 AAAAAAAAAGAAGA
78526 AAAAAAA
1 AAAAAAA
78533 CAAAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGAAGA
Found at i:79910 original size:55 final size:55
Alignment explanation
Indices: 79825--80106 Score: 435
Period size: 55 Copynumber: 5.1 Consensus size: 55
79815 TGAAGCAAAA
79825 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * * *
79880 GAAGATTATTCGAGTCTTATACTCTTTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
79935 GAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
79988 GAAGATTGTTCGAGTCTTATACTCTCTCTGAAGAAATAGGGAGTAGACACGA-CTGTT
1 GAAGATTGTTCGAGTCTTATA--CTCTCTGAAGAAATAGGGGGCAGACGCGATC-GTT
80045 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
80100 GGAGATT
1 GAAGATT
80107 ATTGTTCGAG
Statistics
Matches: 204, Mismatches: 17, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
53 46 0.23
54 6 0.03
55 100 0.49
56 2 0.01
57 50 0.25
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
Found at i:80162 original size:52 final size:52
Alignment explanation
Indices: 80102--80602 Score: 849
Period size: 52 Copynumber: 9.6 Consensus size: 52
80092 CGATCGTTGG
80102 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
80154 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
80206 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * *
80258 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
80310 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
80362 AGATTATTGTTCGAGTTCTAGTCCTTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * * *
80414 AGATTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
80466 AGATTATTGTTCGAGTTCTAGTCCTTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * * *
80518 AGATTATTTTTCGAGTTCTAGTCCTTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
80570 AGATTATCGTTCGAGTTCTACTCCCTGAAGAAA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAA
80603 TAGAGAGCGA
Statistics
Matches: 421, Mismatches: 28, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 421 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.30
Consensus pattern (52 bp):
AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
Found at i:80868 original size:3 final size:3
Alignment explanation
Indices: 80860--80891 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
80850 GGATACTATC
80860 ATT ATT ATT ATT ATT A-T ATT ATT -TT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
80892 ATAATAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:81583 original size:20 final size:20
Alignment explanation
Indices: 81560--81614 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
81550 GCACTAACTC
81560 TATTATACT-GCCACCACTAA
1 TATT-TACTGGCCACCACTAA
*
81580 TATTTGCTGGCCACCACTAA
1 TATTTACTGGCCACCACTAA
*
81600 TATTTGCTGGCCACC
1 TATTTACTGGCCACC
81615 CATGTTTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.25, C:0.31, G:0.13, T:0.31
Consensus pattern (20 bp):
TATTTACTGGCCACCACTAA
Found at i:82216 original size:146 final size:146
Alignment explanation
Indices: 81946--82220 Score: 327
Period size: 146 Copynumber: 1.9 Consensus size: 146
81936 TCTCGCCGGA
* * *
81946 GATCGGGATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATA
1 GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCAACACAAACAACATA
* * ** * ** *
82011 TTGAAAATTCAAGACGATCGGACGGTGGACGGTGACGGATCGGAGAAAACATATCCGGACGGTTT
66 TTGAAAAATCAAGACGATCAGACGGTGGACGACGACAGATCAAAGAAAACACATCCGGACGGTTT
82076 TTAGCCTCTTGCTGGT
131 TTAGCCTCTTGCTGGT
* * * * * * *
82092 GATCGGAATCTTCGTTCAATATTCCGAACGGTGAAAAGTTGTGTG-ATGCCAACACAAACAACCT
1 GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCG-GAAGGCCAACACAAACAACAT
* * * * *
82156 ATTGAAAAATCAGGACGATCAGACGGTGGATGACGGCAGATCAAAGAAAATACATTCGGACGGTT
65 ATTGAAAAATCAAGACGATCAGACGGTGGACGACGACAGATCAAAGAAAACACATCCGGACGGTT
82221 ATCTTTGTAT
Statistics
Matches: 105, Mismatches: 23, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
146 104 0.99
147 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.21
Consensus pattern (146 bp):
GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCAACACAAACAACATA
TTGAAAAATCAAGACGATCAGACGGTGGACGACGACAGATCAAAGAAAACACATCCGGACGGTTT
TTAGCCTCTTGCTGGT
Found at i:87024 original size:14 final size:14
Alignment explanation
Indices: 87004--87042 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
86994 ACACATTCAT
*
87004 AAAAAAATG-AGAA
1 AAAAAAAGGAAGAA
87017 AGAAAAAAGGAAGAA
1 A-AAAAAAGGAAGAA
87032 AAAAAAAGGAA
1 AAAAAAAGGAA
87043 AAATTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 1 0.04
14 17 0.74
15 5 0.22
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (14 bp):
AAAAAAAGGAAGAA
Found at i:90588 original size:75 final size:72
Alignment explanation
Indices: 90464--90663 Score: 206
Period size: 75 Copynumber: 2.7 Consensus size: 72
90454 ATCAACAAGA
* * * * *
90464 AACAAATGCCGGGGTATGCTGAAAGCCCATTTCAATCA-TAATCAT-GAATATTGATGCGTTTTG
1 AACAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAAAT--TGGAATATTGACGCATTTTG
*
90527 AATGTTCACGT
64 AACG-TC-CGT
* * *
90538 CAACAAATGCTGAGGCATGCTGAAAGCCCATTTTAATCAGAAATTGGAATATTGGCGCATTTTGA
1 -AACAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATTGACGCATTTTGA
*
90603 ACGTCTGT
65 ACGTCCGT
* *
90611 ATTAGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATTAGAAATTGGAATA
1 A--A-CAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATA
90664 ACATTTTGAA
Statistics
Matches: 106, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
72 1 0.01
73 2 0.02
74 4 0.04
75 96 0.91
76 3 0.03
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (72 bp):
AACAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATTGACGCATTTTGAA
CGTCCGT
Found at i:90712 original size:70 final size:71
Alignment explanation
Indices: 90541--90712 Score: 195
Period size: 75 Copynumber: 2.4 Consensus size: 71
90531 TTCACGTCAA
* * *
90541 CAAATGCTGAGGCATGCTGAAAGCCCATTTTAATCAGAAATTGGAATATTGGCGCATTTTGAACG
1 CAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATA---G-ACATTTTGAACG
* *
90606 TCTGTATTAG
62 TCTATATCAG
* * *
90616 CAAATGTTGGGGCATGCTGAAAGCCCATTTCAATTAGAAATTGGAATA-ACATTTTGAACAT-TC
1 CAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATAGACATTTTGAACGTCT-
90679 ATATCAG
65 ATATCAG
* *
90686 TAAATGCTGGGGCATGCTGAAGGCCCA
1 CAAATGCTGGGGCATGCTGAAAGCCCA
90713 CATCATTATG
Statistics
Matches: 85, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
69 1 0.01
70 40 0.47
75 44 0.52
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (71 bp):
CAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATAGACATTTTGAACGTCTA
TATCAG
Found at i:92637 original size:31 final size:29
Alignment explanation
Indices: 92599--92660 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
92589 TGCAGTGCAG
*
92599 GACGTTTTCAAAAAGCCTTCGGGAGTTTTTT
1 GACGTTTT--AAAAGCCTTCGGGAGCTTTTT
*
92630 GACGTTTTTAAAGCCTTCGGGAGCTTTTT
1 GACGTTTTAAAAGCCTTCGGGAGCTTTTT
92659 GA
1 GA
92661 TCTTAAAGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 21 0.72
31 8 0.28
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (29 bp):
GACGTTTTAAAAGCCTTCGGGAGCTTTTT
Found at i:92761 original size:73 final size:73
Alignment explanation
Indices: 92639--93077 Score: 664
Period size: 73 Copynumber: 6.0 Consensus size: 73
92629 TGACGTTTTT
* *
92639 AAAGCCTTCGGGAGCTTTTTGATCTTAAAGGCTCAGGGTCATCTGTAAGACCTACAGTGCATGAT
1 AAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTCAGGGTCATCTATAAGACCTACAGTGCATGAT
92704 GTTTTCAA
66 GTTTTCAA
* *
92712 AAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTTAGGGTCATCTATAAGACCTAAAGTGCATGAT
1 AAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTCAGGGTCATCTATAAGACCTACAGTGCATGAT
92777 GTTTTCAA
66 GTTTTCAA
* * * *
92785 AAAACCTTCGGGAGCTTTTTGATATTAAAGCCTCAGGGTCATCTGTAAGATCTACAGTGCATGAT
1 AAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTCAGGGTCATCTATAAGACCTACAGTGCATGAT
92850 GTTTTCAA
66 GTTTTCAA
* *
92858 AAAGCCTTCGGGAGCTTTTTGATCTTAAAACCTCAGGGTCAACTATAAGACCTACAGTGCATGAT
1 AAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTCAGGGTCATCTATAAGACCTACAGTGCATGAT
92923 GTTTTCAA
66 GTTTTCAA
* ** * *
92931 AAAACCTTCAAGAGCTTTTTGATATTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGAT
1 AAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTCAGGGTCATCTATAAGACCTACAGTGCATGAT
92996 GTTTTCAA
66 GTTTTCAA
* * * * * * *
93004 AAAGCCTTCGGGAGCTTTTTGATTTTAAAACCTTAGGG-CAATCCATAAGACCTCCAGTGTAGGA
1 AAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTCAGGGTC-ATCTATAAGACCTACAGTGCATGA
93068 TGTTTTCAA
65 TGTTTTCAA
93077 A
1 A
93078 TGAGATTTTA
Statistics
Matches: 331, Mismatches: 34, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
72 1 0.00
73 330 1.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (73 bp):
AAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTCAGGGTCATCTATAAGACCTACAGTGCATGAT
GTTTTCAA
Found at i:93478 original size:3 final size:3
Alignment explanation
Indices: 93470--93517 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
93460 ATTTTTAAAC
* *
93470 TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
93518 AATAATAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:94771 original size:25 final size:25
Alignment explanation
Indices: 94743--94792 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
94733 AAAAGCATGT
*
94743 TTTTATTTATTTTTTGGCATTTATA
1 TTTTATTTATTTTTAGGCATTTATA
* *
94768 TTTTATTTCTTTTTAGTCATTTATA
1 TTTTATTTATTTTTAGGCATTTATA
94793 CATGTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.20, C:0.06, G:0.06, T:0.68
Consensus pattern (25 bp):
TTTTATTTATTTTTAGGCATTTATA
Found at i:95528 original size:2 final size:2
Alignment explanation
Indices: 95521--95550 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
95511 TATAAAACCC
95521 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
95551 TTTTTCTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:98503 original size:42 final size:42
Alignment explanation
Indices: 98457--98542 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
98447 GAAGTGGAAG
98457 TCCTCCATGAAAGGAGTAGCCACTAATAATCCGAAGTGAGAT
1 TCCTCCATGAAAGGAGTAGCCACTAATAATCCGAAGTGAGAT
98499 TCCTCCATGAAAGGAGTAGCCACTAATAATCCGAAGTGAGAT
1 TCCTCCATGAAAGGAGTAGCCACTAATAATCCGAAGTGAGAT
98541 TC
1 TC
98543 ATCCCGAAGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (42 bp):
TCCTCCATGAAAGGAGTAGCCACTAATAATCCGAAGTGAGAT
Found at i:98577 original size:41 final size:42
Alignment explanation
Indices: 98518--98642 Score: 139
Period size: 41 Copynumber: 3.0 Consensus size: 42
98508 AAAGGAGTAG
* * *
98518 CCACTAATAATCCGAAGTGAGATTCATCC-CGAAGGGT-AAAT
1 CCACTGATAATCCAAAGTGAAATTCA-CCTCGAAGGGTGAAAT
98559 CCACTGATAATCCAAAGTGAAATTCACCTCGAAGGGTGAAAT
1 CCACTGATAATCCAAAGTGAAATTCACCTCGAAGGGTGAAAT
*** * * *
98601 -CACTGATAATATGAAGTGAAATTCATCTCCAAGAGTGAAAT
1 CCACTGATAATCCAAAGTGAAATTCACCTCGAAGGGTGAAAT
98642 C
1 C
98643 ATTGAACTTC
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
40 2 0.03
41 66 0.92
42 4 0.06
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.23
Consensus pattern (42 bp):
CCACTGATAATCCAAAGTGAAATTCACCTCGAAGGGTGAAAT
Found at i:101685 original size:28 final size:28
Alignment explanation
Indices: 101639--101707 Score: 102
Period size: 28 Copynumber: 2.4 Consensus size: 28
101629 TTCAAATTCA
*
101639 AGAAATTAAAAGTTAGTAGTTAGTAGTT
1 AGAAGTTAAAAGTTAGTAGTTAGTAGTT
* *
101667 AGTAGTTAAAAGTTTGTAGTTAGTAGTT
1 AGAAGTTAAAAGTTAGTAGTTAGTAGTT
101695 AGAAGTTAGAAAG
1 AGAAGTTA-AAAG
101708 CCAATAGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 32 0.89
29 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.25, T:0.35
Consensus pattern (28 bp):
AGAAGTTAAAAGTTAGTAGTTAGTAGTT
Found at i:101705 original size:7 final size:7
Alignment explanation
Indices: 101649--101703 Score: 74
Period size: 7 Copynumber: 7.9 Consensus size: 7
101639 AGAAATTAAA
101649 AGTTAGT
1 AGTTAGT
101656 AGTTAGT
1 AGTTAGT
101663 AGTTAGT
1 AGTTAGT
**
101670 AGTTAAA
1 AGTTAGT
*
101677 AGTTTGT
1 AGTTAGT
101684 AGTTAGT
1 AGTTAGT
*
101691 AGTTAGA
1 AGTTAGT
101698 AGTTAG
1 AGTTAG
101704 AAAGCCAATA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.40
Consensus pattern (7 bp):
AGTTAGT
Found at i:103444 original size:110 final size:112
Alignment explanation
Indices: 103260--103508 Score: 317
Period size: 111 Copynumber: 2.2 Consensus size: 112
103250 GTTAAGCTAG
* * * * *
103260 TTCTTCTCATTATGTACTTATTCTCACATCAGATAAGTTCTTCTCATTATAAACTCTCAATTGGA
1 TTCTTCTCATTATGAACTTCTTCT-TCATCAGATAAGTTCTTCTCATTATAAACTCTCAACTGAA
* **
103325 AATGTTGAT-CACCTCTTTCTGTGATGGATGAGCCAAGGTTGAACAAA
65 AATGTTGATCCACCTCCTTCTGTGATGGATGAGCCAAAATTGAACAAA
* * *
103372 TTCTTCTCATTATGAACTCCTTCTTCAT-ATATAAGTTCTTCTCATTATGAAA-TCTCCACTGAA
1 TTCTTCTCATTATGAACTTCTTCTTCATCAGATAAGTTCTTCTCATTAT-AAACTCTCAACTGAA
** *
103435 AAT-TCTGATCCATTTCCTTCTGTGATGGATGAGCCAAAATTGAACAAG
65 AATGT-TGATCCACCTCCTTCTGTGATGGATGAGCCAAAATTGAACAAA
103483 TTCTTCTCATTATGAACTTCTTCTTC
1 TTCTTCTCATTATGAACTTCTTCTTC
103509 CTTATCGGAT
Statistics
Matches: 119, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
109 1 0.01
110 34 0.29
111 63 0.53
112 21 0.18
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.39
Consensus pattern (112 bp):
TTCTTCTCATTATGAACTTCTTCTTCATCAGATAAGTTCTTCTCATTATAAACTCTCAACTGAAA
ATGTTGATCCACCTCCTTCTGTGATGGATGAGCCAAAATTGAACAAA
Done.