Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold351
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: 325634
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 2 of 3
Found at i:160737 original size:13 final size:13
Alignment explanation
Indices: 160702--160737 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
160692 CTATATGTTG
*
160702 TTTTTCTTTTCTT
1 TTTTTTTTTTCTT
*
160715 TTCTTTTTTTCTT
1 TTTTTTTTTTCTT
160728 TTTTTTTTTT
1 TTTTTTTTTT
160738 TTCTATGTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTTCTT
Found at i:165075 original size:2 final size:2
Alignment explanation
Indices: 165068--165110 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
165058 TGAAACTGGA
165068 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
165110 A
1 A
165111 AAGTTTAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:167299 original size:2 final size:2
Alignment explanation
Indices: 167292--167326 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
167282 TATGTGTCAA
167292 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
167327 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:167331 original size:2 final size:2
Alignment explanation
Indices: 167326--167356 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
167316 ATATATATAT
167326 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
167357 ACAAATAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:168654 original size:3 final size:3
Alignment explanation
Indices: 168643--168691 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
168633 TTTTTTCCTT
*
168643 TTC TT- TTC TTC -TC TTC TCC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
168689 TTC
1 TTC
168692 CTCCCCTGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:168754 original size:3 final size:3
Alignment explanation
Indices: 168741--168777 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
168731 CGCAGAGCAA
168741 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
168778 CTGCAAAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:169088 original size:21 final size:20
Alignment explanation
Indices: 169039--169109 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 20
169029 ATTTTTAATA
169039 TATTTTTTAATTTAAA-AAAT
1 TATTTTTT-ATTTAAATAAAT
* * *
169059 AACTATTTATTTAAAATAAAT
1 TATTTTTTATTT-AAATAAAT
*
169080 TATTTTTTATTTTTAACT-AAT
1 TATTTTTTA--TTTAAATAAAT
169101 TATTTTTTA
1 TATTTTTTA
169110 ATAAATTATT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
19 4 0.10
20 8 0.20
21 22 0.55
22 3 0.08
23 3 0.08
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTTTTTATTTAAATAAAT
Found at i:169109 original size:15 final size:15
Alignment explanation
Indices: 169089--169123 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
169079 TTATTTTTTA
169089 TTTTTAACT-AATTAT
1 TTTTTAA-TAAATTAT
169104 TTTTTAATAAATTAT
1 TTTTTAATAAATTAT
169119 TTTTT
1 TTTTT
169124 TACTCACGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 1 0.05
15 18 0.95
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTAATAAATTAT
Found at i:169768 original size:30 final size:30
Alignment explanation
Indices: 169700--169775 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
169690 ATATATTTTT
*
169700 ATTATATCCAAAAAAATCTTTAATCTTTAA
1 ATTATATCTAAAAAAATCTTTAATCTTTAA
* * *
169730 TTTGTATCTAAATAAA-CTCTTAA-CATTTAA
1 ATTATATCTAAAAAAATCT-TTAATC-TTTAA
169760 ATTATATCTAAAAAAA
1 ATTATATCTAAAAAAA
169776 AGCTGCTAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 3 0.08
30 34 0.92
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.39
Consensus pattern (30 bp):
ATTATATCTAAAAAAATCTTTAATCTTTAA
Found at i:170690 original size:19 final size:19
Alignment explanation
Indices: 170650--170690 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
170640 ATGTTATATG
* * *
170650 TTTTATTTTTTAATTAATT
1 TTTTATTATTTAAATAAAT
170669 TTTTATTATTTAAATAAAT
1 TTTTATTATTTAAATAAAT
170688 TTT
1 TTT
170691 AAGAGAGTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTATTATTTAAATAAAT
Found at i:170690 original size:20 final size:19
Alignment explanation
Indices: 170650--170690 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
170640 ATGTTATATG
* *
170650 TTTTATTTTTTAATTAATT
1 TTTTATTTTTAAATAAATT
170669 TTTTATTATTTAAATAAATT
1 TTTTATT-TTTAAATAAATT
170689 TT
1 TT
170691 AAGAGAGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTATTTTTAAATAAATT
Found at i:171039 original size:20 final size:20
Alignment explanation
Indices: 171013--171057 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
171003 AGCAAAATAA
*
171013 TATATTTCAATA-ATTATAT
1 TATATTTAAATATATTATAT
171032 TCATATTTAAATATATTATAT
1 T-ATATTTAAATATATTATAT
171053 TATAT
1 TATAT
171058 AAATATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 14 0.61
21 8 0.35
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (20 bp):
TATATTTAAATATATTATAT
Found at i:171062 original size:18 final size:20
Alignment explanation
Indices: 171021--171064 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 20
171011 AATATATTTC
171021 AATA-ATTATATTCATATTTA
1 AATATATTATATTCATA-TTA
171041 AATATATTATATT-ATA-TA
1 AATATATTATATTCATATTA
171059 AATATA
1 AATATA
171065 AATATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.35
20 7 0.30
21 8 0.35
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
AATATATTATATTCATATTA
Found at i:171172 original size:18 final size:18
Alignment explanation
Indices: 171122--171161 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
171112 TTAATTTTTA
171122 ATTTATCATTA-TAA-AA-
1 ATTTAT-ATTATTAATAAT
171138 ATTTATATTATTAATAAT
1 ATTTATATTATTAATAAT
171156 ATTTAT
1 ATTTAT
171162 TTAGTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 4 0.19
16 9 0.43
17 2 0.10
18 6 0.29
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTATATTATTAATAAT
Found at i:173499 original size:20 final size:20
Alignment explanation
Indices: 173453--173500 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
173443 AAAAATCAAA
*
173453 ATTTTATT-ATAAAATTTAT
1 ATTTTATTAATAAAATATAT
*
173472 -TCTTTATTAATATAATATAT
1 AT-TTTATTAATAAAATATAT
173492 ATTTTATTA
1 ATTTTATTA
173501 GTATTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 1 0.04
19 6 0.25
20 16 0.67
21 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTTATTAATAAAATATAT
Found at i:174054 original size:19 final size:17
Alignment explanation
Indices: 174012--174072 Score: 52
Period size: 19 Copynumber: 3.4 Consensus size: 17
174002 ATTAAATTAT
*
174012 ATTAAATAATTATTATTTA
1 ATTAAAT-ATT-TTATGTA
* *
174031 CTTAAATATTTTTGTGTA
1 ATTAAATA-TTTTATGTA
174049 ATTTAAA-ATTTTATGTA
1 A-TTAAATATTTTATGTA
174066 ATTAAAT
1 ATTAAAT
174073 TTGAAATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 5 0.15
17 9 0.26
18 7 0.21
19 13 0.38
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (17 bp):
ATTAAATATTTTATGTA
Found at i:174830 original size:38 final size:37
Alignment explanation
Indices: 174753--174830 Score: 93
Period size: 38 Copynumber: 2.1 Consensus size: 37
174743 TTATGCAAAA
* * *
174753 AAATAAAATAAATTAAAATACAATATGAACACAACAT
1 AAATAAAAAAAATTAAAATACAATATAAAAACAACAT
* * *
174790 AAATAAAAAATAATTAAAATATAATATAAAAATAATAT
1 AAATAAAAAA-AATTAAAATACAATATAAAAACAACAT
174828 AAA
1 AAA
174831 CATGATACTA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
37 9 0.26
38 25 0.74
ACGTcount: A:0.69, C:0.05, G:0.01, T:0.24
Consensus pattern (37 bp):
AAATAAAAAAAATTAAAATACAATATAAAAACAACAT
Found at i:175101 original size:14 final size:14
Alignment explanation
Indices: 175082--175137 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
175072 ACATGTAAAT
175082 TTTTTATTTTTTTA
1 TTTTTATTTTTTTA
*
175096 TTTTTATTTTTTTC
1 TTTTTATTTTTTTA
* *
175110 TTTTTCTCTTTCTTTT
1 TTTTTAT-TTT-TTTA
*
175126 TTTTTCTTTTTT
1 TTTTTATTTTTT
175138 CATTCTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 21 0.57
15 6 0.16
16 10 0.27
ACGTcount: A:0.05, C:0.09, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTATTTTTTTA
Found at i:175125 original size:17 final size:15
Alignment explanation
Indices: 175088--175151 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 15
175078 AAATTTTTTA
* *
175088 TTTTTTTATTTTT-A
1 TTTTTTTCTTTTTCT
175102 TTTTTTTCTTTTTCT
1 TTTTTTTCTTTTTCT
175117 CTTTCTTTT-TTTTTCT
1 -TTT-TTTTCTTTTTCT
175133 TTTTTCATTCTTTTTCT
1 TTTTT--TTCTTTTTCT
175150 TT
1 TT
175152 CTCTCATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
14 14 0.33
15 3 0.07
16 12 0.29
17 13 0.31
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTTCTTTTTCT
Found at i:175143 original size:21 final size:21
Alignment explanation
Indices: 175081--175153 Score: 83
Period size: 22 Copynumber: 3.4 Consensus size: 21
175071 AACATGTAAA
* * *
175081 TTTTTTATTTTTTTATTTTTAT
1 TTTTTTCTTTTTTCATTCTT-T
*
175103 TTTTTTCTTTTTCTCTTTCTTT
1 TTTTTTCTTTTT-TCATTCTTT
175125 TTTTTTCTTTTTTCATTCTTT
1 TTTTTTCTTTTTTCATTCTTT
*
175146 TTCTTTCT
1 TTTTTTCT
175154 CTCATAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
21 15 0.34
22 24 0.55
23 5 0.11
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTTTCTTTTTTCATTCTTT
Found at i:175530 original size:12 final size:12
Alignment explanation
Indices: 175513--175556 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
175503 AAACATAATA
175513 AATTTATATTAT
1 AATTTATATTAT
175525 AATTTATATTAT
1 AATTTATATTAT
*
175537 -ATTCT-TATCAT
1 AATT-TATATTAT
175548 AATTTATAT
1 AATTTATAT
175557 AAATAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (12 bp):
AATTTATATTAT
Found at i:175646 original size:21 final size:20
Alignment explanation
Indices: 175591--175662 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
175581 ATAAAAGTAT
*
175591 ATAATAATA-AATTTATATT
1 ATAATAATATAATTTATATA
* * *
175610 ATCATTCATAATAATTTATGTA
1 AT-AATAAT-ATAATTTATATA
175632 ATAAATAATATAATTTATATA
1 AT-AATAATATAATTTATATA
*
175653 ATTATAATAT
1 ATAATAATAT
175663 TTATTAATAA
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
19 2 0.05
20 11 0.27
21 14 0.34
22 14 0.34
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (20 bp):
ATAATAATATAATTTATATA
Found at i:175665 original size:38 final size:38
Alignment explanation
Indices: 175555--175672 Score: 104
Period size: 35 Copynumber: 3.1 Consensus size: 38
175545 CATAATTTAT
* * * *
175555 ATAAATAA-ATAATATATAAAATTATAATA--AAAGT-
1 ATAAATAATATAATTTATATAATTATAATATTTATGTA
175589 ATATAATAATA-AATTTATATTATCATTCATAATAATTTATGTA
1 ATA-AATAATATAATTTATA-TA--ATT-ATAAT-ATTTATGTA
175632 ATAAATAATATAATTTATATAATTATAATATTTAT-TA
1 ATAAATAATATAATTTATATAATTATAATATTTATGTA
175669 ATAA
1 ATAA
175673 TTTTATTTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 19
0.75 0.04 0.21
Matches are distributed among these distances:
34 3 0.04
35 12 0.17
36 2 0.03
37 6 0.09
38 9 0.13
39 10 0.14
40 4 0.06
42 12 0.17
43 11 0.16
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (38 bp):
ATAAATAATATAATTTATATAATTATAATATTTATGTA
Found at i:179713 original size:16 final size:16
Alignment explanation
Indices: 179694--179725 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
179684 AATTATCTTT
179694 AATTATTATTAAATTA
1 AATTATTATTAAATTA
179710 AATTATTATTAAATTA
1 AATTATTATTAAATTA
179726 TATGCTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTATTATTAAATTA
Found at i:180777 original size:22 final size:22
Alignment explanation
Indices: 180743--180801 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
180733 TCTGAAACTC
* *
180743 AAATTATTGTTTAAAAATTATT
1 AAATTAATATTTAAAAATTATT
* * *
180765 AAATTAATATTTATATATTTTT
1 AAATTAATATTTAAAAATTATT
180787 ATAATTAA-ATTTAAA
1 A-AATTAATATTTAAA
180802 TAAAAATATT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 24 0.80
23 6 0.20
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
AAATTAATATTTAAAAATTATT
Found at i:184458 original size:34 final size:34
Alignment explanation
Indices: 184415--184481 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
184405 CTCGTCGCAA
184415 GTCAACTCCGATGAATCTGCTAATCCAGAGCTTT
1 GTCAACTCCGATGAATCTGCTAATCCAGAGCTTT
184449 GTCAACTCCGATGAATCTGCTAATCCAGAGCTT
1 GTCAACTCCGATGAATCTGCTAATCCAGAGCTT
184482 ACAGCTAACG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (34 bp):
GTCAACTCCGATGAATCTGCTAATCCAGAGCTTT
Found at i:191356 original size:23 final size:23
Alignment explanation
Indices: 191321--191368 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
191311 AAAATTTTAA
*
191321 TTTTTTAATAATTTAATAATAAT
1 TTTTTTAATAATTTAAAAATAAT
191344 TTTTATTAA-AATTTAAAAATAAT
1 TTTT-TTAATAATTTAAAAATAAT
191367 TT
1 TT
191369 AACATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTTTTAATAATTTAAAAATAAT
Found at i:192373 original size:15 final size:15
Alignment explanation
Indices: 192350--192393 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
192340 ATAAGTTAGG
*
192350 AAAATTTATTTTTAA
1 AAAAATTATTTTTAA
*
192365 AAAAATTATATTTAA
1 AAAAATTATTTTTAA
*
192380 ATTAAATTATTTTT
1 A-AAAATTATTTTT
192394 TTAATTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AAAAATTATTTTTAA
Found at i:192817 original size:13 final size:13
Alignment explanation
Indices: 192799--192823 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
192789 CTTACTTACA
192799 TTATTTTTTTAAT
1 TTATTTTTTTAAT
192812 TTATTTTTTTAA
1 TTATTTTTTTAA
192824 AAATTTAATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTTTTTAAT
Found at i:193947 original size:35 final size:37
Alignment explanation
Indices: 193865--193957 Score: 86
Period size: 37 Copynumber: 2.6 Consensus size: 37
193855 GTAGATTCGA
* * *
193865 TAAT-TTATATATATTTTTATATATTATAGTTATATT
1 TAATATTATATATATTTATATAAATTATAGATATATT
* *
193901 TAAAATAATATATATTTATATAAATTATTA-AT-TA-T
1 TAATATTATATATATTTATATAAATTA-TAGATATATT
*
193936 TAATATTATATAAATTATATAT
1 TAATATTATATATATT-TATAT
193958 TTTTATATCT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
35 14 0.30
36 10 0.22
37 20 0.43
38 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (37 bp):
TAATATTATATATATTTATATAAATTATAGATATATT
Found at i:199247 original size:21 final size:21
Alignment explanation
Indices: 199222--199297 Score: 77
Period size: 20 Copynumber: 3.6 Consensus size: 21
199212 ATTTTATTGA
199222 ATTTATAAAATAAATTTAAAT
1 ATTTATAAAATAAATTTAAAT
* *
199243 ATTTAT-AAATATATTAAAAT
1 ATTTATAAAATAAATTTAAAT
*
199263 -TTTTTAAAAATAAA-TTAAAT
1 ATTTAT-AAAATAAATTTAAAT
199283 ATTATATATAAATAA
1 ATT-TATA-AAATAA
199298 TATCTAATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
19 4 0.09
20 17 0.39
21 15 0.34
22 8 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTTATAAAATAAATTTAAAT
Found at i:199270 original size:19 final size:20
Alignment explanation
Indices: 199222--199295 Score: 71
Period size: 21 Copynumber: 3.7 Consensus size: 20
199212 ATTTTATTGA
*
199222 ATTTATAAAATAAATTTAAAT
1 ATTTAT-AAATAAATTAAAAT
*
199243 ATTTATAAATATATTAAAATT
1 ATTTATAAATAAATTAAAA-T
* *
199264 TTTTAAAAATAAATT-AAAT
1 ATTTATAAATAAATTAAAAT
*
199283 A-TTATATATAAAT
1 ATTTATAAATAAAT
199296 AATATCTAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
18 10 0.23
19 1 0.02
20 14 0.32
21 19 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTATAAATAAATTAAAAT
Found at i:199542 original size:35 final size:35
Alignment explanation
Indices: 199494--199564 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
199484 GAAGTCATGA
*
199494 ATTAATCCGTACCCTTTAAGAAAAACTAAGGAACT
1 ATTAATCCATACCCTTTAAGAAAAACTAAGGAACT
*
199529 ATTAATCCATACCCTTTTAGAAAAACTAAGGAACT
1 ATTAATCCATACCCTTTAAGAAAAACTAAGGAACT
199564 A
1 A
199565 AGAATGGGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.27
Consensus pattern (35 bp):
ATTAATCCATACCCTTTAAGAAAAACTAAGGAACT
Found at i:199659 original size:21 final size:23
Alignment explanation
Indices: 199614--199661 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
199604 ATAAATAAAT
199614 TAAA-CAATATGTTTATTAATAA
1 TAAATCAATATGTTTATTAATAA
*
199636 TAAATCAATAT-TTT-TTAATTA
1 TAAATCAATATGTTTATTAATAA
199657 TAAAT
1 TAAAT
199662 ATTTTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 11 0.46
22 7 0.29
23 6 0.25
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (23 bp):
TAAATCAATATGTTTATTAATAA
Found at i:201575 original size:17 final size:17
Alignment explanation
Indices: 201553--201585 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
201543 CGTCGAAAAA
201553 ATTAAATTAATT-AATTG
1 ATTAAA-TAATTCAATTG
201570 ATTAAATAATTCAATT
1 ATTAAATAATTCAATT
201586 AAAAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (17 bp):
ATTAAATAATTCAATTG
Found at i:202086 original size:28 final size:29
Alignment explanation
Indices: 202027--202087 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 29
202017 TCGCAATGTA
*
202027 AAATAAAAATATATTTTATAATTAAATTT
1 AAATAAAAATATATTTAATAATTAAATTT
*
202056 AAATAAAAA-AT-TTTAATTATTAAATATT
1 AAATAAAAATATATTTAATAATTAAAT-TT
202084 AAAT
1 AAAT
202088 TAAATTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 12 0.41
28 8 0.28
29 9 0.31
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
AAATAAAAATATATTTAATAATTAAATTT
Found at i:204219 original size:402 final size:401
Alignment explanation
Indices: 203442--204237 Score: 1200
Period size: 402 Copynumber: 2.0 Consensus size: 401
203432 TACTGTCGTA
* * *
203442 ACGTGCGCTCGATCCCGGCAATAGGGCGAATGAGGTGCGCTCGACTTAATATCCCTCGCGATTGG
1 ACGTGCGCTCGACCCCGGCAATAGGGCGAATGAGGTACGCCCGACTTAATATCCCTCGCGATTGG
* * * *
203507 GGATTTCTATGGCATGATGAGAAGTATGCTGATAAAAGGGGGAATATCGGTAGATGAATCGCCCA
66 GGATTTCCATGGCATGATGAGAAATATGCTGATAAAAGGGGGAAGATCGATAGATGAATCGCCCA
* * * *
203572 TCTAATTGATCTTCAATGGTCACTACGAGGTGACCGAAATTTTAGAGTCGCCACCGATCATTTCG
131 TCTAATCGATCTTCAACGGTCACTACGAAGTGACCGAAAATTTAGAGTCGCCACCGATCATTTCG
*
203637 AGCTAGGCACGATCGGATGCCTATTGAAACCTATGTCTTGAGTTACGAAACTCAAAACATCGATC
196 AGCTAGGCACGATCGGATGCCTATTGAAACCTATGTCTTGAGTTACAAAACTCAAAACATCGATC
* * * * *
203702 CCGTGATCTACGCAATTTAGAGATTCGTCGGTTGGATTCGGGAGTTGGTTACGCACAAAGAGATA
261 CCGTGATCTACGCAATTCAAAGATTCATCGATTGGATCCGGGAGTTGGTTACGCACAAAGAGATA
* **
203767 CGAACCTCCTCGTGACGCCCGAAATCGGTACCTTACTAGCAATGTTTTGACTCGATATTGGTTAC
326 CGAACCTCCTCGCGACGCCCGAAATCGGTACCTTACTAGCAACATTTTGACTCGATATTGGTTAC
203832 ATTGTGTCGCG
391 ATTGTGTCGCG
* *
203843 ACGTGCGCTCGGACCCCGGCGATAGGGAC-AGATGAGGTATGCCCGACTTAATATCCCTCGCGAT
1 ACGTGCGCTC-GACCCCGGCAATAGGG-CGA-ATGAGGTACGCCCGACTTAATATCCCTCGCGAT
* *
203907 TGGGGATTTCCATGGCATGATGAGAAATATGTTGATTAAAGGGGGAAGATCGATAGATGAATCGC
63 TGGGGATTTCCATGGCATGATGAGAAATATGCTGATAAAAGGGGGAAGATCGATAGATGAATCGC
*
203972 CCATCTAATCGATCTTC-ACGGTCACTACGAAGTGACCGAAAATTTGGAGTCGCCACCGATCATT
128 CCATCTAATCGATCTTCAACGGTCACTACGAAGTGACCGAAAATTTAGAGTCGCCACCGATCATT
* * * *
204036 TCGGGCTAGGCATGATCGGATGCCTATTGAAACCTATGTCTTGAGTTACAAAACTCGAGACATCG
193 TCGAGCTAGGCACGATCGGATGCCTATTGAAACCTATGTCTTGAGTTACAAAACTCAAAACATCG
* * * * * *
204101 ATCTCGTGGTCTACGTAATTCAAAGATTCATCGATTGGGTCCGGGAGTTGGTTACGCGCAAAGGG
258 ATCCCGTGATCTACGCAATTCAAAGATTCATCGATTGGATCCGGGAGTTGGTTACGCACAAAGAG
* * *
204166 GTACGAACCTCCTCGCGACGCCCGAAATCGGTACCTTACTAGCTACATTTTGACTTGATATTGGT
323 ATACGAACCTCCTCGCGACGCCCGAAATCGGTACCTTACTAGCAACATTTTGACTCGATATTGGT
*
204231 TTCATTG
388 TACATTG
204238 GTTTTGACTC
Statistics
Matches: 353, Mismatches: 39, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
401 10 0.03
402 237 0.67
403 106 0.30
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (401 bp):
ACGTGCGCTCGACCCCGGCAATAGGGCGAATGAGGTACGCCCGACTTAATATCCCTCGCGATTGG
GGATTTCCATGGCATGATGAGAAATATGCTGATAAAAGGGGGAAGATCGATAGATGAATCGCCCA
TCTAATCGATCTTCAACGGTCACTACGAAGTGACCGAAAATTTAGAGTCGCCACCGATCATTTCG
AGCTAGGCACGATCGGATGCCTATTGAAACCTATGTCTTGAGTTACAAAACTCAAAACATCGATC
CCGTGATCTACGCAATTCAAAGATTCATCGATTGGATCCGGGAGTTGGTTACGCACAAAGAGATA
CGAACCTCCTCGCGACGCCCGAAATCGGTACCTTACTAGCAACATTTTGACTCGATATTGGTTAC
ATTGTGTCGCG
Found at i:207097 original size:20 final size:20
Alignment explanation
Indices: 207068--207142 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
207058 AAAAAGACAT
*
207068 AATGTATCGATACATTGTAG
1 AATGTATCGATACATTGTAA
*
207088 AATATATCGATACATT-TATA
1 AATGTATCGATACATTGTA-A
* * *
207108 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGTAA
207128 AATGTATCGATACAT
1 AATGTATCGATACAT
207143 CAAGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.04
20 42 0.93
21 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTGTAA
Found at i:210311 original size:49 final size:49
Alignment explanation
Indices: 210150--211104 Score: 518
Period size: 39 Copynumber: 20.8 Consensus size: 49
210140 CGTAAAATGA
* * * * *
210150 CAATGTGCTGATTCATGGCCAACGACATTAGACTTGAAGAAGAA--TGC
1 CAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGC
** * * * * * *
210197 CAATGTGCTGAGACAAGGCTAGCGATATTGGGCTTAGGAATGTTAAAGATGC
1 CAATGTGCTGATTCAAGGCCAACGATATTGGACTTA--AA-GATGAAGGTGC
* * *
210249 CAATATGCTGATTCAAGGCCAACGATATCGAACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGC
* *
210298 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGATG---AAGGTGC
* * *
210350 CAATATGCTGATTCAAGGCCAGA-GATATTTGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCA-ACGATATTGGACTTAAAGATGAAGGTGC
* * *
210399 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGCAAATGTGC
1 CAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGAT-G--AAGGTGC
*
210451 CAATATGCTGATTCAAGGCCAACGATATTGGAC-T-----T----GTGC
1 CAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGC
* * * * *
210490 TAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGC
1 CAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGC
* * * *
210538 CAATATGCTGATTCACGGCCAGCGATATTGGGC-T-----T--A--TGC
1 CAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGC
* * * * * *
210577 CAATGTGCTGATTCAAAGCCAGCGACATTGGTCTTAAAGA-CAAGGCGC
1 CAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGC
* * *
210625 CAATATGCTGATTCAAGGCCAGCGATATTGGGC-T-----T--A--TGC
1 CAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGC
* * *
210664 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAACGATATTGGAC-TTAAAGATGAAGGTGC
* *
210714 CAATATGCTGATTCAAGGCCAACGATATTGGGC-T-----T----GTGC
1 CAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGC
* * * * * *
210753 CAATATGCTAATTCAAGGCCAGCGACATTGGTCTTAAATATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGC
*
210802 CAATATGCTGATTCAAGGCCAACGATATTAGG-C-T-----T----GTGC
1 CAATGTGCTGATTCAAGGCCAACGATATT-GGACTTAAAGATGAAGGTGC
* * * *
210841 CAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAGAGA-CAAGGTGC
1 CAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGC
* ** *
210889 CAATATGCTGATTCAAGGCCAGTGATATTGGGC-T-----T----GTGC
1 CAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGC
* * * * * *
210928 CAATGTGCTGATTCAAGACTAGCGACATTGGTCTTAAAGA-CAAGGTGC
1 CAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGC
* * * *
210976 CAATATGCTGATTCAAGGCTAGCGATATTGGTC-T-----T--A--TGC
1 CAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGC
* * * *
211015 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGC
* * * *
211064 CGATATGCTGATTTAAGGCCAGCGATATTGGACTTAGAAGA
1 CAATGTGCTGATTCAAGGCCAACGATATTGGACTTA-AAGA
211105 AGACGCCACC
Statistics
Matches: 716, Mismatches: 101, Indels: 179
0.72 0.10 0.18
Matches are distributed among these distances:
38 2 0.00
39 224 0.31
40 6 0.01
41 4 0.01
43 2 0.00
45 2 0.00
46 3 0.00
47 32 0.04
48 132 0.18
49 155 0.22
50 43 0.06
51 1 0.00
52 110 0.15
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGC
Found at i:210328 original size:101 final size:90
Alignment explanation
Indices: 210294--211100 Score: 999
Period size: 87 Copynumber: 9.0 Consensus size: 90
210284 AAAGATGAAG
* *
210294 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AA-ATGATAAAGGTGCCAATATGCT
*
210359 GATTCAAGGCCAGA-GATATTTGACTTAAAGATAAA
64 GATTCAAGGCCA-ACGATATTGGAC-T-----T--A
* *
210394 GGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAA-GATGGCAAATGTGCCAATATG
1 -GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAATGAT---AAAGGTGCCAATATG
210458 CTGATTCAAGGCCAACGATATTGGACTT-
62 CTGATTCAAGGCCAACGATATTGGACTTA
* *
210486 GTGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAA-GA-CAAGGTGCCAATATGCTGA
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAATGATAAAGGTGCCAATATGCTGA
* * *
210549 TTCACGGCCAGCGATATTGGGCTTA
66 TTCAAGGCCAACGATATTGGACTTA
* * *
210574 -TGCCAATGTGCTGATTCAAAGCCAGCGACATTGGTCTTAAA-GA-CAAGGCGCCAATATGCTGA
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAATGATAAAGGTGCCAATATGCTGA
* *
210636 TTCAAGGCCAGCGATATTGGGCTTA
66 TTCAAGGCCAACGATATTGGACTTA
*
210661 -TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTTAAA-GATGAAGGTGCCAATATGCTG
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTC-TTAAATGATAAAGGTGCCAATATGCTG
*
210724 ATTCAAGGCCAACGATATTGGGCTT-
65 ATTCAAGGCCAACGATATTGGACTTA
* * *
210749 GTGCCAATATGCTAATTCAAGGCCAGCGACATTGGTCTTAAAT-ATGAAGGTGCCAATATGCTGA
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAATGATAAAGGTGCCAATATGCTGA
210813 TTCAAGGCCAACGATATTAGG-CTT-
66 TTCAAGGCCAACGATATT-GGACTTA
* * *
210837 GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAGA-GA-CAAGGTGCCAATATGCTGA
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAATGATAAAGGTGCCAATATGCTGA
** *
210900 TTCAAGGCCAGTGATATTGGGCTT-
66 TTCAAGGCCAACGATATTGGACTTA
* * *
210924 GTGCCAATGTGCTGATTCAAGACTAGCGACATTGGTCTTAAA-GA-CAAGGTGCCAATATGCTGA
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAATGATAAAGGTGCCAATATGCTGA
* * *
210987 TTCAAGGCTAGCGATATTGGTCTTA
66 TTCAAGGCCAACGATATTGGACTTA
*
211012 -TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAA-GATAAAGGTGCCGATATGCTGA
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAATGATAAAGGTGCCAATATGCTGA
* *
211075 TTTAAGGCCAGCGATATTGGACTTA
66 TTCAAGGCCAACGATATTGGACTTA
211100 G
1 G
211101 AAGAAGACGC
Statistics
Matches: 650, Mismatches: 41, Indels: 42
0.89 0.06 0.06
Matches are distributed among these distances:
86 2 0.00
87 314 0.48
88 132 0.20
89 76 0.12
91 42 0.06
95 1 0.00
98 2 0.00
99 1 0.00
100 4 0.01
101 76 0.12
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (90 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAATGATAAAGGTGCCAATATGCTGA
TTCAAGGCCAACGATATTGGACTTA
Found at i:210582 original size:87 final size:88
Alignment explanation
Indices: 210396--211099 Score: 1065
Period size: 87 Copynumber: 8.0 Consensus size: 88
210386 AAGATAAAGG
* *
210396 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGCAAATGTGCCAATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAT--C-AAGGTGCCAATATGCTG
* * *
210461 ATTCAAGGCCAACGATATTGGACTTG
63 ATTCAAGGCCAGCGATATTGGGCTTA
*
210487 TGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATCAAGGTGCCAATATGCTGATT
*
210551 CACGGCCAGCGATATTGGGCTTA
66 CAAGGCCAGCGATATTGGGCTTA
* *
210574 TGCCAATGTGCTGATTCAAAGCCAGCGACATTGGTCTTAAAGA-CAAGGCGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATCAAGGTGCCAATATGCTGATT
210638 CAAGGCCAGCGATATTGGGCTTA
66 CAAGGCCAGCGATATTGGGCTTA
*
210661 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTTAAAGATGAAGGTGCCAATATGCTGAT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTC-TTAAAGATCAAGGTGCCAATATGCTGAT
* *
210726 TCAAGGCCAACGATATTGGGCTTG
65 TCAAGGCCAGCGATATTGGGCTTA
* * * *
210750 TGCCAATATGCTAATTCAAGGCCAGCGACATTGGTCTTAAATATGAAGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATCAAGGTGCCAATATGCTGATT
* * *
210815 CAAGGCCAACGATATTAGGCTTG
66 CAAGGCCAGCGATATTGGGCTTA
* *
210838 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAGAGA-CAAGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATCAAGGTGCCAATATGCTGATT
* *
210902 CAAGGCCAGTGATATTGGGCTTG
66 CAAGGCCAGCGATATTGGGCTTA
* *
210925 TGCCAATGTGCTGATTCAAGACTAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATCAAGGTGCCAATATGCTGATT
* *
210989 CAAGGCTAGCGATATTGGTCTTA
66 CAAGGCCAGCGATATTGGGCTTA
* *
211012 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCGATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATCAAGGTGCCAATATGCTGATT
* *
211077 TAAGGCCAGCGATATTGGACTTA
66 CAAGGCCAGCGATATTGGGCTTA
211100 GAAGAAGACG
Statistics
Matches: 566, Mismatches: 44, Indels: 9
0.91 0.07 0.01
Matches are distributed among these distances:
87 316 0.56
88 135 0.24
89 74 0.13
91 41 0.07
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (88 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATCAAGGTGCCAATATGCTGATT
CAAGGCCAGCGATATTGGGCTTA
Found at i:210869 original size:351 final size:355
Alignment explanation
Indices: 210295--211099 Score: 1221
Period size: 351 Copynumber: 2.2 Consensus size: 355
210285 AAGATGAAGG
*
210295 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATG---AAGGTGCCAATATGCTG
* * *
210360 ATTCAAGGCCAGA-GATATTTGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGA
63 ATTCAAGGCCA-ACGATATTGGACTT----AT--A-GTGCCAATATGCTAATTCAAGGCCAGCGA
*
210424 CATTGGACTTAAAGATGGCAAATGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTGTG
120 CATTGGACTTAAAGATGG-AAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTGTG
* * *
210489 CTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAC
184 CCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
210554 GGCCAGCGATATTGGGCTTATGCCAATGTGCTGATTCAA-AGCCAGCGACATTGGTCTTAAAGAC
249 GGCCAGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGA-CCAGCGACATTGGTCTTAAAGAC
210618 AAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTA
313 AAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTA
210661 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTTAAAGATGAAGGTGCCAATATGCTGAT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTC-TTAAAGATGAAGGTGCCAATATGCTGAT
* *
210726 TCAAGGCCAACGATATTGGGC-T-T-GTGCCAATATGCTAATTCAAGGCCAGCGACATTGGTCTT
65 TCAAGGCCAACGATATTGGACTTATAGTGCCAATATGCTAATTCAAGGCCAGCGACATTGGACTT
*
210788 AAATAT-G-AAGGTGCCAATATGCTGATTCAAGGCCAACGATATTAGG-CTTGTGCCAATGTGCT
130 AAAGATGGAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATT-GGACTTGTGCCAATGTGCT
* *
210850 GATTCAAGGCCAACGACATTGGTCTTAGAGACAAGGTGCCAATATGCTGATTCAAGGCCAGTGAT
194 GATTCAAGGCCAACGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGAT
* * *
210915 ATTGGGCTTGTGCCAATGTGCTGATTCAAGACTAGCGACATTGGTCTTAAAGACAAGGTGCCAAT
259 ATTGGGCTTATGCCAATGTGCTGATTCAAGACCAGCGACATTGGTCTTAAAGACAAGGCGCCAAT
* *
210980 ATGCTGATTCAAGGCTAGCGATATTGGTCTTA
324 ATGCTGATTCAAGGCCAGCGATATTGGGCTTA
* *
211012 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCGATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGATT
* *
211077 TAAGGCCAGCGATATTGGACTTA
66 CAAGGCCAACGATATTGGACTTA
211100 GAAGAAGACG
Statistics
Matches: 410, Mismatches: 23, Indels: 26
0.89 0.05 0.06
Matches are distributed among these distances:
350 44 0.11
351 238 0.58
352 3 0.01
353 1 0.00
354 41 0.10
358 1 0.00
363 2 0.00
364 36 0.09
366 35 0.09
367 9 0.02
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (355 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGATT
CAAGGCCAACGATATTGGACTTATAGTGCCAATATGCTAATTCAAGGCCAGCGACATTGGACTTA
AAGATGGAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTGTGCCAATGTGCTGA
TTCAAGGCCAACGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATAT
TGGGCTTATGCCAATGTGCTGATTCAAGACCAGCGACATTGGTCTTAAAGACAAGGCGCCAATAT
GCTGATTCAAGGCCAGCGATATTGGGCTTA
Found at i:211179 original size:28 final size:29
Alignment explanation
Indices: 211116--211216 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 29
211106 GACGCCACCA
**
211116 ACTTGTGTGGGCTTTTGAAAGGGTTG-CACCA
1 ACTTGTGT--GCTTTTGAAA-GGTTGCCACTG
211147 ACTTGTGTGCTTTTG-AAGGTTGCCACTG
1 ACTTGTGTGCTTTTGAAAGGTTGCCACTG
* * *
211175 ACTTGTGAGCTTTTGAAAAGGGTGCCATTG
1 ACTTGTGTGCTTTTG-AAAGGTTGCCACTG
*
211205 ACTTGTGGGCTT
1 ACTTGTGTGCTT
211217 AAAAGGAGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
27 5 0.08
28 19 0.31
29 7 0.11
30 22 0.36
31 8 0.13
ACGTcount: A:0.18, C:0.16, G:0.31, T:0.36
Consensus pattern (29 bp):
ACTTGTGTGCTTTTGAAAGGTTGCCACTG
Found at i:211244 original size:33 final size:32
Alignment explanation
Indices: 211207--211830 Score: 391
Period size: 27 Copynumber: 20.3 Consensus size: 32
211197 TGCCATTGAC
* *
211207 TTGTGGGCTTAAAAGGAGAAAGATGCCACAGAG
1 TTGTGGACTTAAAAGGAGAAAG-TGCCACGGAG
*
211240 TTGTGGACTTAAAA-G-G---GTGCCATGGAG
1 TTGTGGACTTAAAAGGAGAAAGTGCCACGGAG
*
211267 TTGTGGACTTAAAA--TG---GTGCCACGGAG
1 TTGTGGACTTAAAAGGAGAAAGTGCCACGGAG
* *
211294 TTGTGGACTTAAAAAGAGCAATGTGCCACGGAG
1 TTGTGGACTTAAAAGGAG-AAAGTGCCACGGAG
* * * *
211327 TTGTGGACTTAAAAAGAAAAAGATGCCATGAAG
1 TTGTGGACTTAAAAGGAGAAAG-TGCCACGGAG
* *
211360 TTGTGGACTTAAAAGGAACAAAATGCCACGGAG
1 TTGTGGACTTAAAAGG-AGAAAGTGCCACGGAG
211393 TTGTGGACTTAAAA-G-G---GTGCCACGGAG
1 TTGTGGACTTAAAAGGAGAAAGTGCCACGGAG
* *
211420 TTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAG
1 TTGTGGACTTAAAAGG-AGAA-AGTGCCACGGAG
* *
211454 TTGTGGGCTTAAAA--AG---GTGCCATGGAG
1 TTGTGGACTTAAAAGGAGAAAGTGCCACGGAG
***
211481 TTGTGGACTTAAAA-G-G---GTGCCATATAG
1 TTGTGGACTTAAAAGGAGAAAGTGCCACGGAG
* *
211508 TTGTGGACTTAAAAAGAAAAAGAGTGCCACGGAG
1 TTGTGGACTT-AAAAGGAGAA-AGTGCCACGGAG
* *
211542 TTGTGGGCTTAAAAGGAAAAAGATGCCACGGAG
1 TTGTGGACTTAAAAGGAGAAAG-TGCCACGGAG
* * *
211575 TTGTAGACTT-ACAGG-G---GTGCCACAGAG
1 TTGTGGACTTAAAAGGAGAAAGTGCCACGGAG
* * *
211602 TTGGGGGCTTAAAAGGAAAAAAAGTGCCACGGAG
1 TTGTGGACTTAAAAGG--AGAAAGTGCCACGGAG
*
211636 TTGTGGGCTTAAAA-G-G---GTGCCACGGAG
1 TTGTGGACTTAAAAGGAGAAAGTGCCACGGAG
* * *
211663 TTGTGAACTTAAAAGGAAAAAGAGTGCCACAGAG
1 TTGTGGACTTAAAAGG-AGAA-AGTGCCACGGAG
* *
211697 TTGTGGACTTAAAAGGA-ACAAGGTGGCATGGAG
1 TTGTGGACTTAAAAGGAGA-AA-GTGCCACGGAG
*
211730 TTGTGGACTTAAAA-G-G--A-TGCCACAGAG
1 TTGTGGACTTAAAAGGAGAAAGTGCCACGGAG
* * *
211757 TTGTGGACTTTGAAAAGAAAAAAGTGCCACAGAG
1 TTGTGGAC-TT-AAAAGGAGAAAGTGCCACGGAG
* * * *
211791 TCGTGGACTTAGAAA--AGAAA-TACCGCTGAG
1 TTGTGGACTTA-AAAGGAGAAAGTGCCACGGAG
211821 TTGTGGACTT
1 TTGTGGACTT
211831 TGAAGAAAAA
Statistics
Matches: 477, Mismatches: 64, Indels: 103
0.74 0.10 0.16
Matches are distributed among these distances:
27 167 0.35
28 14 0.03
29 6 0.01
30 16 0.03
31 6 0.01
32 15 0.03
33 144 0.30
34 109 0.23
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (32 bp):
TTGTGGACTTAAAAGGAGAAAGTGCCACGGAG
Found at i:211481 original size:61 final size:61
Alignment explanation
Indices: 211250--211746 Score: 458
Period size: 61 Copynumber: 8.0 Consensus size: 61
211240 TTGTGGACTT
* * * *
211250 AAAAGGGTGCCATGGAGTTGTGGACTTAAAATGGTGCCACGGAGTTGTGGACTTAAAAAGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGA
** * * *
211311 GCAA-TGTGCCACGGAGTTGTGGACTTAAAAAGAAAAAGATGCCATGAAGTTGTGGACTTAAAAG
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAAG-----G-TGCCACGGAGTTGTGGACTTAAAAG
211375 GA
60 GA
*
211377 ACAAA-A-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGA
1 A-AAAGAGTGCCACGGAGTTGTGGACTTAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGA
* * *
211437 AAAAGAGTGCCACAGAGTTGTGGGCTTAAAAAGGTGCCATGGAGTTGTGGACTTAAAA-G-
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGA
*** *
211496 ----G-GTGCCATATAGTTGTGGACTTAAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAA
1 AAAAGAGTGCCACGGAGTTGTGGACTT------AAAAAG-GTGCCACGGAGTTGTGGACTTAAAA
211556 GGA
59 GGA
* * ** * * *
211559 AAAAGA-TGCCACGGAGTTGTAGACTTACAGGGGTGCCACAGAGTTGGGGGCTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGA
* * * *
211619 AAAAAAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGAACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGA
* * *
211680 AAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGAACAAGGTGGCATGGAGTTGTGGACTTAAAAG
1 AAAAGAGTGCCACGGAGTTGTGGACTT---A--AA-AAGGTGCCACGGAGTTGTGGACTTAAAAG
211745 GA
60 GA
211747 TGCCACAGAG
Statistics
Matches: 358, Mismatches: 48, Indels: 54
0.78 0.10 0.12
Matches are distributed among these distances:
54 18 0.05
55 1 0.00
59 3 0.01
60 90 0.25
61 146 0.41
62 1 0.00
64 1 0.00
65 1 0.00
66 51 0.14
67 46 0.13
ACGTcount: A:0.35, C:0.12, G:0.32, T:0.21
Consensus pattern (61 bp):
AAAAGAGTGCCACGGAGTTGTGGACTTAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGA
Found at i:211613 original size:94 final size:94
Alignment explanation
Indices: 211284--211746 Score: 479
Period size: 94 Copynumber: 4.9 Consensus size: 94
211274 CTTAAAATGG
*
211284 TGCCACGGAGTTGTGGACTTAAAAAGAGCAATGTGCCACGGAGTTGTGGACTTAAAAAGAAAAAG
1 TGCCACGGAGTTGTGGACTT-AAAAG-G----GTGCCACAGAGTTGTGGACTTAAAAAGAAAAAG
* * *
211349 A-TGCCATGAAGTTGTGGACTTAAAAGGAACAAA-A
60 AGTGCCACGGAGTTGTGGGCTTAAAAGGAA-AAAGA
* *
211383 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCC
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGAAAAAGAGTGCC
* *
211448 ACAGAGTTGTGGGCTT------AAAAAGG
66 ACGGAGTTGTGGGCTTAAAAGGAAAAAGA
* * *
211471 TGCCATGGAGTTGTGGACTTAAAAGGGTGCCATATAGTTGTGGACTTAAAAAGAAAAAGAGTGCC
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGAAAAAGAGTGCC
211536 ACGGAGTTGTGGGCTTAAAAGGAAAAAGA
66 ACGGAGTTGTGGGCTTAAAAGGAAAAAGA
* * * * * * *
211565 TGCCACGGAGTTGTAGACTTACAGGGGTGCCACAGAGTTGGGGGCTTAAAAGGAAAAAAAGTGCC
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGAAAAAGAGTGCC
211630 ACGGAGTTGTGGGCTTAAAAGG-----G-
66 ACGGAGTTGTGGGCTTAAAAGGAAAAAGA
* * *
211653 TGCCACGGAGTTGTGAACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGAACAA
1 TGCCACGGAGTTGTGGACTTAAAA-G-----G-GTGCCACAGAGTTGTGGACTTAAAAAGAAAAA
* * *
211718 G-GTGGCATGGAGTTGTGGACTTAAAAGGA
59 GAGTGCCACGGAGTTGTGGGCTTAAAAGGA
211747 TGCCACAGAG
Statistics
Matches: 314, Mismatches: 34, Indels: 36
0.82 0.09 0.09
Matches are distributed among these distances:
87 3 0.01
88 97 0.31
89 2 0.01
93 33 0.11
94 124 0.39
95 29 0.09
97 1 0.00
98 5 0.02
99 20 0.06
ACGTcount: A:0.35, C:0.13, G:0.32, T:0.21
Consensus pattern (94 bp):
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGAAAAAGAGTGCC
ACGGAGTTGTGGGCTTAAAAGGAAAAAGA
Found at i:211615 original size:182 final size:184
Alignment explanation
Indices: 211250--211746 Score: 653
Period size: 182 Copynumber: 2.7 Consensus size: 184
211240 TTGTGGACTT
* * * *
211250 AAAAGGGTGCCATGGAGTTGTGGACTTAAAATGGTGCCACGGAGTTGTGGACTTAAAAAGAGCAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGGTGCCACGGAGTTGTGGACTT-AAAAGAG--A
* *
211315 TGTGCCACGGAGTTGTGGACTTAAAAAGAAAAAGA-TGCCATGAAGTTGTGGACTTAAAAGGAAC
63 -GTGCCACAGAGTTGTGGACTTAAAAAGAAAAAGAGTGCCATGGAGTTGTGGACTTAAAAGGAAC
* * *
211379 AAAATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGA
127 AAAATGCCACGGAGTTGTAGACTTAAAAGGGTGCCACAGAGTTGGGGACTTAAAAGGA
* *
211437 AAAAGAGTGCCACAGAGTTGTGGGCTTAAAAAGGTGCCATGGAGTTGTGGACTTAAAAG-G-GTG
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGAGAGTG
* * * *
211500 CCATATAGTTGTGGACTTAAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA-AAAG
66 CCACAGAGTTGTGGACTTAAAAAGAAAAAGAGTGCCATGGAGTTGTGGACTTAAAAGGAACAAA-
* * *
211564 ATGCCACGGAGTTGTAGACTTACAGGGGTGCCACAGAGTTGGGGGCTTAAAAGGA
130 ATGCCACGGAGTTGTAGACTTAAAAGGGTGCCACAGAGTTGGGGACTTAAAAGGA
* * *
211619 AAAAAAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGAACTTAAAAGGAAAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGGTGCCACGGAGTTGTGGACTTAAAA-G----A
* * *
211684 GAGTGCCACAGAGTTGTGGACTTAAAAGGAACAAG-GTGGCATGGAGTTGTGGACTTAAAAGGA
61 GAGTGCCACAGAGTTGTGGACTTAAAAAGAAAAAGAGTGCCATGGAGTTGTGGACTTAAAAGGA
211747 TGCCACAGAG
Statistics
Matches: 271, Mismatches: 30, Indels: 17
0.85 0.09 0.05
Matches are distributed among these distances:
181 34 0.13
182 127 0.47
183 1 0.00
185 1 0.00
186 5 0.02
187 48 0.18
188 26 0.10
189 29 0.11
ACGTcount: A:0.35, C:0.12, G:0.32, T:0.21
Consensus pattern (184 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGAGAGTG
CCACAGAGTTGTGGACTTAAAAAGAAAAAGAGTGCCATGGAGTTGTGGACTTAAAAGGAACAAAA
TGCCACGGAGTTGTAGACTTAAAAGGGTGCCACAGAGTTGGGGACTTAAAAGGA
Found at i:211641 original size:155 final size:146
Alignment explanation
Indices: 211190--211801 Score: 565
Period size: 155 Copynumber: 4.0 Consensus size: 146
211180 TGAGCTTTTG
* * *
211190 AAAAGGGTGCCAT-TGACTTGTGGGCTTAAAAGGAGAAAGATGCCACAGAGTTGTGGACTTAAAA
1 AAAAGGGTGCCATAT-AGTTGTGGACTTAAAAGGAAAAAGATGCCACAGAGTTGTGGACTTAAAA
* * * ** *
211254 GGGTGCCATGGAGTTGTGGACTTAAAATGGTGCCACGGAGTTGTGGACTTAAAAAGAGCAATGTG
65 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTT-AAAAGAAAAAAGTG
211319 CCACGGAGTTGTGGACTT
129 CCACGGAGTTGTGGACTT
* *
211337 AAAAAGAAAAAGATGCCATGA-AGTTGTGGACTTAAAAGGAACAAA-ATGCCACGGAGTTGTGGA
1 -AAAAG-----GGTGCCAT-ATAGTTGTGGACTTAAAAGGAA-AAAGATGCCACAGAGTTGTGGA
*
211400 CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT-
58 CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA-G-----G-GTGCCACAGAGTTGTGGACTTA
* *
211464 ----AAAAAGGTGCCATGGAGTTGTGGACTT
116 AAAGAAAAAAGTGCCACGGAGTTGTGGACTT
* * *
211491 AAAAGGGTGCCATATAGTTGTGGACTTAAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAA
1 AAAAGGGTGCCATATAGTTGTGGACTTAAAAGGAAAAAGA-TGCCACAGAGTTGTGGACTTAAAA
* * * * *
211556 GGAAAAAGATGCCACGGAGTTGTAGACTTACAGGGGTGCCACAGAGTTGGGGGCTTAAAAGGAAA
65 GG-----G-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA-G-AA
*
211621 AAAAGTGCCACGGAGTTGTGGGCTT
122 AAAAGTGCCACGGAGTTGTGGACTT
*** *
211646 AAAAGGGTGCCACGGAGTTGTGAACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGACTTAAAA
1 AAAAGGGTGCCATATAGTTGTGGACTTAAAAGGAAAAAGA-TGCCACAGAGTTGTGGACTTAAAA
* * *
211711 GGAACAAGGTGGCATGGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTTGAAAAGAA
65 -G-----GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TT-AAAAGAA
* *
211776 AAAAGTGCCACAGAGTCGTGGACTT
122 AAAAGTGCCACGGAGTTGTGGACTT
211801 A
1 A
211802 GAAAAGAAAT
Statistics
Matches: 384, Mismatches: 41, Indels: 71
0.77 0.08 0.14
Matches are distributed among these distances:
147 4 0.01
148 52 0.14
149 26 0.07
153 79 0.21
154 28 0.07
155 165 0.43
156 5 0.01
157 4 0.01
159 1 0.00
160 19 0.05
161 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (146 bp):
AAAAGGGTGCCATATAGTTGTGGACTTAAAAGGAAAAAGATGCCACAGAGTTGTGGACTTAAAAG
GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAAAAAAGTGCC
ACGGAGTTGTGGACTT
Found at i:211954 original size:31 final size:31
Alignment explanation
Indices: 211740--212239 Score: 571
Period size: 31 Copynumber: 15.9 Consensus size: 31
211730 TTGTGGACTT
* *
211740 AAAAGGATGCCACAGAGTTGTGGACTTTGAAAAG
1 AAAA-GATGCCACTGAGTCGTGGACTTTG--AAG
* * *
211774 AAAAAAGTGCCACAGAGTCGTGGACTTAGAA-
1 AAAAGA-TGCCACTGAGTCGTGGACTTTGAAG
* * *
211805 AAGAA-ATACCGCTGAGTTGTGGACTTTGAAG
1 AA-AAGATGCCACTGAGTCGTGGACTTTGAAG
* *
211836 AAAAAGATGTCACTGAGTCGTGGACTTTG-GG
1 -AAAAGATGCCACTGAGTCGTGGACTTTGAAG
* *
211867 AAGAGATGCCACTGAGTCGTGGACTTGGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
* * * *
211898 AAAAAGGATGCTACTGATTTGTGGACTTAGAAG
1 -AAAA-GATGCCACTGAGTCGTGGACTTTGAAG
* *
211931 AAAATATGCCACTGAGTCATGGACTTTG--G
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
*
211960 AAAGAGATGCCACTGAGTCGTGGACTTGGAAG
1 AAA-AGATGCCACTGAGTCGTGGACTTTGAAG
*
211992 AAAATGATGCCACTGAGTCATGGACTTTGAAG
1 AAAA-GATGCCACTGAGTCGTGGACTTTGAAG
*
212024 AAAAAAAATGCCACTGAGTCGTGGACTTTGAAG
1 --AAAAGATGCCACTGAGTCGTGGACTTTGAAG
* *
212057 AAAAAATGCCATTGAGTCGTGGACTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
212088 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
* * *
212119 AAAAGATACCACTGAGTCGTAGACTTTAAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
*
212150 AAAAGATGCCACTGAGTCGTGGACTTAGAA-
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
* * * *
212180 AAGAGATGCCACTAAGTGGTGGATTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
212211 AAAAGATGCCACTGAGTCGTGGACTTTGA
1 AAAAGATGCCACTGAGTCGTGGACTTTGA
212240 GAAGAGAGAT
Statistics
Matches: 397, Mismatches: 54, Indels: 33
0.82 0.11 0.07
Matches are distributed among these distances:
29 4 0.01
30 91 0.23
31 164 0.41
32 61 0.15
33 49 0.12
34 28 0.07
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (31 bp):
AAAAGATGCCACTGAGTCGTGGACTTTGAAG
Found at i:211954 original size:126 final size:122
Alignment explanation
Indices: 211740--212242 Score: 591
Period size: 126 Copynumber: 4.0 Consensus size: 122
211730 TTGTGGACTT
* * *
211740 AAAAGGATGCCACAGAGTTGTGGACTTTGAAAAGAAAAA-AGTGCCACAGAGTCGTGGACTTAGA
1 AAAA-GATGCCACTGAGTCGTGGACTTTG--AAGAAAAAGA-TGCCACTGAGTCGTGGACTTAGA
* * * * *
211804 AAAGAAATACCGCTGAGTTGTGGACTTTGAAGAAAAAGATGTCACTGAGTCGTGGACTTTGGG
62 AAA-AAATGCCACTGAGTCGTGGACTTTGAAG-AAAAGATGCCACTGAGTCGTGGACTTTGAG
* * * * *
211867 AAGAGATGCCACTGAGTCGTGGACTTGGAAGAAAAAGGATGCTACTGATTTGTGGACTTAGAAGA
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAA-GATGCCACTGAGTCGTGGACTTAGAA-A
* *
211932 AAATATGCCACTGAGTCATGGACTTTG--GAAAGAGATGCCACTGAGTCGTGGACTTGGAAG
64 AAA-ATGCCACTGAGTCGTGGACTTTGAAGAAA-AGATGCCACTGAGTCGTGGACTTTG-AG
* * *
211992 AAAATGATGCCACTGAGTCATGGACTTTGAAGAAAAAAAATGCCACTGAGTCGTGGACTTTGAAG
1 AAAA-GATGCCACTGAGTCGTGGACTTTGAAG-AAAAAGATGCCACTGAGTCGTGGACTTAG-A-
*
212057 AAAAAATGCCATTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAG
62 AAAAAATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTG-AG
* * *
212119 AAAAGATACCACTGAGTCGTAGACTTTAAAG-AAAAGATGCCACTGAGTCGTGGACTTAGAAAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAGATGCCACTGAGTCGTGGACTTAGAAAA-
* * * *
212183 AGATGCCACTAAGTGGTGGATTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAG
65 AAATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAG
212241 AA
1 AA
212243 GAGAGATTTG
Statistics
Matches: 326, Mismatches: 37, Indels: 31
0.83 0.09 0.08
Matches are distributed among these distances:
122 7 0.02
123 55 0.17
124 58 0.18
125 26 0.08
126 131 0.40
127 44 0.13
128 5 0.02
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (122 bp):
AAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAGATGCCACTGAGTCGTGGACTTAGAAAAA
AATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAG
Found at i:213524 original size:12 final size:12
Alignment explanation
Indices: 213509--213564 Score: 60
Period size: 12 Copynumber: 4.6 Consensus size: 12
213499 GCCTTTGCAC
213509 TATTTTTTTTTG
1 TATTTTTTTTTG
213521 TATTTTTTTTTG
1 TATTTTTTTTTG
*
213533 T-TTTTTTTTCTT
1 TATTTTTTTT-TG
*
213545 TCTTTCTTTTTTG
1 TATTT-TTTTTTG
*
213558 TGTTTTT
1 TATTTTT
213565 ACTTGTGACT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
11 8 0.21
12 17 0.45
13 8 0.21
14 5 0.13
ACGTcount: A:0.04, C:0.05, G:0.07, T:0.84
Consensus pattern (12 bp):
TATTTTTTTTTG
Found at i:221159 original size:13 final size:13
Alignment explanation
Indices: 221138--221172 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
221128 AAATTGAAGA
* *
221138 TTTAGTTTTTTTT
1 TTTAATTTTGTTT
221151 TTTAATTTTGTTT
1 TTTAATTTTGTTT
221164 TTTAATTTT
1 TTTAATTTT
221173 AATTGAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (13 bp):
TTTAATTTTGTTT
Found at i:221172 original size:19 final size:18
Alignment explanation
Indices: 221137--221182 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
221127 CAAATTGAAG
*
221137 ATTTAGTTTTTTTTTTTA
1 ATTTAGTTTTTTATTTTA
*
221155 ATTTTGTTTTTTAATTTTA
1 ATTTAGTTTTTT-ATTTTA
*
221174 ATTGAGTTT
1 ATTTAGTTT
221183 ACATGGACTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.72
Consensus pattern (18 bp):
ATTTAGTTTTTTATTTTA
Found at i:221456 original size:16 final size:16
Alignment explanation
Indices: 221415--221457 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
221405 TGTAATAATA
*
221415 AATTATTTAAAAAATT
1 AATTATATAAAAAATT
*
221431 AATTTTATATAACAAATT
1 AA--TTATATAAAAAATT
221449 AATTATATA
1 AATTATATA
221458 TATAAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 9 0.39
18 14 0.61
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTATATAAAAAATT
Found at i:221560 original size:30 final size:31
Alignment explanation
Indices: 221478--221560 Score: 75
Period size: 30 Copynumber: 2.7 Consensus size: 31
221468 GATTTCAATA
*
221478 AATA-AATAATTAAATATATTAAAAATATAAT
1 AATATAATAATTAAAT-TTTTAAAAATATAAT
*
221509 AGTATAATAA--AAATTTATTTAAAAAT-TAAT
1 AATATAATAATTAAA-TT-TTTAAAAATATAAT
* *
221539 AATTTAATAATTAACTTTTTAA
1 AATATAATAATTAAATTTTTAA
221561 GGATAAATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
30 21 0.50
31 14 0.33
32 7 0.17
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (31 bp):
AATATAATAATTAAATTTTTAAAAATATAAT
Found at i:221944 original size:11 final size:11
Alignment explanation
Indices: 221928--221993 Score: 54
Period size: 11 Copynumber: 6.5 Consensus size: 11
221918 ATGATAATTT
221928 TAAATATAATA
1 TAAATATAATA
221939 TAAATA-AA-A
1 TAAATATAATA
*
221948 T--AT-TAAAA
1 TAAATATAATA
*
221956 TAAATAAAATA
1 TAAATATAATA
*
221967 TAAA-ATGATA
1 TAAATATAATA
*
221977 TAAAAATAATA
1 TAAATATAATA
221988 TAAATA
1 TAAATA
221994 CCAGAATACA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
7 4 0.09
8 2 0.05
9 2 0.05
10 12 0.28
11 23 0.53
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (11 bp):
TAAATATAATA
Found at i:221958 original size:17 final size:16
Alignment explanation
Indices: 221929--221993 Score: 78
Period size: 17 Copynumber: 4.0 Consensus size: 16
221919 TGATAATTTT
*
221929 AAATATAATATAAATA
1 AAATATAAAATAAATA
221945 AAATATTAAAATAAATA
1 AAATA-TAAAATAAATA
*
221962 AAATATAAAATGATATA
1 AAATATAAAAT-AAATA
*
221979 AAA-ATAATATAAATA
1 AAATATAAAATAAATA
221994 CCAGAATACA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
15 4 0.09
16 17 0.40
17 22 0.51
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (16 bp):
AAATATAAAATAAATA
Found at i:222628 original size:18 final size:18
Alignment explanation
Indices: 222605--222643 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
222595 ATTATCAGAA
222605 AATATTTTTT-AAAAATAT
1 AATATTTTTTGAAAAA-AT
222623 AATATTTTTTGAAAAAAT
1 AATATTTTTTGAAAAAAT
222641 AAT
1 AAT
222644 TTGAATGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
AATATTTTTTGAAAAAAT
Found at i:222784 original size:14 final size:13
Alignment explanation
Indices: 222742--222793 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
222732 AAATAATTAA
222742 AATATTAATATTTT
1 AATA-TAATATTTT
* * *
222756 AGTATTATTTTTT
1 AATATAATATTTT
222769 AATAGTAATATTTT
1 AATA-TAATATTTT
222783 AATCATAATAT
1 AAT-ATAATAT
222794 ATAATAATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
13 10 0.33
14 19 0.63
15 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (13 bp):
AATATAATATTTT
Found at i:222988 original size:21 final size:22
Alignment explanation
Indices: 222964--223005 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
222954 TTATTTATCA
* *
222964 TTAAACTATTAAT-TTTTAATG
1 TTAAAATAGTAATATTTTAATG
222985 TTAAAATAGTAATATTTTAAT
1 TTAAAATAGTAATATTTTAAT
223006 AAAAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (22 bp):
TTAAAATAGTAATATTTTAATG
Found at i:223264 original size:24 final size:24
Alignment explanation
Indices: 223236--223324 Score: 71
Period size: 24 Copynumber: 3.8 Consensus size: 24
223226 TATCAAATAT
223236 TTTATTAAAATAATAAATTTATTA
1 TTTATTAAAATAATAAATTTATTA
* * *
223260 TTTATTTAAA-AAT-AGTAT-TTA
1 TTTATTAAAATAATAAATTTATTA
*
223281 -TTATTAAAATAAATAATATTAAATTA
1 TTTATTAAAAT-AATAA-ATT-TATTA
223307 TGTTATTAAAAT-ATAAAT
1 T-TTATTAAAATAATAAAT
223325 ATGTATGTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
20 8 0.16
21 3 0.06
22 6 0.12
23 4 0.08
24 10 0.20
25 2 0.04
26 7 0.14
28 10 0.20
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TTTATTAAAATAATAAATTTATTA
Found at i:227144 original size:22 final size:22
Alignment explanation
Indices: 227115--227168 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
227105 GTAAATTCAC
227115 CTAACACACCTAATATATTTA-
1 CTAACACACCTAATATATTTAT
* *
227136 CTTAACACACTTAATATGTTTAT
1 C-TAACACACCTAATATATTTAT
227159 CTAACACACC
1 CTAACACACC
227169 ACCTAACATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 26 0.93
23 1 0.04
ACGTcount: A:0.39, C:0.26, G:0.02, T:0.33
Consensus pattern (22 bp):
CTAACACACCTAATATATTTAT
Found at i:227207 original size:12 final size:12
Alignment explanation
Indices: 227192--227217 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
227182 AATATATTAC
227192 TCACCTAACATA
1 TCACCTAACATA
227204 TCACCTAACATA
1 TCACCTAACATA
227216 TC
1 TC
227218 TAATATGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.27
Consensus pattern (12 bp):
TCACCTAACATA
Found at i:231804 original size:22 final size:22
Alignment explanation
Indices: 231768--231832 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
231758 ATTTATACAA
* * **
231768 AATAAGTTCAGCTAACACGTCT
1 AATAAGTTTACCTAACACACCT
*
231790 AATACGTTTACCTAACACACCT
1 AATAAGTTTACCTAACACACCT
231812 AATAAGTTTACCTAACACACC
1 AATAAGTTTACCTAACACACC
231833 ACCTAACACA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.26
Consensus pattern (22 bp):
AATAAGTTTACCTAACACACCT
Found at i:231886 original size:37 final size:35
Alignment explanation
Indices: 231799--231902 Score: 124
Period size: 37 Copynumber: 3.0 Consensus size: 35
231789 TAATACGTTT
231799 ACCTAACACACCTAATA-AGTTTACCTAACACACC
1 ACCTAACACACCTAATATAGTTTACCTAACACACC
** * *
231833 ACCTAACACATTTAATATA-TTACTCACTTAACATACC
1 ACCTAACACACCTAATATAGTT--T-ACCTAACACACC
231870 ACCTAACACACCTAATAT-GTTTACCTAACACAC
1 ACCTAACACACCTAATATAGTTTACCTAACACAC
231903 TTAATAAAGA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
34 26 0.46
35 2 0.04
36 1 0.02
37 28 0.49
ACGTcount: A:0.40, C:0.32, G:0.02, T:0.26
Consensus pattern (35 bp):
ACCTAACACACCTAATATAGTTTACCTAACACACC
Found at i:232138 original size:20 final size:19
Alignment explanation
Indices: 232083--232144 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 19
232073 TATTCTAAAT
* *
232083 ATATTTGAATATAAATATA
1 ATATTTAAAAATAAATATA
* * *
232102 AGATTTAAACATGAATATCA
1 ATATTTAAAAATAAATAT-A
232122 ATATTTAAAAATAAATAT-
1 ATATTTAAAAATAAATATA
232140 ATATT
1 ATATT
232145 ATTTTAGGTA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
18 5 0.14
19 14 0.40
20 16 0.46
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (19 bp):
ATATTTAAAAATAAATATA
Found at i:233878 original size:3 final size:3
Alignment explanation
Indices: 233870--233905 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
233860 AATAAAAATA
*
233870 TAT TAT TAT TAT TAT TAT TAT TAT GAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
233906 GGGGATTGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:237421 original size:15 final size:15
Alignment explanation
Indices: 237401--237431 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
237391 ATTTCGTTTG
*
237401 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
237416 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
237431 G
1 G
237432 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:239263 original size:21 final size:21
Alignment explanation
Indices: 239234--239278 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
239224 AAGTTTTCAT
*
239234 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
239254 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
239276 TTT
1 TTT
239279 CAACTTGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:241509 original size:13 final size:13
Alignment explanation
Indices: 241491--241516 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
241481 CAATTTTTTG
241491 TGTATCGATACAT
1 TGTATCGATACAT
241504 TGTATCGATACAT
1 TGTATCGATACAT
241517 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:241531 original size:32 final size:33
Alignment explanation
Indices: 241471--241534 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
241461 TACAAGCCAA
** *
241471 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
241504 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
241535 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:242178 original size:18 final size:17
Alignment explanation
Indices: 242148--242189 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
242138 CATTTTCTTG
*
242148 TTATTTTTTATTTAAGT
1 TTATTTTTCATTTAAGT
*
242165 TTATTTTCTCATTTATGT
1 TTATTTT-TCATTTAAGT
242183 TT-TTTTT
1 TTATTTTT
242190 TTTTACTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 1 0.05
17 11 0.50
18 10 0.45
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.74
Consensus pattern (17 bp):
TTATTTTTCATTTAAGT
Found at i:245972 original size:29 final size:28
Alignment explanation
Indices: 245908--245973 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
245898 ATGTATAAAA
*
245908 TATTTTATATAAATTTTTACATAATTATT
1 TATTTAATATAAATTTTTACAT-ATTATT
245937 TATTTAATAT-AATTTTTGACAT-TTATAT
1 TATTTAATATAAATTTTT-ACATATTAT-T
245965 TATATTAAT
1 TAT-TTAAT
245974 TTTTTATACC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 4 0.12
28 11 0.33
29 18 0.55
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (28 bp):
TATTTAATATAAATTTTTACATATTATT
Found at i:247015 original size:15 final size:15
Alignment explanation
Indices: 246995--247023 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
246985 ATTAAAACAA
246995 AGAAGTTAACACTTT
1 AGAAGTTAACACTTT
247010 AGAAGTTAACACTT
1 AGAAGTTAACACTT
247024 AATGACTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (15 bp):
AGAAGTTAACACTTT
Found at i:250353 original size:16 final size:15
Alignment explanation
Indices: 250334--250375 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 15
250324 TTGAACCAAA
250334 AAAAAAAAAGAAAAAG
1 AAAAAAAAAG-AAAAG
250350 AAAAAGAAAAGAAAAG
1 AAAAA-AAAAGAAAAG
250366 AAATAAAAAA
1 AAA-AAAAAA
250376 ATACTGGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (15 bp):
AAAAAAAAAGAAAAG
Found at i:250353 original size:17 final size:16
Alignment explanation
Indices: 250333--250376 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
250323 TTTGAACCAA
250333 AAAAAAAAAAGAAAAAG
1 AAAAAAAAAAG-AAAAG
*
250350 AAAAAGAAAAGAAAAG
1 AAAAAAAAAAGAAAAG
250366 AAATAAAAAAA
1 AAA-AAAAAAA
250377 TACTGGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.02
Consensus pattern (16 bp):
AAAAAAAAAAGAAAAG
Found at i:250359 original size:22 final size:22
Alignment explanation
Indices: 250334--250376 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
250324 TTGAACCAAA
250334 AAAAAAAAAGAAA-AAGAAAAAG
1 AAAAAAAAAGAAATAA-AAAAAG
*
250356 AAAAGAAAAGAAATAAAAAAA
1 AAAAAAAAAGAAATAAAAAAA
250377 TACTGGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (22 bp):
AAAAAAAAAGAAATAAAAAAAG
Found at i:250937 original size:19 final size:19
Alignment explanation
Indices: 250913--250952 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
250903 TTTTTAAAAA
*
250913 TATATTTTGT-ATTAATATT
1 TATATTTTATAATTAA-ATT
250932 TATATTTTATAATTAAATT
1 TATATTTTATAATTAAATT
250951 TA
1 TA
250953 AATAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (19 bp):
TATATTTTATAATTAAATT
Found at i:254542 original size:13 final size:13
Alignment explanation
Indices: 254524--254548 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
254514 ACTGAAGTAA
254524 TGTATCGATACAT
1 TGTATCGATACAT
254537 TGTATCGATACA
1 TGTATCGATACA
254549 ATCTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:257210 original size:15 final size:15
Alignment explanation
Indices: 257190--257228 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
257180 TAAAAATGTC
* *
257190 CAAAATGAGGATGCT
1 CAAAATGAAGAAGCT
257205 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
257220 CCAAATGAA
1 CAAAATGAA
257229 ATTGATGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.49, C:0.15, G:0.21, T:0.15
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:259305 original size:20 final size:21
Alignment explanation
Indices: 259235--259318 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 21
259225 ATGTCCAAAA
259235 TGTATCGATACA-TGTTT-CT
1 TGTATCGATACATTGTTTCCT
* **
259254 GTGTATCGATACATCTGGAAATTCAA
1 -TGTATCGATACAT-T-G--TTTCCT
259280 TGTATCGATACATT-TTTCCT
1 TGTATCGATACATTGTTTCCT
259300 TGTATCGATACATTGTTTC
1 TGTATCGATACATTGTTTC
259319 GATACAGGGT
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
20 29 0.57
21 4 0.08
22 1 0.02
23 1 0.02
24 1 0.02
25 15 0.29
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.43
Consensus pattern (21 bp):
TGTATCGATACATTGTTTCCT
Found at i:259488 original size:20 final size:20
Alignment explanation
Indices: 259445--259490 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
259435 AAATCTTTTG
259445 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
259466 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
259486 CAAAA
1 CAAAA
259491 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:262545 original size:16 final size:16
Alignment explanation
Indices: 262524--262576 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
262514 TCTTTAATTT
262524 TTTTATTTATATTTTA
1 TTTTATTTATATTTTA
*
262540 TTTTA-TTATAATTATA
1 TTTTATTTAT-ATTTTA
262556 TTTTATTTATTATATTTA
1 TTTTATTTA-TAT-TTTA
262574 TTT
1 TTT
262577 AAATTTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 4 0.13
16 15 0.48
17 5 0.16
18 7 0.23
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTATTTATATTTTA
Found at i:262566 original size:20 final size:21
Alignment explanation
Indices: 262530--262574 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
262520 ATTTTTTTAT
262530 TTATATTTTATTTTATTATAA
1 TTATATTTTATTTTATTATAA
*
262551 TTATATTTTA-TTTATTATAT
1 TTATATTTTATTTTATTATAA
262571 TTAT
1 TTAT
262575 TTAAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TTATATTTTATTTTATTATAA
Found at i:262584 original size:20 final size:21
Alignment explanation
Indices: 262530--262584 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
262520 ATTTTTTTAT
*
262530 TTATATTTTATTTTATTATAA
1 TTATATTTAATTTTATTATAA
*
262551 TTATATTTTA-TTTATTAT-A
1 TTATATTTAATTTTATTATAA
262570 TT-TATTTAAATTTTA
1 TTATATTT-AATTTTA
262585 ATGTATTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 5 0.16
19 4 0.13
20 12 0.39
21 10 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTATATTTAATTTTATTATAA
Found at i:263268 original size:15 final size:15
Alignment explanation
Indices: 263248--263279 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
263238 GGGTACTATA
263248 ATATTTTGTCATGAC
1 ATATTTTGTCATGAC
263263 ATATTTTGTCATGAC
1 ATATTTTGTCATGAC
263278 AT
1 AT
263280 TACCGTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (15 bp):
ATATTTTGTCATGAC
Found at i:265740 original size:18 final size:18
Alignment explanation
Indices: 265687--265750 Score: 67
Period size: 18 Copynumber: 3.5 Consensus size: 18
265677 CTAGAGAGAA
* *
265687 AAAAAGATAGAAAAAAGG
1 AAAAAGAAAGAAAAAAAG
265705 AAAAAGTTAAAG-AAAAAAG
1 AAAAAG--AAAGAAAAAAAG
*
265724 AAAAAGAGAGAAAAAAAG
1 AAAAAGAAAGAAAAAAAG
*
265742 AGAAAGAAA
1 AAAAAGAAA
265751 ATGGATAGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 3 0.08
18 20 0.53
19 12 0.32
20 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (18 bp):
AAAAAGAAAGAAAAAAAG
Found at i:266993 original size:20 final size:20
Alignment explanation
Indices: 266968--267017 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
266958 CCCTCATTTT
266968 TATCGATAAAA-GTAAAAATG
1 TATCGATAAAATG-AAAAATG
* * *
266988 TATCGATACAATGCACAATG
1 TATCGATAAAATGAAAAATG
267008 TATCGATAAA
1 TATCGATAAA
267018 TTATGTGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (20 bp):
TATCGATAAAATGAAAAATG
Found at i:267115 original size:113 final size:112
Alignment explanation
Indices: 266892--267107 Score: 258
Period size: 112 Copynumber: 1.9 Consensus size: 112
266882 TTCAGGATTG
** * *
266892 AATGTATCGATGCATCATGTGAATGTATCGATACATATGGTTAGCAGTAGCTAAGATATGCTGAA
1 AATGTATCGATAAATCATGTGAATGTATCGATACATATGGTTAGCAATAGCTAAGAAATGCTGAA
* *
266957 ACCCTCATTTTTATCGATAAAAGTAAAAATGTATCGATACAATGCAC
66 ACCCTCATTTGTATCGATAAAAGTAAAAATATATCGATACAATGCAC
* * * *
267004 AATGTATCGATAAATTATGTGAATGTATCGTTACATCTGGTT-GCTAATAGGTAAAGAAAT-CTT
1 AATGTATCGATAAATCATGTGAATGTATCGATACATATGGTTAGC-AATAGCT-AAGAAATGC-T
* * *
267067 GAAACTCTCATTTGTATCGATACACA-TGAAAATATATCGAT
63 GAAACCCTCATTTGTATCGATA-AAAGTAAAAATATATCGAT
267108 GTAATGCATA
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
111 2 0.02
112 43 0.49
113 40 0.46
114 2 0.02
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (112 bp):
AATGTATCGATAAATCATGTGAATGTATCGATACATATGGTTAGCAATAGCTAAGAAATGCTGAA
ACCCTCATTTGTATCGATAAAAGTAAAAATATATCGATACAATGCAC
Found at i:269172 original size:29 final size:28
Alignment explanation
Indices: 269031--269213 Score: 103
Period size: 29 Copynumber: 6.3 Consensus size: 28
269021 TATTTCAGGG
*
269031 TCATTTCAGTAATTTTACATGATTTAAGA
1 TCATTT-AGTAATTTTTCATGATTTAAGA
* * * *
269060 CCGTTTATGCAA-TTTT-ATGAATTTTAGGA
1 TCATTTA-GTAATTTTTCATG-A-TTTAAGA
* *
269089 TTATTTTAGTAATTTTAT-AAGATTTAAGA
1 TCA-TTTAGTAATTTT-TCATGATTTAAGA
269118 TCATTTATGTAA--TTTCATGCATTTTAAGA
1 TCATTTA-GTAATTTTTCATG-A-TTTAAGA
269147 TCATCTTAGTAATTTTTCATGATTT-AGTA
1 TCAT-TTAGTAATTTTTCATGATTTAAG-A
*
269176 TCATTTATGT-A-TTTTCATGCATTTTAAGG
1 TCATTTA-GTAATTTTTCATG-A-TTTAAGA
*
269205 TTATTTAGT
1 TCATTTAGT
269214 TAAATGTACC
Statistics
Matches: 121, Mismatches: 15, Indels: 37
0.70 0.09 0.21
Matches are distributed among these distances:
26 1 0.01
27 15 0.12
28 19 0.16
29 62 0.51
30 14 0.12
31 10 0.08
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50
Consensus pattern (28 bp):
TCATTTAGTAATTTTTCATGATTTAAGA
Found at i:269203 original size:58 final size:58
Alignment explanation
Indices: 268834--269201 Score: 282
Period size: 58 Copynumber: 6.3 Consensus size: 58
268824 AGGGGCTATC
* * * * * *
268834 ATGTAATTTCATACATTTAAAGG-CCATTTTAGTTATTTTTTATGATTTAGGGATCA-TT
1 ATGTAATTTCATGCATTT-TAGGATCATTTTAGTAATTTTTCATGATTTA-AGATCATTT
* * * * * * * *
268892 GT-TAAATTCATACATTTTAGGGTCATATTAGTTAATTTTTTATGATTTAGGGATTA-TT
1 ATGTAATTTCATGCATTTTAGGATCATTTTAG-TAATTTTTCATGATTTA-AGATCATTT
* * * * * * *
268950 ATGTGATTTCATACATTTTAGGACCATTTTAATTATTTTCCATGATTTAAGGACCA-TT
1 ATGTAATTTCATGCATTTTAGGATCATTTTAGTAATTTTTCATGATTTAA-GATCATTT
* * * * * * * * *
269008 ATTTAAATTCATGTATTTCAGGGTCATTTCAGTAATTTTACATGATTTAAGACCGTTT
1 ATGTAATTTCATGCATTTTAGGATCATTTTAGTAATTTTTCATGATTTAAGATCATTT
* * * * *
269066 ATGCAATTTTATGAATTTTAGGATTATTTTAGTAATTTTAT-AAGATTTAAGATCATTT
1 ATGTAATTTCATGCATTTTAGGATCATTTTAGTAATTTT-TCATGATTTAAGATCATTT
* *
269124 ATGTAATTTCATGCATTTTAAGATCATCTTAGTAATTTTTCATGATTT-AGTATCATTT
1 ATGTAATTTCATGCATTTTAGGATCATTTTAGTAATTTTTCATGATTTAAG-ATCATTT
*
269182 ATGTATTTTCATGCATTTTA
1 ATGTAATTTCATGCATTTTA
269202 AGGTTATTTA
Statistics
Matches: 248, Mismatches: 54, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
56 3 0.01
57 28 0.11
58 194 0.78
59 23 0.09
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (58 bp):
ATGTAATTTCATGCATTTTAGGATCATTTTAGTAATTTTTCATGATTTAAGATCATTT
Found at i:269431 original size:78 final size:77
Alignment explanation
Indices: 269227--269438 Score: 196
Period size: 78 Copynumber: 2.7 Consensus size: 77
269217 ATGTACCTTC
** * * * *
269227 AAACTAAGTTTTTATGGTCATGTGGGAACCTTCACGTCAAAAAATGTCCATTGAA-GTCATTTAG
1 AAACTAAGTCCTTAAGGTCATGTGGGAACCTTCATGTC-AAACATGTCCATT-AAGGGCATTTAG
*
269291 GTAAAAGCACCTTA
64 GTAAAAGCACATTA
* ** * ** * *
269305 AAA-TCAAGTCCTTAAGATCATGTAAGAATCTTTGTGTTGAAACATGTCCGTTAAGGGCATTTAG
1 AAACT-AAGTCCTTAAGGTCATGTGGGAACCTTCATG-TCAAACATGTCCATTAAGGGCATTTAG
*
269369 GTAATA-CTACATTA
64 GTAAAAGC-ACATTA
*
269383 AAACTAAGTCCTTAAGGTCATGTGGGAACCTTCATGTCAATACGTGTCCATTAAGG
1 AAACTAAGTCCTTAAGGTCATGTGGGAACCTTCATGTCAA-ACATGTCCATTAAGG
269439 TCATGCAGGG
Statistics
Matches: 103, Mismatches: 25, Indels: 12
0.74 0.18 0.09
Matches are distributed among these distances:
77 7 0.07
78 94 0.91
79 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (77 bp):
AAACTAAGTCCTTAAGGTCATGTGGGAACCTTCATGTCAAACATGTCCATTAAGGGCATTTAGGT
AAAAGCACATTA
Found at i:270605 original size:18 final size:18
Alignment explanation
Indices: 270584--270618 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
270574 TTTATTACAT
270584 TTTATTT-TATTTTATTTA
1 TTTATTTGT-TTTTATTTA
270602 TTTATTTGTTTTTATTT
1 TTTATTTGTTTTTATTT
270619 GTTGCTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (18 bp):
TTTATTTGTTTTTATTTA
Found at i:272015 original size:22 final size:23
Alignment explanation
Indices: 271987--272061 Score: 93
Period size: 22 Copynumber: 3.3 Consensus size: 23
271977 TAATAAAATT
271987 ATATAATATAAAAATAAT-TAAA
1 ATATAATATAAAAATAATATAAA
272009 ATATAATATAAAATATAATATATAA
1 ATATAATATAAAA-ATAATATA-AA
*
272034 ATA-AA-ATAAATATAATATAAA
1 ATATAATATAAAAATAATATAAA
272055 TATATAA
1 -ATATAA
272062 ATTTATTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
21 2 0.04
22 24 0.51
23 12 0.26
24 4 0.09
25 5 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATATAATATAAAAATAATATAAA
Found at i:272027 original size:34 final size:35
Alignment explanation
Indices: 271975--272061 Score: 117
Period size: 34 Copynumber: 2.5 Consensus size: 35
271965 TACTTTTAGT
*
271975 TATAATA-AAATTATATAATATAAAAAT-AATTAAAA
1 TATAATATAAA-TATATAATATAAAAATAAAAT-AAA
*
272010 TATAATATAAA-ATATAATATATAAATAAAATAAA
1 TATAATATAAATATATAATATAAAAATAAAATAAA
272044 TATAATATAAATATATAA
1 TATAATATAAATATATAA
272062 ATTTATTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
34 28 0.60
35 16 0.34
36 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (35 bp):
TATAATATAAATATATAATATAAAAATAAAATAAA
Found at i:272072 original size:28 final size:28
Alignment explanation
Indices: 271978--272063 Score: 106
Period size: 28 Copynumber: 3.1 Consensus size: 28
271968 TTTTAGTTAT
*
271978 AATAAAAT-TATATAATATAAA-A-ATA
1 AATAAAATAAATATAATATAAATATATA
* *
272003 ATTAAAATATAATATAAAATATAATATATA
1 AATAAAATA-AATATAATATA-AATATATA
272033 AATAAAATAAATATAATATAAATATATA
1 AATAAAATAAATATAATATAAATATATA
272061 AAT
1 AAT
272064 TTATTAAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
25 7 0.14
27 9 0.18
28 13 0.25
29 11 0.22
30 11 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (28 bp):
AATAAAATAAATATAATATAAATATATA
Found at i:272079 original size:28 final size:27
Alignment explanation
Indices: 271978--272063 Score: 95
Period size: 29 Copynumber: 3.1 Consensus size: 27
271968 TTTTAGTTAT
* *
271978 AATAAAAT-TATATAATATAA-AAATA
1 AATAAAATAAATATAATATAATATATA
*
272003 ATTAAAATATAATATAAAATATAATATATA
1 AATAAAATA-AATAT--AATATAATATATA
272033 AATAAAATAAATATAATATAAATATATA
1 AATAAAATAAATATAATAT-AATATATA
272061 AAT
1 AAT
272064 TTATTAAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
25 7 0.14
27 9 0.18
28 11 0.22
29 12 0.24
30 12 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (27 bp):
AATAAAATAAATATAATATAATATATA
Found at i:272086 original size:5 final size:5
Alignment explanation
Indices: 271975--272061 Score: 53
Period size: 5 Copynumber: 18.0 Consensus size: 5
271965 TACTTTTAGT
* * *
271975 TATAA TA-AA -ATTA TATAA TATAAA AATAA TTAAAA TATAA TATAAAA
1 TATAA TATAA TATAA TATAA TAT-AA TATAA -TATAA TATAA TAT--AA
*
272022 TATAA TAT-A TA-AA TAAAA TA-AA TATAA TATAA -AT-A TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
272062 ATTTATTAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 22
0.70 0.06 0.24
Matches are distributed among these distances:
3 2 0.03
4 17 0.26
5 34 0.52
6 7 0.11
7 5 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (5 bp):
TATAA
Found at i:273979 original size:31 final size:31
Alignment explanation
Indices: 273944--274047 Score: 110
Period size: 31 Copynumber: 3.5 Consensus size: 31
273934 CAAATTCGCA
273944 TTCTCCCCCTTAATCATAAGCACTTATCTCT
1 TTCTCCCCCTTAATCATAAGCACTTATCTCT
** ** * *
273975 TTCT-CCCC--AATTTTAA-CAAAT-TCGCA
1 TTCTCCCCCTTAATCATAAGCACTTATCTCT
274001 TTCTCCCCCTTAATCATAAGCACTTATCTCT
1 TTCTCCCCCTTAATCATAAGCACTTATCTCT
*
274032 TTCTCCTCCTTAATCA
1 TTCTCCCCCTTAATCA
274048 AAAATTTATT
Statistics
Matches: 55, Mismatches: 13, Indels: 10
0.71 0.17 0.13
Matches are distributed among these distances:
26 7 0.13
27 7 0.13
28 6 0.11
29 6 0.11
30 7 0.13
31 22 0.40
ACGTcount: A:0.24, C:0.35, G:0.03, T:0.38
Consensus pattern (31 bp):
TTCTCCCCCTTAATCATAAGCACTTATCTCT
Found at i:273995 original size:57 final size:57
Alignment explanation
Indices: 273926--274037 Score: 224
Period size: 57 Copynumber: 2.0 Consensus size: 57
273916 TTAATAAGGT
273926 AATTTTAACAAATTCGCATTCTCCCCCTTAATCATAAGCACTTATCTCTTTCTCCCC
1 AATTTTAACAAATTCGCATTCTCCCCCTTAATCATAAGCACTTATCTCTTTCTCCCC
273983 AATTTTAACAAATTCGCATTCTCCCCCTTAATCATAAGCACTTATCTCTTTCTCC
1 AATTTTAACAAATTCGCATTCTCCCCCTTAATCATAAGCACTTATCTCTTTCTCC
274038 TCCTTAATCA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.27, C:0.32, G:0.04, T:0.38
Consensus pattern (57 bp):
AATTTTAACAAATTCGCATTCTCCCCCTTAATCATAAGCACTTATCTCTTTCTCCCC
Found at i:282066 original size:20 final size:20
Alignment explanation
Indices: 282023--282075 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
282013 GCCAATGACT
*
282023 TGTATCGATACATGCTTTTCA
1 TGTATCGATACAT-CTTGTCA
282044 TGTATCGATACAT-TTGGTCA
1 TGTATCGATACATCTT-GTCA
282064 TGTATCGATACA
1 TGTATCGATACA
282076 ATGTATCGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 2 0.07
20 15 0.50
21 13 0.43
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATCTTGTCA
Found at i:282081 original size:13 final size:13
Alignment explanation
Indices: 282063--282087 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
282053 ACATTTGGTC
282063 ATGTATCGATACA
1 ATGTATCGATACA
282076 ATGTATCGATAC
1 ATGTATCGATAC
282088 TGTGCAACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:286551 original size:12 final size:13
Alignment explanation
Indices: 286534--286562 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
286524 GAAAAAATCA
286534 AAAATTAAAATT-
1 AAAATTAAAATTC
286546 AAAATTAAAATTC
1 AAAATTAAAATTC
286559 AAAA
1 AAAA
286563 AAAAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATTAAAATTC
Found at i:286613 original size:35 final size:35
Alignment explanation
Indices: 286574--286784 Score: 377
Period size: 35 Copynumber: 6.0 Consensus size: 35
286564 AAAATAAATA
286574 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
*
286609 ATAAAAATGAAGGCGTGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
*
286644 ATAAAAATGAAGGCGTGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
286679 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
*
286714 ATAAAAATGGAGGCATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
* *
286749 ATAAAAATGGAGGCATGAAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
286784 A
1 A
286785 ATGGGCATGC
Statistics
Matches: 172, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 172 1.00
ACGTcount: A:0.42, C:0.06, G:0.33, T:0.20
Consensus pattern (35 bp):
ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
Found at i:286677 original size:49 final size:49
Alignment explanation
Indices: 286624--286824 Score: 165
Period size: 49 Copynumber: 4.0 Consensus size: 49
286614 AATGAAGGCG
*
286624 TGGAATGATGGGCATGGAATATAAAAATGAAGGCGTGGAATGATGGGCA
1 TGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGCA
**** * ** * *
286673 TGGAAT-ATAAAAAT-GAAGGCAT-GGAATGATGGGCATGGAATATAAAAATGGAGGCA
1 TGGAATGATGGGCATGGAA--TATAAAAATGA-AGGCATGG-A-AT---GAT-G-GGCA
* *
286729 TGGAATGATGGGCATGGAATATAAAAATGGAGGCATGAAATGATGGGCA
1 TGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGCA
* *
286778 TGGAATAATGGGCATGCAATATAAAAATGAAGGCATGGAATGATGGG
1 TGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGG
286825 GATAAAAAAT
Statistics
Matches: 114, Mismatches: 25, Indels: 26
0.69 0.15 0.16
Matches are distributed among these distances:
47 3 0.03
48 9 0.08
49 61 0.54
50 2 0.02
51 4 0.04
54 4 0.04
55 2 0.02
56 18 0.16
57 8 0.07
58 3 0.03
ACGTcount: A:0.40, C:0.06, G:0.33, T:0.20
Consensus pattern (49 bp):
TGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGCA
Found at i:286694 original size:21 final size:20
Alignment explanation
Indices: 286599--286765 Score: 67
Period size: 21 Copynumber: 9.3 Consensus size: 20
286589 TGGAATGATG
286599 GGCATGGAATATAAAAATGAA
1 GGCATGGAATATAAAAATG-A
* *
286620 GGCGTGG-A-AT---GATG-
1 GGCATGGAATATAAAAATGA
286634 GGCATGGAATATAAAAATGAA
1 GGCATGGAATATAAAAATG-A
* *
286655 GGCGTGG-A-AT---GATG-
1 GGCATGGAATATAAAAATGA
286669 GGCATGGAATATAAAAATGAA
1 GGCATGGAATATAAAAATG-A
*
286690 GGCATGG-A-AT---GATG-
1 GGCATGGAATATAAAAATGA
286704 GGCATGGAATATAAAAATGGA
1 GGCATGGAATATAAAAAT-GA
*
286725 GGCATGG-A-AT---GATG-
1 GGCATGGAATATAAAAATGA
286739 GGCATGGAATATAAAAATGGA
1 GGCATGGAATATAAAAAT-GA
286760 GGCATG
1 GGCATG
286766 AAATGATGGG
Statistics
Matches: 106, Mismatches: 12, Indels: 56
0.61 0.07 0.32
Matches are distributed among these distances:
14 26 0.25
15 5 0.05
16 19 0.18
19 18 0.17
20 6 0.06
21 32 0.30
ACGTcount: A:0.41, C:0.06, G:0.34, T:0.20
Consensus pattern (20 bp):
GGCATGGAATATAAAAATGA
Found at i:286779 original size:14 final size:14
Alignment explanation
Indices: 286760--286798 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
286750 TAAAAATGGA
*
286760 GGCATGAAATGATG
1 GGCATGAAATAATG
*
286774 GGCATGGAATAATG
1 GGCATGAAATAATG
*
286788 GGCATGCAATA
1 GGCATGAAATA
286799 TAAAAATGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.10, G:0.33, T:0.21
Consensus pattern (14 bp):
GGCATGAAATAATG
Found at i:288346 original size:51 final size:51
Alignment explanation
Indices: 288266--288384 Score: 204
Period size: 51 Copynumber: 2.3 Consensus size: 51
288256 TATTTCTGAG
*
288266 GGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATC-
1 GGGATACTCCAACCCCGGTTTTATCTCTAAAACATCAATTTTTCATAATCA
*
288316 GTGGATACTCCAACCTCGGTTTTATCTCTAAAACATCAATTTTTCATAATCA
1 G-GGATACTCCAACCCCGGTTTTATCTCTAAAACATCAATTTTTCATAATCA
288368 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
288385 TTATTTCTGA
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
50 1 0.02
51 62 0.97
52 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGATACTCCAACCCCGGTTTTATCTCTAAAACATCAATTTTTCATAATCA
Found at i:288451 original size:79 final size:79
Alignment explanation
Indices: 288318--288885 Score: 836
Period size: 79 Copynumber: 7.2 Consensus size: 79
288308 TCATAATCGT
* * *
288318 GGATACTCCAACCTCGGTTTTATCTCTAAAACATCAATTTTTCATAATCAGGGATACTCCAACCC
1 GGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCC
288383 CGTTATTTCTGAGG
66 CGTTATTTCTGAGG
* * * *
288397 GGATACTCTAACCCCGATTTTATTTCTAAAATATTAATTTTTCATAATCGGGGATACTCCAACCC
1 GGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCC
*
288462 CGTTATTTCCGAGG
66 CGTTATTTCTGAGG
* * * *
288476 GGATACTCCAACCTCGGTTTTATCTCTAAAACATCAATTTTTCATAATCGTGGATACTCTAACCC
1 GGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCC
*
288541 CCTTATTTCTGAGG
66 CGTTATTTCTGAGG
* * *
288555 GGATACTCCAACCCCGGTTTTATCTCTAAAACATCAATTTTTCATAATCGAGGATACTCCAATCC
1 GGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCC
288620 CGTTATTT-TCGAGG
66 CGTTATTTCT-GAGG
*
288634 GGATACTACAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCC
1 GGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCC
288699 CGTTATTTCTGAGG
66 CGTTATTTCTGAGG
* *
288713 GGATACTTCAACCTCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCC
1 GGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCC
288778 CGTTATTTCTGAGG
66 CGTTATTTCTGAGG
* * * * * * * *
288792 GGATACTCCAGCTCCGATTTTAGTTCCAAAACACCAATTTCTT-ACAATCAGGGATACTCCAACC
1 GGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTT-TTCATAATCGGGGATACTCCAACC
*
288856 CCGTTATTT-TCACGG
65 CCGTTATTTCTGA-GG
288871 GGATACTCCAACCCC
1 GGATACTCCAACCCC
288886 ATTATTTTCA
Statistics
Matches: 443, Mismatches: 42, Indels: 8
0.90 0.09 0.02
Matches are distributed among these distances:
78 3 0.01
79 437 0.99
80 3 0.01
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (79 bp):
GGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCC
CGTTATTTCTGAGG
Found at i:288454 original size:130 final size:130
Alignment explanation
Indices: 288221--288460 Score: 399
Period size: 130 Copynumber: 1.8 Consensus size: 130
288211 TTTAATTTTC
* * *
288221 TCAATTTTTCACAATCGGGGATACTCCAACCTCATTATTTCTGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCACAATCAGGGATACTCCAACCCCATTATTTCTGAGGGGATACTCCAACCCCGATT
*
288286 TTATTTCTAAAACATCAATTTTTCATAATCGTGGATACTCCAACCTCGGTTTTATCTCTAAAACA
66 TTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCTCGGTTTTATCTCTAAAACA
* * *
288351 TCAATTTTTCATAATCAGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCTAACCCCGATT
1 TCAATTTTTCACAATCAGGGATACTCCAACCCCATTATTTCTGAGGGGATACTCCAACCCCGATT
* *
288416 TTATTTCTAAAATATTAATTTTTCATAATCGGGGATACTCCAACC
66 TTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACC
288461 CCGTTATTTC
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 101 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (130 bp):
TCAATTTTTCACAATCAGGGATACTCCAACCCCATTATTTCTGAGGGGATACTCCAACCCCGATT
TTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCTCGGTTTTATCTCTAAAACA
Found at i:288874 original size:28 final size:28
Alignment explanation
Indices: 288842--288914 Score: 137
Period size: 28 Copynumber: 2.6 Consensus size: 28
288832 CTTACAATCA
*
288842 GGGATACTCCAACCCCGTTATTTTCACG
1 GGGATACTCCAACCCCATTATTTTCACG
288870 GGGATACTCCAACCCCATTATTTTCACG
1 GGGATACTCCAACCCCATTATTTTCACG
288898 GGGATACTCCAACCCCA
1 GGGATACTCCAACCCCA
288915 GCCCTTATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (28 bp):
GGGATACTCCAACCCCATTATTTTCACG
Found at i:291107 original size:4 final size:4
Alignment explanation
Indices: 291098--291126 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
291088 TATTTTGAGG
291098 TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
291127 GTTTTGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:302517 original size:55 final size:55
Alignment explanation
Indices: 302433--302594 Score: 220
Period size: 55 Copynumber: 2.9 Consensus size: 55
302423 CGCCTTCTCC
302433 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGA-TGCA
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGACT-CA
* ** *
302488 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGTAAAACTCC
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGACTCA
* * * *
302543 TTTTAAAGCCCACACAAGTTGGTGGC-GCTTCCTAGTCCTCAAAGAGCAGGAC
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCTTCAAAGAGCAGGAC
302595 GCTCCCTCTT
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
54 4 0.04
55 89 0.95
56 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (55 bp):
TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGACTCA
Found at i:302768 original size:211 final size:204
Alignment explanation
Indices: 302431--302805 Score: 536
Period size: 211 Copynumber: 1.8 Consensus size: 204
302421 GACGCCTTCT
*
302431 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGATGCATTTCAAAG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCATTTCAAAG
* * * * *
302496 CCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGTAAAACTCCTTTTAAAGCCCACACAAG
66 CCCACACAAGTTGATGGCACCTTTCAGTCTTCAAAAAGCAAAACGCCTTTCAAAGCCCACACAAG
*
302561 TTGGTGGCGCT-TCCTAGTCCTCAAAGAGCAGGACGCTCCCTCTTTTCGCCCTTTAGTCCTCAAA
131 TTGGTGGCACTATCC-AGTCCTCAAAGAGCAGGACGCTCCCTCTTTTCGCCCTTTAGTCCTCAAA
302625 CAGCAGGACG
195 CAGCAGGACG
* * *
302635 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCGCCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGA-----T-GCAT
** *
302700 TTCAAAGCCCACACAAGTTGATGGCACCTTTCAGTCTTCAAAAAGCAGGACGCCTTTCAAATCCC
59 TTCAAAGCCCACACAAGTTGATGGCACCTTTCAGTCTTCAAAAAGCAAAACGCCTTTCAAAGCCC
* *
302765 ACACAAGTTGGTGGCACTATTCAGTCTTCAAAGAGCAGGAC
124 ACACAAGTTGGTGGCACTATCCAGTCCTCAAAGAGCAGGAC
302806 TCCTTTTAAA
Statistics
Matches: 148, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
204 33 0.22
205 17 0.11
210 1 0.01
211 95 0.64
212 2 0.01
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.24
Consensus pattern (204 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCATTTCAAAG
CCCACACAAGTTGATGGCACCTTTCAGTCTTCAAAAAGCAAAACGCCTTTCAAAGCCCACACAAG
TTGGTGGCACTATCCAGTCCTCAAAGAGCAGGACGCTCCCTCTTTTCGCCCTTTAGTCCTCAAAC
AGCAGGACG
Found at i:302780 original size:55 final size:55
Alignment explanation
Indices: 302610--302862 Score: 305
Period size: 55 Copynumber: 4.5 Consensus size: 55
302600 CTCTTTTCGC
* *
302610 CCTTT-AGTCCTCAAACAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
302664 CTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCGCCTTTCAAAGCCCACACAAGTTGATGGCA
1 CCTTTC-AGTCCTCAAAGAGCAGGA------CGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
302726 CCTTTCAGTCTTCAAAAAGCAGGACGCCTTTCAAATCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
302781 -CTATTCAGTCTTCAAAGAGCAGGACTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCT-TTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
*
302836 -CTTCCTAGTCCTCAAAGAGCAGGACGC
1 CCTTTC-AGTCCTCAAAGAGCAGGACGC
302863 TCTCTCCTTT
Statistics
Matches: 173, Mismatches: 16, Indels: 19
0.83 0.08 0.09
Matches are distributed among these distances:
54 8 0.05
55 98 0.57
56 17 0.10
61 16 0.09
62 34 0.20
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (55 bp):
CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:302881 original size:266 final size:265
Alignment explanation
Indices: 302396--303064 Score: 1010
Period size: 266 Copynumber: 2.5 Consensus size: 265
302386 CTTCTTCTTC
* *
302396 CACTTTTCTAGTCCTCAAAGATCAGGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCAC
1 CACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCACCTTTCAAAGCCCACACAAGTTGGTGGCAC
* *
302461 CTTTCAGTCTTCAAAGAGCAGGATGCATTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCT
66 CTTTCAGTCTTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCT
* ** *
302526 TCAAAGAGTAAAACTCCTTTTAAAGCCCACACAAGTTGGTGGCGCTTCCTAGTCCTCAAAGAGCA
130 TCAAAGAGCAGGACTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCA
* *
302591 GGACGCTCCCTCTTTTCGCCCTTTAGTCCTCAAACAGCAGGACGCCTTTTAAAGCCCACACAAGT
195 GGACGCTCCCTCCTTTCGCCCTTTAGTCCTCAAACAGCAGGACGCCTTTCAAAGCCCACACAAGT
302656 TGGTGG
260 TGGTGG
* *
302662 CACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCGCCTTTCAAAGCCCACACAAGTTGATGGCAC
1 CACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCACCTTTCAAAGCCCACACAAGTTGGTGGCAC
* *
302727 CTTTCAGTCTTCAAAAAGCAGGACGCCTTTCAAATCCCACACAAGTTGGTGGCACTATTCAGTCT
66 CTTTCAGTCTTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACT-TTCAGTCT
302792 TCAAAGAGCAGGACTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCA
130 TCAAAGAGCAGGACTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCA
* * *
302857 GGACGCTCTCTCCTTTCTCCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGT
195 GGACGCTCCCTCCTTTCGCCCTTTAGTCCTCAAACAGCAGGACGCCTTTCAAAGCCCACACAAGT
302922 TGGTGG
260 TGGTGG
* * * *
302928 CACCTTTC-AGTCTTCAAATAGCAGGA------CACCTTTCAAAGCACACACAAGTTGGTGGCAC
1 CACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCACCTTTCAAAGCCCACACAAGTTGGTGGCAC
* * * * * * *
302986 CTTTCAGTCCTCAAAGAGCAAGACTCCTTTTAAAGCCCACACAAGTTGGTGGCGCTTCCTAGTCC
66 CTTTCAGTCTTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTC-AGTCT
303051 TCAAAGAGCAGGAC
130 TCAAAGAGCAGGAC
303065 GCTCCTTTCT
Statistics
Matches: 370, Mismatches: 31, Indels: 11
0.90 0.08 0.03
Matches are distributed among these distances:
258 2 0.01
259 96 0.26
265 18 0.05
266 254 0.69
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.25
Consensus pattern (265 bp):
CACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCACCTTTCAAAGCCCACACAAGTTGGTGGCAC
CTTTCAGTCTTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCAGTCTT
CAAAGAGCAGGACTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAG
GACGCTCCCTCCTTTCGCCCTTTAGTCCTCAAACAGCAGGACGCCTTTCAAAGCCCACACAAGTT
GGTGG
Found at i:302951 original size:55 final size:55
Alignment explanation
Indices: 302876--303066 Score: 278
Period size: 55 Copynumber: 3.5 Consensus size: 55
302866 CTCCTTTCTC
302876 CCTTT-AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
302930 CCTTTCAGTCTTCAAATAGCAGGACACCTTTCAAAGCACACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
302985 CCTTTCAGTCCTCAAAGAGCAAGACTCCTTTTAAAGCCCACACAAGTTGGTGGC-
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
303039 GCTTCCTAGTCCTCAAAGAGCAGGACGC
1 CCTTTC-AGTCCTCAAAGAGCAGGACGC
303067 TCCTTTCTTT
Statistics
Matches: 121, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
54 9 0.07
55 112 0.93
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (55 bp):
CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:302953 original size:204 final size:204
Alignment explanation
Indices: 302695--303703 Score: 963
Period size: 204 Copynumber: 4.8 Consensus size: 204
302685 AGGACGCCTT
* *
302695 CGCCTTTCAAAGCCCACACAAGTTGATGGCACCTTTCAGTCTTCAAAAAGCAGGACGCCTTTCAA
1 CGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAAAGCAGGACGCCTTTCAA
* *
302760 ATCCCACACAAGTTGGTGGCACTATTCAGTCTTCAAAGAGCAGGACTCCTTTTAAAGCCCACACA
66 AGCCCACACAAGTTGGTGGCACT-TTCAGTCCTCAAAGAGCAGGACTCCTTTTAAAGCCCACACA
302825 AGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCTCCCTTTAGTCCTCA
130 AGTTGGTGGCACCTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCTCCCTTTAGTCCTCA
302889 AAGAGCAGGA
195 AAGAGCAGGA
* * *
302899 CGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAATAGCAGGACACCTTTCAA
1 CGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAAAGCAGGACGCCTTTCAA
* *
302964 AGCACACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGACTCCTTTTAAAGCCCACACA
66 AGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGACTCCTTTTAAAGCCCACACA
* * * *
303029 AGTTGGTGGC-GCTTCCTAGTCCTCAAAGAGCAGGACGCTC-CTTTCTTTCGCCCTTTATTCCTC
130 AGTTGGTGGCACCTTCCTAGTCCTCAAAGAGCAGGACGCTCTC-TCCTTTCTCCCTTTAGTCCTC
303092 AAAGAGCAGGA
194 AAAGAGCAGGA
* * * *
303103 CGCCTTTTAAAGTCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAAAGCAGAACGCCTTCGC
1 CGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAAAGCAG---G---ACGC
* * *
303168 CTTTCAAAGCCTACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGA-TGCCTTTCAAAG
59 CTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGACT-CCTTTTAAAG
* * * *
303232 CCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACTCCTTTTAAAGCCCACACAA
122 CCCACACAAGTTGGTGGCACCTTCCTAGTCCTCAAAGAGCAGGAC-GC---T----CTCTC-C--
* *
303296 GTTGGTGGT-ACTTCCTAGTCCTCAAAGAGCAGGA
176 -TT--T-CTCCCTT--TAGTCCTCAAAGAGCAGGA
* * * * *
303330 CG-C--T-----CTCTC-C---TT--TCGC-CCTTT-AGTCCTCAAAGAGCAGGACGCCTTTTAA
1 CGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAAAGCAGGACGCCTTTCAA
* * * *
303379 AGCCCACACAAGTCGGTGGCATTTTTCTAGTCCTCAAAGAGTAGGACGCCTTTGCCTTTCAAAGC
66 AGCCCACACAAGTTGGTGGCA-CTTTC-AGTCCTCAAAGAGCAGGA---C--T-CCTTTTAAAGC
* *
303444 CCACACAAGTTGGTGGCACCTT-TTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCACCCTTTA
123 CCACACAAGTTGGTGGCACCTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCTCCCTTTA
303508 GTCCTCAAAGAGCAGGA
188 GTCCTCAAAGAGCAGGA
* *
303525 CGCCTTTCAAAGCCCACACAAGTTGAG-GGCACC-TTCAGTCCTCAAAGAGTAGGACGCCTTCTC
1 CGCCTTTCAAAGCCCACACAAGTTG-GTGGCACCTTTCAGTCCTCAAAAAGCAGGACGCCTT-T-
* *
303588 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGAATGCTTTCTTTTTG
63 C----AAAGCCCACACAAGTTGGTGGCAC-TTTCAGTCCTCAAAGAGCAGGA--C--TCCTTTT-
* * * **
303653 CAAATCCCACACTAGTTGGTGGCATCTTCC-AGTCCTTGAAGAGCAGGACGC
118 -AAAGCCCACACAAGTTGGTGGCACCTTCCTAGTCCTCAAAGAGCAGGACGC
303704 CTTTTCTTTT
Statistics
Matches: 668, Mismatches: 71, Indels: 121
0.78 0.08 0.14
Matches are distributed among these distances:
195 21 0.03
196 1 0.00
197 4 0.01
198 1 0.00
199 2 0.00
202 1 0.00
203 7 0.01
204 255 0.38
205 32 0.05
207 4 0.01
208 1 0.00
209 4 0.01
210 42 0.06
211 151 0.23
212 9 0.01
213 7 0.01
214 4 0.01
215 62 0.09
216 26 0.04
218 1 0.00
219 3 0.00
220 2 0.00
223 2 0.00
224 1 0.00
225 4 0.01
226 1 0.00
227 20 0.03
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (204 bp):
CGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAAAGCAGGACGCCTTTCAA
AGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACTCCTTTTAAAGCCCACACAA
GTTGGTGGCACCTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCTCCCTTTAGTCCTCAA
AGAGCAGGA
Found at i:303094 original size:149 final size:154
Alignment explanation
Indices: 302941--303219 Score: 374
Period size: 149 Copynumber: 1.8 Consensus size: 154
302931 CTTTCAGTCT
* *
302941 TCAAATAGCAGGACACCTTTCAAAG-CACACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAG
1 TCAAAGAGCAGGACACCTTTCAAAGTC-CACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAAAG
* *
303004 C-AA-GAC-T-CCTTTTAAAGCCCACACAAGTTGGTGGC-GCTTCCTAGTCCTCAAAGAGCAGGA
65 CAAACGACTTCCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCC-AGTCCTCAAAGAGCAGGA
303064 CGCTCCTTTCTTTCGCCCTTTATTCC
129 CGCTCCTTTCTTTCGCCCTTTATTCC
* * *
303090 TCAAAGAGCAGGACGCCTTTTAAAGTCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAAAGC
1 TCAAAGAGCAGGACACCTTTCAAAGTCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAAAGC
* * * *
303155 AGAACGCCTTCGCCTTTCAAAGCCTACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGA
66 A-AACGACTTC-CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGA
303220 TGCCTTTCAA
Statistics
Matches: 110, Mismatches: 11, Indels: 11
0.83 0.08 0.08
Matches are distributed among these distances:
149 44 0.40
150 14 0.13
152 2 0.02
153 2 0.02
154 1 0.01
156 43 0.39
157 4 0.04
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (154 bp):
TCAAAGAGCAGGACACCTTTCAAAGTCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAAAGC
AAACGACTTCCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACG
CTCCTTTCTTTCGCCCTTTATTCC
Found at i:303228 original size:266 final size:266
Alignment explanation
Indices: 302899--303486 Score: 989
Period size: 266 Copynumber: 2.2 Consensus size: 266
302889 AAGAGCAGGA
*
302899 CGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAATAGCAGGACACCTTTCAA
1 CGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGACACCTTTCAA
302964 AGCACACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGACTCCTTTTAAAGCCCACACA
66 AGCACACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGACTCCTTTTAAAGCCCACACA
* * *
303029 AGTTGGTGGCGCTTCCTAGTCCTCAAAGAGCAGGACGCTC-CTTTCTTTCGCCCTTTATTCCTCA
131 AGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTC-TCCTTTCGCCCTTTAGTCCTCA
* *
303093 AAGAGCAGGACGCCTTTTAAAGTCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAAAGCAGA
195 AAGAGCAGGACGCCTTTTAAAGCCCACACAAGTCGGTGGCACTTTTCTAGTCCTCAAAAAGCAGA
303158 ACGCCTT
260 ACGCCTT
* **
303165 CGCCTTTCAAAGCCTACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGATGCCTTTCAA
1 CGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGACACCTTTCAA
* *
303230 AGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACTCCTTTTAAAGCCCACACA
66 AGCACACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGACTCCTTTTAAAGCCCACACA
*
303295 AGTTGGTGGTACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCGCCCTTTAGTCCTCAA
131 AGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCGCCCTTTAGTCCTCAA
* * * *
303360 AGAGCAGGACGCCTTTTAAAGCCCACACAAGTCGGTGGCATTTTTCTAGTCCTCAAAGAGTAGGA
196 AGAGCAGGACGCCTTTTAAAGCCCACACAAGTCGGTGGCACTTTTCTAGTCCTCAAAAAGCAGAA
303425 CGCCTT
261 CGCCTT
* * *
303431 TGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGAC
1 CGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGAC
303487 GCTCTCTCCT
Statistics
Matches: 300, Mismatches: 21, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
266 299 1.00
267 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (266 bp):
CGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGACACCTTTCAA
AGCACACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGACTCCTTTTAAAGCCCACACA
AGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCGCCCTTTAGTCCTCAA
AGAGCAGGACGCCTTTTAAAGCCCACACAAGTCGGTGGCACTTTTCTAGTCCTCAAAAAGCAGAA
CGCCTT
Done.