Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold196
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: 7488280
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 125249 characters in sequence are not A, C, G, or T
File 2 of 47
Found at i:164403 original size:11 final size:12
Alignment explanation
Indices: 164368--164439 Score: 76
Period size: 12 Copynumber: 6.1 Consensus size: 12
164358 TTTTTTTATA
*
164368 TTATATCATATT
1 TTATATTATATT
*
164380 TTATATAATATT
1 TTATATTATATT
164392 TTA-ATTATATT
1 TTATATTATATT
164403 TTATATTATA-T
1 TTATATTATATT
* *
164414 TTATAATATATAA
1 TTATATTATAT-T
*
164427 TAATATTATATT
1 TTATATTATATT
164439 T
1 T
164440 AAAATTATCA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
11 20 0.40
12 21 0.42
13 9 0.18
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (12 bp):
TTATATTATATT
Found at i:165116 original size:13 final size:14
Alignment explanation
Indices: 165094--165123 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
165084 CCCCCCACCT
165094 AAAAGAAAAAAGAA
1 AAAAGAAAAAAGAA
165108 AAAAG-AAAAAGAA
1 AAAAGAAAAAAGAA
165121 AAA
1 AAA
165124 GGGCATGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAGAA
Found at i:165124 original size:6 final size:7
Alignment explanation
Indices: 165094--165123 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
165084 CCCCCCACCT
165094 AAAAGAA
1 AAAAGAA
165101 AAAAGAA
1 AAAAGAA
165108 AAAAG-A
1 AAAAGAA
165114 AAAAGAA
1 AAAAGAA
165121 AAA
1 AAA
165124 GGGCATGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:165981 original size:19 final size:18
Alignment explanation
Indices: 165956--166019 Score: 84
Period size: 18 Copynumber: 3.8 Consensus size: 18
165946 TTTCAAACGA
165956 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
165974 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
165990 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
166006 TTTGTATCGATACA
1 TTTGTATCGATACA
166020 ATGTATTGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
18 13 0.32
19 12 0.30
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:165995 original size:13 final size:13
Alignment explanation
Indices: 165977--166025 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 13
165967 ACATAAGTGT
165977 TGTATCGATACAA
1 TGTATCGATACAA
165990 TGTATCGATACATAA
1 TGTATCGATAC--AA
166005 GTTTGTATCGATACAA
1 ---TGTATCGATACAA
166021 TGTAT
1 TGTAT
166026 TGCTACGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 16 0.52
15 2 0.06
16 2 0.06
18 11 0.35
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:166014 original size:31 final size:32
Alignment explanation
Indices: 165958--166025 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 32
165948 TCAAACGATT
165958 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
165990 TGTATCGATACATAAGT-TTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
166021 TGTAT
1 TGTAT
166026 TGCTACGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 19 0.53
32 17 0.47
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:176410 original size:2 final size:2
Alignment explanation
Indices: 176398--176439 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
176388 ATTAAATGGT
* *
176398 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TG TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
176439 T
1 T
176440 CTAAGTTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:181341 original size:3 final size:3
Alignment explanation
Indices: 181333--181423 Score: 86
Period size: 3 Copynumber: 31.7 Consensus size: 3
181323 TAAATATGAT
* *
181333 ATA ATA AT- ATA AT- ATA AAA ATA ATTA A-A ATA TTAA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA AT-A ATA ATA ATA
* *
181376 AAA ATA ATA TTA AT- ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
181422 AT
1 AT
181424 TATTATTATT
Statistics
Matches: 72, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
2 12 0.17
3 55 0.76
4 5 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:181428 original size:3 final size:3
Alignment explanation
Indices: 181422--181447 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
181412 AATAATAATA
181422 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
181448 GTGATTAGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:182772 original size:2 final size:2
Alignment explanation
Indices: 182765--182793 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
182755 AAAAATACCA
182765 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
182794 GGTTATTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:183294 original size:80 final size:80
Alignment explanation
Indices: 183157--183384 Score: 314
Period size: 80 Copynumber: 2.9 Consensus size: 80
183147 GAAAGACAAA
* * *
183157 AAAATAACTCTTCACTTCAATTTAGGGACAG-AGCAAACATAAATGTAAAATTCCTCAACAGCTC
1 AAAATAACTCTCCACTTTAATTTAGGGACAGAAGCAAGCATAAATGTAAAATTCCTCAACAGCTC
*
183221 ATAATCAAATATTAG
66 ATAAGCAAATATTAG
* * * *
183236 AACATAACTCTCCACTTTACTTTAGGGACAGAAGCAAGCATAAATGTAATATTCCTCAATAGCTC
1 AAAATAACTCTCCACTTTAATTTAGGGACAGAAGCAAGCATAAATGTAAAATTCCTCAACAGCTC
*
183301 ATAAGCAAATATTAT
66 ATAAGCAAATATTAG
** * * * *
183316 AAAATAACTCTCCGTTTTAGTTTAGGGAGAAAAGCAAGCATAAATATAAAATTCCTCAACAGCTC
1 AAAATAACTCTCCACTTTAATTTAGGGACAGAAGCAAGCATAAATGTAAAATTCCTCAACAGCTC
183381 ATAA
66 ATAA
183385 CCACACACTC
Statistics
Matches: 130, Mismatches: 18, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
79 27 0.21
80 103 0.79
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.27
Consensus pattern (80 bp):
AAAATAACTCTCCACTTTAATTTAGGGACAGAAGCAAGCATAAATGTAAAATTCCTCAACAGCTC
ATAAGCAAATATTAG
Found at i:185893 original size:142 final size:142
Alignment explanation
Indices: 185637--185915 Score: 549
Period size: 142 Copynumber: 2.0 Consensus size: 142
185627 CTTTTAATCC
185637 CTGTTTCTAGCTTATTGTCTTTCCAATGTTCTAGCAAGTACAATTTAATCAATACTGAATAAAAA
1 CTGTTTCTAGCTTATTGTCTTTCCAATGTTCTAGCAAGTACAATTTAATCAATACTGAATAAAAA
185702 CAGAAGTGCAAATGCTCAAAGGAAACAAGTGATAGAACAAGTCAATAATGAAAGAGAGGAAAGAA
66 CAGAAGTGCAAATGCTCAAAGGAAACAAGTGATAGAACAAGTCAATAATGAAAGAGAGGAAAGAA
185767 AAAAAAAAACTT
131 AAAAAAAAACTT
185779 CTGTTTCTAGCTTATTGTCTTTCCAATGTTCTAGCAAGTACAATTTAATCAATACTGAATAAAAA
1 CTGTTTCTAGCTTATTGTCTTTCCAATGTTCTAGCAAGTACAATTTAATCAATACTGAATAAAAA
*
185844 CAGAAGTGCAAATGCTCAAAGGAAACAAGTGATAGAACAAGTCAGTAATGAAAGAGAGGAAAGAA
66 CAGAAGTGCAAATGCTCAAAGGAAACAAGTGATAGAACAAGTCAATAATGAAAGAGAGGAAAGAA
185909 AAAAAAA
131 AAAAAAA
185916 CTTACTTCTC
Statistics
Matches: 136, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 136 1.00
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.24
Consensus pattern (142 bp):
CTGTTTCTAGCTTATTGTCTTTCCAATGTTCTAGCAAGTACAATTTAATCAATACTGAATAAAAA
CAGAAGTGCAAATGCTCAAAGGAAACAAGTGATAGAACAAGTCAATAATGAAAGAGAGGAAAGAA
AAAAAAAAACTT
Found at i:187773 original size:100 final size:98
Alignment explanation
Indices: 187582--187762 Score: 240
Period size: 100 Copynumber: 1.8 Consensus size: 98
187572 AAGCTAAATA
* * * * *
187582 AATAAATATATTAAAATTTTAATAAAAATTATTAATAAATTAAAATTTATATAAATATATAATAT
1 AATAAACATATTAAAATTTTAAAAAAAATTATTAACAAATCAAAATTTATATAAATATATAATAG
* *
187647 TTTGAATATGATATTAAATAGTAATATGATATG
66 TTTAAATATGATAATAAATAGTAATATGATATG
* *
187680 AATAAACATGTTAAAATTTTTATAAAATAAATTATTAACATATCAAAA-TTATATAAATATATAA
1 AATAAACATATTAAAA-TTTTA-AAAA-AAATTATTAACAAATCAAAATTTATATAAATATATAA
187744 TAGTTTAAATAT-ATAATAA
63 TAGTTTAAATATGATAATAA
187763 TATATAAATA
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
98 14 0.20
99 11 0.15
100 29 0.41
101 17 0.24
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (98 bp):
AATAAACATATTAAAATTTTAAAAAAAATTATTAACAAATCAAAATTTATATAAATATATAATAG
TTTAAATATGATAATAAATAGTAATATGATATG
Found at i:188684 original size:20 final size:20
Alignment explanation
Indices: 188661--188716 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 20
188651 TGATACAAAC
188661 ATATTAACATATTAAAATTT
1 ATATTAACATATTAAAATTT
188681 ATA-TAA-A-A-T-AAA--T
1 ATATTAACATATTAAAATTT
188694 -TATTAACATATTAAAATTT
1 ATATTAACATATTAAAATTT
188713 ATAT
1 ATAT
188717 AAATATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
12 2 0.07
13 4 0.14
14 1 0.04
15 4 0.14
16 2 0.07
17 4 0.14
18 1 0.04
19 4 0.14
20 6 0.21
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATTAACATATTAAAATTT
Found at i:188720 original size:27 final size:29
Alignment explanation
Indices: 188661--188748 Score: 101
Period size: 32 Copynumber: 3.0 Consensus size: 29
188651 TGATACAAAC
188661 ATATTAACATATTAAAATTTATATAAAATAA
1 ATATTAACATATTAAAATTTATAT--AATAA
*
188692 ATTATTAACATATTAAAATTTATATAA-AT
1 A-TATTAACATATTAAAATTTATATAATAA
* *
188721 ATA-TAACATATT-AAATATAAATAATAA
1 ATATTAACATATTAAAATTTATATAATAA
188748 A
1 A
188749 AATATTCAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
26 10 0.20
27 11 0.22
28 2 0.04
29 2 0.04
30 2 0.04
31 1 0.02
32 23 0.45
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (29 bp):
ATATTAACATATTAAAATTTATATAATAA
Found at i:188753 original size:15 final size:14
Alignment explanation
Indices: 188733--188780 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
188723 ATAACATATT
188733 AAATATAAATAATAA
1 AAATATAAA-AATAA
*
188748 AAATATTCAAAATAA
1 AAATA-TAAAAATAA
*
188763 AAAAATAAAAATAA
1 AAATATAAAAATAA
188777 AAAT
1 AAAT
188781 GAAGTAATCC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 11 0.39
15 14 0.50
16 3 0.11
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATATAAAAATAA
Found at i:188753 original size:22 final size:23
Alignment explanation
Indices: 188713--188775 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
188703 ATTAAAATTT
*
188713 ATATAAAT-ATATAACATATT-AA
1 ATATAAATAATA-AAAATATTCAA
188735 ATATAAATAATAAAAATATTCAA
1 ATATAAATAATAAAAATATTCAA
*
188758 A-ATAAAAAAATAAAAATA
1 ATAT-AAATAATAAAAATA
188776 AAAATGAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
22 17 0.47
23 19 0.53
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (23 bp):
ATATAAATAATAAAAATATTCAA
Found at i:197388 original size:3 final size:3
Alignment explanation
Indices: 197380--197434 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
197370 CATCATATCT
197380 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
197428 ATA ATA A
1 ATA ATA A
197435 ATTAATTAGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:197610 original size:36 final size:39
Alignment explanation
Indices: 197533--197610 Score: 108
Period size: 40 Copynumber: 2.1 Consensus size: 39
197523 TTTAAAAGAT
*
197533 TTATTTAATTAAAAAATTAATTAATGATTCAAAATTTTAA
1 TTATTTAATTAAAAAATGAATTAAT-ATTCAAAATTTTAA
*
197573 TTATTTAATTAAAAGATGAA-TAAT-TT-AAAATTTTAA
1 TTATTTAATTAAAAAATGAATTAATATTCAAAATTTTAA
197609 TT
1 TT
197611 TTTCACAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
36 12 0.33
37 2 0.06
39 4 0.11
40 18 0.50
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (39 bp):
TTATTTAATTAAAAAATGAATTAATATTCAAAATTTTAA
Found at i:198225 original size:20 final size:20
Alignment explanation
Indices: 198200--198237 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
198190 GGAGACTTTT
*
198200 TTTTTTTGACAGAATTTTGG
1 TTTTTTTGACAAAATTTTGG
198220 TTTTTTTGACAAAATTTT
1 TTTTTTTGACAAAATTTT
198238 ATTGGGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.05, G:0.13, T:0.58
Consensus pattern (20 bp):
TTTTTTTGACAAAATTTTGG
Found at i:202434 original size:2 final size:2
Alignment explanation
Indices: 202427--202453 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
202417 AAGCGTGCAC
202427 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 A
202454 GTAGCTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:203399 original size:17 final size:19
Alignment explanation
Indices: 203366--203400 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
203356 TCTTAAAAAT
203366 TTAAAATATATTTATATAA
1 TTAAAATATATTTATATAA
203385 TTAAAATA-A-TTATATA
1 TTAAAATATATTTATATA
203401 TTTTAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAAAATATATTTATATAA
Found at i:204883 original size:14 final size:14
Alignment explanation
Indices: 204846--204901 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
204836 AATCATTATT
204846 TATTAATTATAATAA
1 TATTAATTATAA-AA
* *
204861 TATT-TTTATTTAAA
1 TATTAATTA-TAAAA
204875 T-TTAATTATAAAA
1 TATTAATTATAAAA
204888 TATTAATTA-AAAA
1 TATTAATTATAAAA
204901 T
1 T
204902 TTATTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 12 0.35
14 16 0.47
15 6 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATTAATTATAAAA
Found at i:204900 original size:13 final size:13
Alignment explanation
Indices: 204872--204904 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
204862 ATTTTTATTT
204872 AAATTTAATTATA
1 AAATTTAATTATA
204885 AAATATTAATTA-A
1 AAAT-TTAATTATA
204898 AAATTTA
1 AAATTTA
204905 TTTTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 9 0.47
14 7 0.37
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AAATTTAATTATA
Found at i:205396 original size:11 final size:11
Alignment explanation
Indices: 205366--205405 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
205356 AAATCTGATT
*
205366 AAATTGATAAA
1 AAATTAATAAA
205377 AAA-T-A-AAA
1 AAATTAATAAA
205385 AAATTAATAAA
1 AAATTAATAAA
205396 AAATTAATAA
1 AAATTAATAA
205406 TTCAACTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 6 0.23
9 2 0.08
10 2 0.08
11 16 0.62
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (11 bp):
AAATTAATAAA
Found at i:206242 original size:19 final size:20
Alignment explanation
Indices: 206203--206246 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
206193 ATAAATCAAT
*
206203 AATTATTTAAATTGATAAAA
1 AATTAATTAAATTGATAAAA
*
206223 AATTAATTAAATT-TTAAAA
1 AATTAATTAAATTGATAAAA
206242 AATTA
1 AATTA
206247 TTGATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
AATTAATTAAATTGATAAAA
Found at i:206281 original size:20 final size:20
Alignment explanation
Indices: 206245--206282 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
206235 TTTAAAAAAT
206245 TATTGATTTTAAGTTTTTTG
1 TATTGATTTTAAGTTTTTTG
*
206265 TATT-ATTTTAAATTTTTT
1 TATTGATTTTAAGTTTTTT
206283 ATTATATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (20 bp):
TATTGATTTTAAGTTTTTTG
Found at i:206383 original size:16 final size:15
Alignment explanation
Indices: 206359--206409 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
206349 CAAATATATA
*
206359 AATATTTATTATATTT
1 AATAATTATT-TATTT
*
206375 AATACTTATTTAATATT
1 AATAATTATTT-AT-TT
206392 AA-AATTATTTATTT
1 AATAATTATTTATTT
206406 AATA
1 AATA
206410 TTTTAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
14 4 0.13
15 4 0.13
16 18 0.60
17 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
AATAATTATTTATTT
Found at i:206417 original size:20 final size:20
Alignment explanation
Indices: 206361--206424 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
206351 AATATATAAA
* *
206361 TATTTATTATATTTAA-TACT
1 TATTTAATAT-TTTAATTATT
**
206381 TATTTAATATTAAAATTATT
1 TATTTAATATTTTAATTATT
*
206401 TATTTAATATTTTAATTTTT
1 TATTTAATATTTTAATTATT
206421 TATT
1 TATT
206425 ACAATCAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 3 0.08
20 33 0.92
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTAATATTTTAATTATT
Found at i:212910 original size:20 final size:20
Alignment explanation
Indices: 212859--212926 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
212849 TTTAAAAGAT
*
212859 TTATTTAATTAAAAAATTAA
1 TTATTTAATTAAAAGATTAA
* * * *
212879 TTAATGATTTAAAAGTTTAA
1 TTATTTAATTAAAAGATTAA
*
212899 TTATTTAATTAAAAGATAAA
1 TTATTTAATTAAAAGATTAA
*
212919 TAATTTAA
1 TTATTTAA
212927 AATTTCAATT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (20 bp):
TTATTTAATTAAAAGATTAA
Found at i:213573 original size:20 final size:20
Alignment explanation
Indices: 213538--213575 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
213528 TGGAGACCTT
*
213538 TTTTTTTGACAGAATTTTGG
1 TTTTTTTGACAAAATTTTGG
*
213558 TTTTTTTGATAAAATTTT
1 TTTTTTTGACAAAATTTT
213576 ATTGGGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.13, T:0.61
Consensus pattern (20 bp):
TTTTTTTGACAAAATTTTGG
Found at i:214069 original size:20 final size:20
Alignment explanation
Indices: 214032--214070 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
214022 GTTGAAAAGA
*
214032 CTAGAATTTCATCGAAAATG
1 CTAGAATTTCATCAAAAATG
*
214052 CTAGAATTTCATTAAAAAT
1 CTAGAATTTCATCAAAAAT
214071 ACAAAATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (20 bp):
CTAGAATTTCATCAAAAATG
Found at i:214357 original size:8 final size:8
Alignment explanation
Indices: 214338--214377 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
214328 TCATTTTTTT
214338 AATATA-A
1 AATATATA
214345 AATATATA
1 AATATATA
214353 AATATATA
1 AATATATA
214361 AA-A-ATA
1 AATATATA
*
214367 AATATTTA
1 AATATATA
214375 AAT
1 AAT
214378 TTAAAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
6 5 0.17
7 8 0.28
8 16 0.55
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AATATATA
Found at i:228913 original size:2 final size:2
Alignment explanation
Indices: 228908--228935 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
228898 TGTTTTTTTA
228908 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
228936 TCGTTTTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:231014 original size:19 final size:21
Alignment explanation
Indices: 230973--231019 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
230963 ACGCATTAAA
230973 ATTTATATAAAAATATAATAT
1 ATTTATATAAAAATATAATAT
*
230994 ATTTATATAAATATATAATAT
1 ATTTATATAAAAATATAATAT
*
231015 TTTTA
1 ATTTA
231020 ATACAGTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTTATATAAAAATATAATAT
Found at i:231336 original size:2 final size:2
Alignment explanation
Indices: 231329--231366 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
231319 GCATGGAAGA
231329 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
231367 GTTTACCCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:231452 original size:3 final size:3
Alignment explanation
Indices: 231444--231478 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
231434 GTTAAAAGAC
231444 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
231479 ATAGATATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:232205 original size:20 final size:20
Alignment explanation
Indices: 232180--232218 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
232170 TCATGTTTTA
232180 TTTAATAATTAAAAA-ATATT
1 TTTAATAA-TAAAAATATATT
*
232200 TTTAATTATAAAAATATAT
1 TTTAATAATAAAAATATAT
232219 AAATATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTAATAATAAAAATATATT
Found at i:239836 original size:18 final size:17
Alignment explanation
Indices: 239813--239857 Score: 58
Period size: 15 Copynumber: 2.7 Consensus size: 17
239803 TCCTATCAGA
239813 TATAATTTATATAATTTT
1 TATAATTTATAT-ATTTT
239831 TATAA--TATATATTTT
1 TATAATTTATATATTTT
*
239846 TATTATTTATAT
1 TATAATTTATAT
239858 TATGTTGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 9 0.38
16 5 0.21
17 5 0.21
18 5 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATAATTTATATATTTT
Found at i:243320 original size:83 final size:84
Alignment explanation
Indices: 243158--243330 Score: 208
Period size: 83 Copynumber: 2.1 Consensus size: 84
243148 ACTATATAAT
* * * *
243158 ATTTACAATCAATCAACTTTTCTCATTTTCTACCATAAGGAAATCAATTCTTAAATATAATCTAT
1 ATTTACAATCAATCAACTTTTCTCATTTTCTACCAAAAGGAAATCAATACTAAAAAATAATCTAT
**
243223 GCATTAATCTAATCCTTAGC
66 AAATTAATCTAATCCTT-GC
* * *
243243 ATTTACAATCAATCAACTTTT-T-TTTTTCTATCAAAAGG-AATCCAATACTAAAAAATAATTTA
1 ATTTACAATCAATCAACTTTTCTCATTTTCTACCAAAAGGAAAT-CAATACTAAAAAATAATCTA
*
243305 TAAATTAGTCTAATCCTTGC
65 TAAATTAATCTAATCCTTGC
243325 ACTTTA
1 A-TTTA
243331 ACATTTACAA
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
82 6 0.08
83 48 0.63
84 1 0.01
85 21 0.28
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.39
Consensus pattern (84 bp):
ATTTACAATCAATCAACTTTTCTCATTTTCTACCAAAAGGAAATCAATACTAAAAAATAATCTAT
AAATTAATCTAATCCTTGC
Found at i:250398 original size:2 final size:2
Alignment explanation
Indices: 250391--250438 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
250381 TTTTAAACGA
250391 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
250433 AT AT AT
1 AT AT AT
250439 CAGGCAAACC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:250700 original size:20 final size:20
Alignment explanation
Indices: 250677--250717 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
250667 TTATATTTAA
*
250677 TACTTATTTAATATTAAAAT
1 TACTTATTTAACATTAAAAT
* *
250697 TACTTGTTTAACATTTAAAT
1 TACTTATTTAACATTAAAAT
250717 T
1 T
250718 TTTTTAATAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.51
Consensus pattern (20 bp):
TACTTATTTAACATTAAAAT
Found at i:253335 original size:16 final size:17
Alignment explanation
Indices: 253305--253338 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
253295 TTTAATTATT
*
253305 TAATAATTAATATTAAA
1 TAATAATTAAAATTAAA
253322 TAAT-ATTAAAATTAAA
1 TAATAATTAAAATTAAA
253338 T
1 T
253339 TAAATTAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATAATTAAAATTAAA
Found at i:253343 original size:10 final size:11
Alignment explanation
Indices: 253309--253345 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
253299 ATTATTTAAT
253309 AATTAATATTA
1 AATTAATATTA
253320 AA-TAATATTAA
1 AATTAATATT-A
253331 AATTAA-ATTA
1 AATTAATATTA
253341 AATTA
1 AATTA
253346 GTTTTAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 13 0.54
11 8 0.33
12 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AATTAATATTA
Found at i:253786 original size:20 final size:20
Alignment explanation
Indices: 253749--253788 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
253739 AATTAATGAT
* * *
253749 TTAAAAGTTTAATTATTTAA
1 TTAAAAGGTAAATAATTTAA
253769 TTAAAAGGTAAATAATTTAA
1 TTAAAAGGTAAATAATTTAA
253789 AAATTCAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (20 bp):
TTAAAAGGTAAATAATTTAA
Found at i:255952 original size:23 final size:24
Alignment explanation
Indices: 255904--255953 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 24
255894 ATATTTTTTA
* *
255904 TTTTTTAAAACAAATAAAGATCAT
1 TTTTTTAAAACAAATAAACATAAT
*
255928 TTTTTTAAAA-AAA-AAACATAAA
1 TTTTTTAAAACAAATAAACATAAT
255950 TTTT
1 TTTT
255954 GAACTTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 10 0.43
23 3 0.13
24 10 0.43
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (24 bp):
TTTTTTAAAACAAATAAACATAAT
Found at i:256693 original size:21 final size:21
Alignment explanation
Indices: 256668--256714 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
256658 CGACCTCCTC
*
256668 TTTTCAAATCAGGAATTCGAT
1 TTTTCAAATCAGGAATTAGAT
*
256689 TTTTCAAATCCGGAATTAGAT
1 TTTTCAAATCAGGAATTAGAT
256710 TTTTC
1 TTTTC
256715 TAGATCTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (21 bp):
TTTTCAAATCAGGAATTAGAT
Found at i:257663 original size:49 final size:45
Alignment explanation
Indices: 257610--257711 Score: 107
Period size: 45 Copynumber: 2.2 Consensus size: 45
257600 CAAGGTCAAT
*
257610 GACATCGGGCTAAAGGAAAAGTGGACCAATGTGCTGACTT-AAGGCCAGC
1 GACATCGGGCT-AA-GAAAAGT-G-CCAATATGCTGA-TTCAAGGCCAGC
* * *
257659 GACATTGGGCTTAGAAAGGTGCCAATATGCTGATTCAAGGCCAGC
1 GACATCGGGCTAAGAAAAGTGCCAATATGCTGATTCAAGGCCAGC
*
257704 GATATCGG
1 GACATCGG
257712 ACTTTAAGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
44 2 0.04
45 26 0.57
46 1 0.02
47 6 0.13
48 1 0.02
49 10 0.22
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (45 bp):
GACATCGGGCTAAGAAAAGTGCCAATATGCTGATTCAAGGCCAGC
Found at i:257859 original size:64 final size:64
Alignment explanation
Indices: 257736--258337 Score: 734
Period size: 64 Copynumber: 9.6 Consensus size: 64
257726 AAAATGGTGA
* * * * * * * * ** *
257736 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGTTTTTAAAAGGGTTTCCATCGA-AAGTGTGGAC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
* * *
257799 TTTTGAAA-GAGGTT-CCAATCAACTTGTGTGGGC-TTAAAAAAGGTTGCCACCGACTTGTGTGG
1 -TTTGAAATG-GGTTGCC-ACCGACTTGTGTGGGCTTTGAAAAAGGTTGCCACCGACTTGTGTGG
257861 GC
63 GC
* ** * *
257863 TTTGAAATGGATTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTACCACCGATTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
* * * *
257927 TTTGAAATGGGTTGCTATCAATTTGTGTGGGCTTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
**
257991 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
* * * *
258055 TTTGAAATAGGTTGCCATCGACTTGTGTGGGCTTTGAAATAGGTTGCCACCGACTTATGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
* *
258119 TTTGAAAT-GG-TGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCAACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
*
258181 TTTAAAATGGGTTGCCACCGACTTGTGTGGGCTTT-AAAATA-G-TGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAA-AGGTTGCCACCGACTTGTGTGGGC
* *
258243 TTTGAAAT-GG-TGCCACCGACCTGTGTGGGCTTT-AAAATGG-TGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
*
258303 TTTGAAAT-GG-TGCCACTGAC-T-TGTGGGCTTTGAAA
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAA
258338 TAGTGCCACA
Statistics
Matches: 476, Mismatches: 51, Indels: 27
0.86 0.09 0.05
Matches are distributed among these distances:
58 10 0.02
59 4 0.01
60 66 0.14
61 2 0.00
62 80 0.17
63 52 0.11
64 262 0.55
ACGTcount: A:0.20, C:0.17, G:0.31, T:0.31
Consensus pattern (64 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
Found at i:257883 original size:32 final size:31
Alignment explanation
Indices: 257820--258352 Score: 722
Period size: 32 Copynumber: 17.1 Consensus size: 31
257810 GTTCCAATCA
** *
257820 ACTTGTGTGGGCTTAAAAAAGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAATGGTTGCCACCG
257851 ACTTGTGTGGGCTTTGAAATGGATTGCCACCG
1 ACTTGTGTGGGCTTTGAAATGG-TTGCCACCG
*
257883 ACTTGTGTGGGCTTTGAAATGGGTTACCACCG
1 ACTTGTGTGGGCTTTGAAAT-GGTTGCCACCG
* * * *
257915 ATTTGTGTGGGCTTTGAAATGGGTTGCTATCA
1 ACTTGTGTGGGCTTTGAAAT-GGTTGCCACCG
* *
257947 ATTTGTGTGGGCTTTGAAAAAGGTTGCCACCG
1 ACTTGTGTGGGCTTTG-AAATGGTTGCCACCG
257979 ACTTGTGTGGGCTTTGAAATGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAAT-GGTTGCCACCG
258011 ACTTGTGTGGGCTTTGAAATGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAAT-GGTTGCCACCG
*
258043 ACTTGTGTGGGCTTTGAAATAGGTTGCCATCG
1 ACTTGTGTGGGCTTTGAAAT-GGTTGCCACCG
258075 ACTTGTGTGGGCTTTGAAATAGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAAT-GGTTGCCACCG
*
258107 ACTTATGTGGGCTTTGAAATGG-TGCCACCG
1 ACTTGTGTGGGCTTTGAAATGGTTGCCACCG
* *
258137 ACTTGTGTGGGCTTTGAAAAGGGTTGCCACCA
1 ACTTGTGTGGGCTTTG-AAATGGTTGCCACCG
*
258169 ACTTGTGTGGGCTTTAAAATGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAAT-GGTTGCCACCG
* *
258201 ACTTGTGTGGGCTTTAAAATAG-TGCCACCG
1 ACTTGTGTGGGCTTTGAAATGGTTGCCACCG
258231 ACTTGTGTGGGCTTTGAAATGG-TGCCACCG
1 ACTTGTGTGGGCTTTGAAATGGTTGCCACCG
* *
258261 ACCTGTGTGGGCTTTAAAATGG-TGCCACCG
1 ACTTGTGTGGGCTTTGAAATGGTTGCCACCG
*
258291 ACTTGTGTGGGCTTTGAAATGG-TGCCACTG
1 ACTTGTGTGGGCTTTGAAATGGTTGCCACCG
* *
258321 AC-T-TGTGGGCTTTGAAATAG-TGCCACAG
1 ACTTGTGTGGGCTTTGAAATGGTTGCCACCG
258349 ACTT
1 ACTT
258353 ATGGACTTAA
Statistics
Matches: 459, Mismatches: 35, Indels: 18
0.90 0.07 0.04
Matches are distributed among these distances:
28 25 0.05
29 2 0.00
30 116 0.25
31 33 0.07
32 278 0.61
33 5 0.01
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (31 bp):
ACTTGTGTGGGCTTTGAAATGGTTGCCACCG
Found at i:258432 original size:27 final size:27
Alignment explanation
Indices: 258340--259702 Score: 1997
Period size: 27 Copynumber: 49.8 Consensus size: 27
258330 CTTTGAAATA
* * * *
258340 GTGCCACAGACTTATGGACTTAAAAAGA
1 GTGCCACGGAGTTGTGGACTT-AAAAGG
* *
258368 GTGCCACGAAGTTGTGAACTTAAAAGGG
1 GTGCCACGGAGTTGTGGACTTAAAA-GG
258396 GTGCCACGGAGTTGTGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
*
258423 GTACCACGGAGTTGTGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
*
258450 GTGCCACGGAGTTGTGGACTTAGAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
*
258477 GTGCCACGGAGTTGTAGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
258504 GTGCCACGGAGTTGTGGACTTTAAAAGG
1 GTGCCACGGAGTTGTGGAC-TTAAAAGG
258532 GTGCCACGGAGTTGTGGACTTAAAAAGG
1 GTGCCACGGAGTTGTGGACTT-AAAAGG
* *
258560 ATGCCATGGAGTTGTGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
258587 GTGCCACGGAGTTGTGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
258614 GATGCCACGGAGTTGTGGACTTAAAAGG
1 G-TGCCACGGAGTTGTGGACTTAAAAGG
* *
258642 GATGCCACAGAGTTGTGGACTTAAGAGG
1 G-TGCCACGGAGTTGTGGACTTAAAAGG
*
258670 ATGCCACGGAGTTGTGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
* *
258697 ATGCCACAGAGTTGTGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
258724 GTGCCACGGAGTTGTGGACTTTAAAAGG
1 GTGCCACGGAGTTGTGGAC-TTAAAAGG
*
258752 GTGCCACAGAGTTGTGGACTTTAAAAGG
1 GTGCCACGGAGTTGTGGAC-TTAAAAGG
*
258780 GTGCGACGGAGTTGTGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
* *
258807 GTGCCACAGAGTTGTGGACTTAAAAAG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
* *
258834 GTGCCACAGAGTTGTGGACTTTAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
*
258861 GTGCCACAGAGTTGTGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
* *
258888 GTGCCACGGAGTTGTAGACTTAAAAGA
1 GTGCCACGGAGTTGTGGACTTAAAAGG
* *
258915 GTACCACGGAGTTATGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
*
258942 GTGCCACGGAGTTATGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
*
258969 GTGCCACGGAGTTATGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
* **
258996 GTGCAACAAAGTTGTGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
259023 GTGCCACGGAGTTGTGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
* *
259050 GTGCCACAGAGTTGTGGACTTAAAAGA
1 GTGCCACGGAGTTGTGGACTTAAAAGG
*
259077 GTGCCACGGAGTTGTGGACTTAAATGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
*
259104 GTGCCACGGAGTTGTGGTCTTTAAAAGG
1 GTGCCACGGAGTTGTGGAC-TTAAAAGG
259132 GTGCCACGGAGTTGTGGACTTCAAAAGG
1 GTGCCACGGAGTTGTGGACTT-AAAAGG
*
259160 GTGCAACGGAGTTGTGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
* *
259187 GTGCCACGGAGTTATAGACTTTAAAAGG
1 GTGCCACGGAGTTGTGGAC-TTAAAAGG
*
259215 GATGCCACGAAGTTGTGGACTTAAAAGG
1 G-TGCCACGGAGTTGTGGACTTAAAAGG
* *
259243 GTGCCACAGAGTTGTGGACTTTAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
* *
259270 GTGCCCCGGAGTTGTGGACTTTAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
259297 GTGCCACGGAGTTGTGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
*
259324 GTGCCACGGAGTTGTGGACTTAAAAGA
1 GTGCCACGGAGTTGTGGACTTAAAAGG
* *
259351 GTGCCATGGAGTTATGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
*
259378 GTGCCACGGAGTTATGGACTTTAAAAGG
1 GTGCCACGGAGTTGTGGAC-TTAAAAGG
* *
259406 GTGCAACAGAGTTGTGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
**
259433 GTGCCATTGAGTTGTGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
259460 GTGCCACGGAGTTGTGGACTTTAAAAGG
1 GTGCCACGGAGTTGTGGAC-TTAAAAGG
* ***
259488 GTGTCGTAGAGTTGTGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
259515 GATGCCACGGAGTTGTGGACTTAAAAGG
1 G-TGCCACGGAGTTGTGGACTTAAAAGG
259543 GTGCCACGGAGTTGTGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
259570 GATGCCACGGAGTTGTGGACTTAAAAGG
1 G-TGCCACGGAGTTGTGGACTTAAAAGG
*
259598 GATGCCACGGAGTTGTGGACTTAAAAGA
1 G-TGCCACGGAGTTGTGGACTTAAAAGG
* *
259626 ATGCCACGGAGTTTTGGACTTTAAAAGG
1 GTGCCACGGAGTTGTGGAC-TTAAAAGG
* * *
259654 ATACCACGAAGTTGTGGACTCTAAAAGG
1 GTGCCACGGAGTTGTGGACT-TAAAAGG
259682 GTGCCACGGAGTTGTGGACTT
1 GTGCCACGGAGTTGTGGACTT
259703 TAGAGAGGTC
Statistics
Matches: 1217, Mismatches: 103, Indels: 31
0.90 0.08 0.02
Matches are distributed among these distances:
27 767 0.63
28 435 0.36
29 15 0.01
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (27 bp):
GTGCCACGGAGTTGTGGACTTAAAAGG
Found at i:258592 original size:83 final size:81
Alignment explanation
Indices: 258340--259702 Score: 1997
Period size: 83 Copynumber: 16.6 Consensus size: 81
258330 CTTTGAAATA
* * * * * *
258340 GTGCCACAGACTTATGGACTTAAAAAGAGTGCCACGAAGTTGTGAACTTAAAAGGGGTGCCACGG
1 GTGCCACGGAGTTGTGGACTT-AAAAGGGTGCCACGGAGTTGTGGACTTAAAA-GGGTGCCACGG
258405 AGTTGTGGACTTAAAAGG
64 AGTTGTGGACTTAAAAGG
* *
258423 GTACCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGGTGCCACGGAG
1 GTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
*
258488 TTGTAGACTTAAAAGG
66 TTGTGGACTTAAAAGG
* *
258504 GTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAAGGATGCCATGG
1 GTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTT-AAAAGGGTGCCACGG
258569 AGTTGTGGACTTAAAAGG
64 AGTTGTGGACTTAAAAGG
*
258587 GTGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACAG
1 GTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGG
*
258652 AGTTGTGGACTTAAGAGG
64 AGTTGTGGACTTAAAAGG
* * *
258670 ATGCCACGGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
1 GTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
258735 TTGTGGACTTTAAAAGG
66 TTGTGGAC-TTAAAAGG
* * *
258752 GTGCCACAGAGTTGTGGACTTTAAAAGGGTGCGACGGAGTTGTGGACTTAAAAGGGTGCCACAGA
1 GTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGA
*
258817 GTTGTGGACTTAAAAAG
65 GTTGTGGACTTAAAAGG
* * *
258834 GTGCCACAGAGTTGTGGACTTTAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
1 GTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
* *
258899 TTGTAGACTTAAAAGA
66 TTGTGGACTTAAAAGG
* * *
258915 GTACCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAG
1 GTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
*
258980 TTATGGACTTAAAAGG
66 TTGTGGACTTAAAAGG
* ** *
258996 GTGCAACAAAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAG
1 GTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
*
259061 TTGTGGACTTAAAAGA
66 TTGTGGACTTAAAAGG
* *
259077 GTGCCACGGAGTTGTGGACTTAAATGGGTGCCACGGAGTTGTGGTCTTTAAAAGGGTGCCACGGA
1 GTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGA
259142 GTTGTGGACTTCAAAAGG
65 GTTGTGGACTT-AAAAGG
* * * *
259160 GTGCAACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTATAGACTTTAAAAGGGATGCCACGA
1 GTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGG-TGCCACGG
259225 AGTTGTGGACTTAAAAGG
64 AGTTGTGGACTTAAAAGG
* * * *
259243 GTGCCACAGAGTTGTGGACTTTAAAGGGTGCCCCGGAGTTGTGGACTTTAAAGGGTGCCACGGAG
1 GTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
259308 TTGTGGACTTAAAAGG
66 TTGTGGACTTAAAAGG
* * *
259324 GTGCCACGGAGTTGTGGACTTAAAAGAGTGCCATGGAGTTATGGACTTAAAAGGGTGCCACGGAG
1 GTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
*
259389 TTATGGACTTTAAAAGG
66 TTGTGGAC-TTAAAAGG
* * **
259406 GTGCAACAGAGTTGTGGACTTAAAAGGGTGCCATTGAGTTGTGGACTTAAAAGGGTGCCACGGAG
1 GTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
259471 TTGTGGACTTTAAAAGG
66 TTGTGGAC-TTAAAAGG
* ***
259488 GTGTCGTAGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGA
1 GTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGA
259553 GTTGTGGACTTAAAAGG
65 GTTGTGGACTTAAAAGG
**
259570 GATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGAATGCCACGG
1 G-TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
*
259635 AGTTTTGGACTTTAAAAGG
64 AGTTGTGGAC-TTAAAAGG
* * *
259654 ATACCACGAAGTTGTGGACTCTAAAAGGGTGCCACGGAGTTGTGGACTT
1 GTGCCACGGAGTTGTGGACT-TAAAAGGGTGCCACGGAGTTGTGGACTT
259703 TAGAGAGGTC
Statistics
Matches: 1160, Mismatches: 106, Indels: 28
0.90 0.08 0.02
Matches are distributed among these distances:
81 393 0.34
82 300 0.26
83 432 0.37
84 35 0.03
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (81 bp):
GTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
TTGTGGACTTAAAAGG
Found at i:267084 original size:8 final size:8
Alignment explanation
Indices: 267071--267103 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
267061 CCATTTCATA
267071 TTTTTTTC
1 TTTTTTTC
267079 TTTTTTT-
1 TTTTTTTC
*
267086 TCTTTTTC
1 TTTTTTTC
267094 TTTTTTTC
1 TTTTTTTC
267102 TT
1 TT
267104 CTTCATCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTC
Found at i:269354 original size:50 final size:50
Alignment explanation
Indices: 269272--269560 Score: 380
Period size: 50 Copynumber: 5.8 Consensus size: 50
269262 ATATACTTAG
* * * * *
269272 CGTCAACAATTACGGTCACCTTTCTTTCTTGTCAAAGGTCGGTGAAGAAT
1 CGTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
* * *
269322 CGTCAACAATTATGACCACCTCTCTCTATTGTCAAAAGTTGGTGAAGAAT
1 CGTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
* * * *
269372 CATCAACAATAATGGCCAACTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
1 CGTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
* *
269422 CGTCAACAATTACGGTCACATCTCTCTATTGTCAAAGGTTGGTGAAGAAT
1 CGTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
* * * * * *
269472 CGTCAACAATTATGGCTATCTCTCTCTATTATCAAAAGTTAGTGAAGAAT
1 CGTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
* *
269522 CGTCAATAATTACGACCACCTCTCTCTATTGTCAAAGGT
1 CGTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGT
269561 ACTTTCCACC
Statistics
Matches: 205, Mismatches: 34, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 205 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (50 bp):
CGTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
Found at i:269545 original size:150 final size:150
Alignment explanation
Indices: 269272--269560 Score: 434
Period size: 150 Copynumber: 1.9 Consensus size: 150
269262 ATATACTTAG
* * * *
269272 CGTCAACAATTACGGTCACCTTTCTTTCTTGTCAAAGGTCGGTGAAGAATCGTCAACAATTATGA
1 CGTCAACAATTACGGTCACATCTCTCTATTGTCAAAGGTCGGTGAAGAATCGTCAACAATTATGA
* * * *
269337 CCACCTCTCTCTATTGTCAAAAGTTGGTGAAGAATCATCAACAATAATGGCCAACTCTCTCTATT
66 CCACCTCTCTCTATTATCAAAAGTTAGTGAAGAATCATCAACAATAACGACCAACTCTCTCTATT
269402 GTCAAAGGTTGGTGAAGAAT
131 GTCAAAGGTTGGTGAAGAAT
* *
269422 CGTCAACAATTACGGTCACATCTCTCTATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGG
1 CGTCAACAATTACGGTCACATCTCTCTATTGTCAAAGGTCGGTGAAGAATCGTCAACAATTATGA
* * * * * *
269487 CTATCTCTCTCTATTATCAAAAGTTAGTGAAGAATCGTCAATAATTACGACCACCTCTCTCTATT
66 CCACCTCTCTCTATTATCAAAAGTTAGTGAAGAATCATCAACAATAACGACCAACTCTCTCTATT
269552 GTCAAAGGT
131 GTCAAAGGT
269561 ACTTTCCACC
Statistics
Matches: 123, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
150 123 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (150 bp):
CGTCAACAATTACGGTCACATCTCTCTATTGTCAAAGGTCGGTGAAGAATCGTCAACAATTATGA
CCACCTCTCTCTATTATCAAAAGTTAGTGAAGAATCATCAACAATAACGACCAACTCTCTCTATT
GTCAAAGGTTGGTGAAGAAT
Found at i:270048 original size:17 final size:16
Alignment explanation
Indices: 270006--270049 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
269996 ATTTAGTACG
270006 AAGGAA-GAAAAATAA
1 AAGGAATGAAAAATAA
270021 AAGGAAGTGAAAAATAA
1 AAGGAA-TGAAAAATAA
270038 AAGGGAATGAAA
1 AA-GGAATGAAA
270050 GTTATCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.23
17 16 0.62
18 4 0.15
ACGTcount: A:0.66, C:0.00, G:0.25, T:0.09
Consensus pattern (16 bp):
AAGGAATGAAAAATAA
Found at i:271557 original size:16 final size:16
Alignment explanation
Indices: 271505--271562 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
271495 AATCTAATTT
*
271505 TTTTAAATTTATATAA
1 TTTTAAATATATATAA
*
271521 -TATAAAT-TAT-TAA
1 TTTTAAATATATATAA
271534 TATATTAAATATATATAA
1 T-T-TTAAATATATATAA
271552 TTTTAAATATA
1 TTTTAAATATA
271563 ATCATAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
13 3 0.09
14 3 0.09
15 7 0.20
16 14 0.40
17 4 0.11
18 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTAAATATATATAA
Found at i:271572 original size:25 final size:23
Alignment explanation
Indices: 271505--271574 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 23
271495 AATCTAATTT
*
271505 TTTTAAAT-TTATATAATATAAA
1 TTTTAAATATAATATAATATAAA
271527 TTATTAATATATTAA-AT-ATATATAA
1 TT-TTAA-ATA-TAATATAATATA-AA
271552 TTTTAAATATAATCATAATATAA
1 TTTTAAATATAAT-ATAATATAA
271575 TAAAATATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
22 5 0.13
23 7 0.18
24 14 0.36
25 11 0.28
26 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTTAAATATAATATAATATAAA
Found at i:271808 original size:69 final size:69
Alignment explanation
Indices: 271731--271868 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
271721 CCACACTCTC
* *
271731 TCCTCCATCATCCTTATGTCCTTAACTCTTTCTCTCTCCAATGAAACTATCATGCAGTCAATCCT
1 TCCTCCATCATCCTTATGTCCTTAACTCTTTCTCTCTCCAATGAAACTATCACGCAATCAATCCT
271796 AGGT
66 AGGT
*
271800 TCCTCCATCATCCTTTTGTCCTTAACTCTTTCTCTCTCCAATGAAACTATCACGCAATCAATCCT
1 TCCTCCATCATCCTTATGTCCTTAACTCTTTCTCTCTCCAATGAAACTATCACGCAATCAATCCT
271865 AGGT
66 AGGT
271869 CAACCAGCTT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.23, C:0.33, G:0.08, T:0.36
Consensus pattern (69 bp):
TCCTCCATCATCCTTATGTCCTTAACTCTTTCTCTCTCCAATGAAACTATCACGCAATCAATCCT
AGGT
Found at i:272255 original size:3 final size:3
Alignment explanation
Indices: 272247--272276 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
272237 TATAAATTTA
*
272247 ATT ATT ATT ATT ATT ATT ATT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
272277 TGTTATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:272935 original size:22 final size:23
Alignment explanation
Indices: 272887--272935 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
272877 TTCTTCTATG
* * * *
272887 TTTTTCTTTTTTTTTTCCTTCAC
1 TTTTTCTCTTTTCTTTCATCCAC
272910 TTTTTCTCTTTTCTTTCATCCA-
1 TTTTTCTCTTTTCTTTCATCCAC
272932 TTTT
1 TTTT
272936 ATATAAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTTCTCTTTTCTTTCATCCAC
Found at i:274144 original size:18 final size:19
Alignment explanation
Indices: 274121--274184 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 19
274111 TTTTGAATAT
274121 AATATAA-AAAATAATAAA
1 AATATAAGAAAATAATAAA
*
274139 AATATAATACAAATTAA-AAA
1 AATATAAGA-AAA-TAATAAA
*
274159 AATATGAAGAAGAT-ATAAA
1 AATAT-AAGAAAATAATAAA
*
274178 TATATAA
1 AATATAA
274185 ACGTGTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
18 10 0.26
19 9 0.24
20 13 0.34
21 6 0.16
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.25
Consensus pattern (19 bp):
AATATAAGAAAATAATAAA
Found at i:274236 original size:19 final size:21
Alignment explanation
Indices: 274195--274241 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
274185 ACGTGTTAAA
*
274195 ATTTATATAAAAATGTAATAT
1 ATTTATATAAAAATATAATAT
*
274216 ATTTATATAAATATATAATAT
1 ATTTATATAAAAATATAATAT
*
274237 CTTTA
1 ATTTA
274242 GTACAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
ATTTATATAAAAATATAATAT
Found at i:274648 original size:3 final size:3
Alignment explanation
Indices: 274640--274701 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
274630 GTTAAAAGAC
274640 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
274688 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
274702 AAGTATATAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:276045 original size:16 final size:16
Alignment explanation
Indices: 276026--276083 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
276016 AAAAGTTAAA
*
276026 AACTCAAACTTGAAAG
1 AACTCAAACCTGAAAG
*
276042 AACTCAAACCTGAAAA
1 AACTCAAACCTGAAAG
* * *
276058 AACCCGAATCT-AAGAG
1 AACTCAAACCTGAA-AG
276074 AACTCAAACC
1 AACTCAAACC
276084 CAAATTTAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 2 0.06
16 30 0.94
ACGTcount: A:0.50, C:0.26, G:0.10, T:0.14
Consensus pattern (16 bp):
AACTCAAACCTGAAAG
Found at i:276257 original size:22 final size:22
Alignment explanation
Indices: 276232--276274 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
276222 GAAATAGTAA
276232 TTTATCAAAA-AGTAAATTATAC
1 TTTAT-AAAATAGTAAATTATAC
*
276254 TTTATAAAATATTAAATTATA
1 TTTATAAAATAGTAAATTATA
276275 TCATGAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (22 bp):
TTTATAAAATAGTAAATTATAC
Found at i:277216 original size:20 final size:19
Alignment explanation
Indices: 277182--277219 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
277172 TTAAAAATTA
*
277182 ATTTTATATATAAATATAG
1 ATTTTATAAATAAATATAG
277201 ATTTTAATAAATAAATATA
1 ATTTT-ATAAATAAATATA
277220 TTAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
ATTTTATAAATAAATATAG
Found at i:277388 original size:16 final size:16
Alignment explanation
Indices: 277367--277443 Score: 66
Period size: 16 Copynumber: 4.8 Consensus size: 16
277357 AAATCGACTT
*
277367 GAACTCGAAAAAGTTC
1 GAACTCGAAAAAGCTC
*
277383 GAACTCGAAAAGGCTC
1 GAACTCGAAAAAGCTC
* * *
277399 GAACTTGACAATGCTC
1 GAACTCGAAAAAGCTC
* * *
277415 AAACTCGAATAGGC-C
1 GAACTCGAAAAAGCTC
277430 TGAACTCGAAAAAG
1 -GAACTCGAAAAAG
277444 ACCCAATCTG
Statistics
Matches: 47, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
15 1 0.02
16 46 0.98
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (16 bp):
GAACTCGAAAAAGCTC
Found at i:277403 original size:32 final size:32
Alignment explanation
Indices: 277366--277443 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
277356 GAAATCGACT
* *
277366 TGAACTCGAAAAAGTTCGAACTCGAAAAGG-C
1 TGAACTCGAAAAAGCTCAAACTCGAAAAGGCC
* * * *
277397 TCGAACTTGACAATGCTCAAACTCGAATAGGCC
1 T-GAACTCGAAAAAGCTCAAACTCGAAAAGGCC
277430 TGAACTCGAAAAAG
1 TGAACTCGAAAAAG
277444 ACCCAATCTG
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
31 1 0.03
32 33 0.92
33 2 0.06
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.18
Consensus pattern (32 bp):
TGAACTCGAAAAAGCTCAAACTCGAAAAGGCC
Found at i:277799 original size:3 final size:3
Alignment explanation
Indices: 277791--277819 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
277781 AGCAGTAATT
277791 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
277820 GCTTTTGGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:283825 original size:38 final size:38
Alignment explanation
Indices: 283771--283861 Score: 119
Period size: 38 Copynumber: 2.4 Consensus size: 38
283761 TCTATTCTAA
* ** *
283771 AAAAATTTATGCATTAGTCTTATCTTTCGAATTTTAAT
1 AAAAATTTATACATTAGTCAAATCTTTCAAATTTTAAT
*
283809 AAAAATTTATATATTAGTCAAATCTTTCAAATTTTAAT
1 AAAAATTTATACATTAGTCAAATCTTTCAAATTTTAAT
*
283847 AAATAATCTATACAT
1 AAA-AATTTATACAT
283862 GATTATCATC
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
38 36 0.80
39 9 0.20
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (38 bp):
AAAAATTTATACATTAGTCAAATCTTTCAAATTTTAAT
Found at i:285235 original size:27 final size:27
Alignment explanation
Indices: 285158--285242 Score: 73
Period size: 32 Copynumber: 3.0 Consensus size: 27
285148 AAAATATGAC
* *
285158 ATAAATATATGAACATATTAAAATCTAT
1 ATAAATGTAT-AACATATTAAAATTTAT
* *
285186 TTAAAATGAATTATTAATATATTAAAATTTAT
1 AT-AAATG---TA-TAACATATTAAAATTTAT
285218 ATAAATGTATAACATATT-AAATTTA
1 ATAAATGTATAACATATTAAAATTTA
285243 AACATGAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
26 7 0.15
27 8 0.17
28 3 0.07
29 4 0.09
31 5 0.11
32 18 0.39
33 1 0.02
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (27 bp):
ATAAATGTATAACATATTAAAATTTAT
Found at i:285345 original size:2 final size:2
Alignment explanation
Indices: 285338--285366 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
285328 TAGTGTTGTG
285338 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
285367 GTCGAGTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:285512 original size:23 final size:22
Alignment explanation
Indices: 285485--285552 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 22
285475 TTTTCTATAA
285485 TTTTAATTATATTATATTAAAT
1 TTTTAATTATATTATATTAAAT
*
285507 TATTTATTTCAATATT-TATT-AAT
1 T-TTTAATT--ATATTATATTAAAT
*
285530 TTTTAATATATTTATATATTAAA
1 TTTTAAT-TATAT-TATATTAAA
285553 ATAATTATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
21 3 0.08
22 7 0.19
23 15 0.42
24 6 0.17
25 5 0.14
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTAATTATATTATATTAAAT
Found at i:293675 original size:27 final size:27
Alignment explanation
Indices: 293643--293715 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 27
293633 AGCCACCCTT
293643 TGTTTGTCAAAAATGGTGGTTACTTTG
1 TGTTTGTCAAAAATGGTGGTTACTTTG
* *
293670 TGTTTGTCAAAAATGGTGGTTTCTTTT
1 TGTTTGTCAAAAATGGTGGTTACTTTG
*
293697 TATTTGTCAAAAATGGTGG
1 TGTTTGTCAAAAATGGTGG
293716 CATGTTGTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.23, C:0.07, G:0.25, T:0.45
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTACTTTG
Found at i:293726 original size:24 final size:25
Alignment explanation
Indices: 293641--293732 Score: 105
Period size: 27 Copynumber: 3.6 Consensus size: 25
293631 AAAGCCACCC
*
293641 TTTGTTTGTCAAAAATGGTGGTTACT
1 TTTGTTTGTCAAAAATGGTGGTCA-T
*
293667 TTGTGTTTGTCAAAAATGGTGGTTTCTT
1 TT-TGTTTGTCAAAAATGGTGG--TCAT
*
293695 TTTATTTGTCAAAAATGGTGG-CAT
1 TTTGTTTGTCAAAAATGGTGGTCAT
*
293719 GTTGTTTGTCAAAA
1 TTTGTTTGTCAAAA
293733 TTTGTGGCTA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
24 14 0.25
26 2 0.04
27 37 0.65
28 3 0.05
29 1 0.02
ACGTcount: A:0.24, C:0.08, G:0.23, T:0.46
Consensus pattern (25 bp):
TTTGTTTGTCAAAAATGGTGGTCAT
Found at i:293748 original size:51 final size:54
Alignment explanation
Indices: 293645--293751 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 54
293635 CCACCCTTTG
* * * **
293645 TTTGTCAAAAATGGTGGTTACTTTGTGTTTGTCAAAAATGGTGGTTTCTTTTTA
1 TTTGTCAAAAATGGTGGTCACTGTGTGTTTGTCAAAAATGGTGGCTAATTTTTA
* *
293699 TTTGTCAAAAATGGTGG-CA-TGT-TGTTTGTCAAAATTTGTGGCTAATTTTTA
1 TTTGTCAAAAATGGTGGTCACTGTGTGTTTGTCAAAAATGGTGGCTAATTTTTA
293750 TT
1 TT
293752 ACAAAATAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
51 26 0.57
52 2 0.04
53 1 0.02
54 17 0.37
ACGTcount: A:0.23, C:0.07, G:0.21, T:0.48
Consensus pattern (54 bp):
TTTGTCAAAAATGGTGGTCACTGTGTGTTTGTCAAAAATGGTGGCTAATTTTTA
Found at i:294768 original size:51 final size:49
Alignment explanation
Indices: 294697--294864 Score: 201
Period size: 51 Copynumber: 3.3 Consensus size: 49
294687 TTTCATCTCG
* * *
294697 GGGATACTCCAATCCCGGTTTCATTTCCAAAACATCAATTTTTCTTAATC
1 GGGATACTCCAA-CCCGGTTTTATTTCCAAAACACCAATTTTTCATAATC
* *
294747 AGGGATACTCCAACCCGGGTTTTATTTCTAAAACACCTATTTTTCATAATC
1 -GGGATACTCCAACCC-GGTTTTATTTCCAAAACACCAATTTTTCATAATC
* * * *
294798 GGGGATACTCCAACTCCGATTTTATTTTCAAAACACCATTTTTTCACAATC
1 -GGGATACTCCAAC-CCGGTTTTATTTCCAAAACACCAATTTTTCATAATC
294849 GAGGATACTCCAACCC
1 G-GGATACTCCAACCC
294865 TGTTATTTCA
Statistics
Matches: 102, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
50 6 0.06
51 94 0.92
52 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.33
Consensus pattern (49 bp):
GGGATACTCCAACCCGGTTTTATTTCCAAAACACCAATTTTTCATAATC
Found at i:294911 original size:28 final size:28
Alignment explanation
Indices: 294851--294919 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
294841 TCACAATCGA
**
294851 GGATACTCCAACCCTGTTATTTCATTAG
1 GGATACTCCAACCCTGTTATTTCACGAG
*
294879 AGATACTCCAACCCTGTTATTTC-CGAGG
1 GGATACTCCAACCCTGTTATTTCACGA-G
294907 GGATACTCCAACC
1 GGATACTCCAACC
294920 TCGGCTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
27 1 0.03
28 35 0.97
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (28 bp):
GGATACTCCAACCCTGTTATTTCACGAG
Found at i:295088 original size:79 final size:78
Alignment explanation
Indices: 294880--295080 Score: 231
Period size: 79 Copynumber: 2.5 Consensus size: 78
294870 TTTCATTAGA
** * * *
294880 GATACTCCAACCCTGTTATTTCCGAGGGGATACTCCAACCTCGGCTTTATTTCTAAAATATTAAT
1 GATACTCCAACCC-GTTATTTTTGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAACATCAAT
294945 TTCTCACAATCGAG
65 TTCTCACAATCGAG
* * * *
294959 GATACTCCAACCCCGTTATTTTTGTGAGGATACTCCAACCCCGGCCTTATTTCTAAAGCATCAAT
1 GATACTCCAA-CCCGTTATTTTTGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAACATCAAT
* * * *
295024 TTTTCATAATTGGG
65 TTCTCACAATCGAG
* * *
295038 GATACTCTAATCCCGTTATTTTTGAGGGGATATTACAACCCCG
1 GATACTCCAA-CCCGTTATTTTTGAGGGGATACTCCAACCCCG
295081 ATTTTATTCT
Statistics
Matches: 102, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
79 99 0.97
80 3 0.03
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.33
Consensus pattern (78 bp):
GATACTCCAACCCGTTATTTTTGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAACATCAATT
TCTCACAATCGAG
Found at i:299135 original size:12 final size:11
Alignment explanation
Indices: 299069--299126 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
299059 CTTTTTTCTC
*
299069 TCTTTTATTTT
1 TCTTCTATTTT
*
299080 TCTTTTATTTAT
1 TCTTCTATTT-T
*
299092 TCATTC-ATTCT
1 TC-TTCTATTTT
299103 TCTTC--TTTT
1 TCTTCTATTTT
299112 TCTTCTATTTT
1 TCTTCTATTTT
299123 TCTT
1 TCTT
299127 TTTATTTTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 8 0.20
10 3 0.08
11 21 0.52
12 6 0.15
13 2 0.05
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.72
Consensus pattern (11 bp):
TCTTCTATTTT
Found at i:300016 original size:62 final size:62
Alignment explanation
Indices: 299914--300100 Score: 338
Period size: 62 Copynumber: 3.0 Consensus size: 62
299904 GACTTTGATC
* *
299914 TATAAATGAAATGGACCACAAAGCCAGGCATTGAATTGGCAATTGGCATATGTCCACTAAAT
1 TATATATGAAATGGACCACAAAGCCAGCCATTGAATTGGCAATTGGCATATGTCCACTAAAT
299976 TATATATGAAATGGACCACAAAGCCAGCCATTGAATTGGCAATTGGCATATGTCCACTAAAT
1 TATATATGAAATGGACCACAAAGCCAGCCATTGAATTGGCAATTGGCATATGTCCACTAAAT
* *
300038 TATATATGAAATGGACCACAAAGCCAGCCATTGAATTGGCAATTGACATATGTCCATTAAAT
1 TATATATGAAATGGACCACAAAGCCAGCCATTGAATTGGCAATTGGCATATGTCCACTAAAT
300100 T
1 T
300101 TTTTCAAGTT
Statistics
Matches: 121, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 121 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (62 bp):
TATATATGAAATGGACCACAAAGCCAGCCATTGAATTGGCAATTGGCATATGTCCACTAAAT
Found at i:301073 original size:17 final size:18
Alignment explanation
Indices: 301051--301094 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
301041 ATCGCTGATA
*
301051 ATATTTTTGTT-AATAAT
1 ATATTTTTGTTGAAAAAT
301068 ATATTTTTTGTTGAAAAAT
1 ATA-TTTTTGTTGAAAAAT
301087 ATTATTTT
1 A-TATTTT
301095 CAATGAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.13
18 8 0.35
19 10 0.43
20 2 0.09
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (18 bp):
ATATTTTTGTTGAAAAAT
Found at i:301077 original size:18 final size:20
Alignment explanation
Indices: 301054--301094 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
301044 GCTGATAATA
*
301054 TTTTTGTT-AATAATA-TAT
1 TTTTTGTTGAAAAATATTAT
301072 TTTTTGTTGAAAAATATTAT
1 TTTTTGTTGAAAAATATTAT
301092 TTT
1 TTT
301095 CAATGAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 6 0.30
20 6 0.30
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (20 bp):
TTTTTGTTGAAAAATATTAT
Found at i:301468 original size:37 final size:36
Alignment explanation
Indices: 301419--301488 Score: 104
Period size: 37 Copynumber: 1.9 Consensus size: 36
301409 TAATAAATAT
*
301419 ATAAAATATAAATGTATAATAAATAAAATAAAATAAA
1 ATAAAATATAAATATATAATAAAT-AAATAAAATAAA
* *
301456 ATAAAATGTAAATATATAATAAATTAATAAAAT
1 ATAAAATATAAATATATAATAAATAAATAAAAT
301489 CGTACATCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 8 0.27
37 22 0.73
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (36 bp):
ATAAAATATAAATATATAATAAATAAATAAAATAAA
Found at i:301474 original size:15 final size:15
Alignment explanation
Indices: 301422--301474 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
301412 TAAATATATA
301422 AAATATAAATGTATAAT
1 AAATA-AAATGTA-AAT
*
301439 AAATAAAAT-AAAAT
1 AAATAAAATGTAAAT
301453 AAAATAAAATGTAAAT
1 -AAATAAAATGTAAAT
*
301469 ATATAA
1 AAATAA
301475 TAAATTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 3 0.10
15 15 0.48
16 8 0.26
17 5 0.16
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (15 bp):
AAATAAAATGTAAAT
Found at i:304920 original size:8 final size:8
Alignment explanation
Indices: 304901--304940 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
304891 TCATTTTTTT
304901 AATATA-A
1 AATATATA
304908 AATATATA
1 AATATATA
304916 AATATATA
1 AATATATA
304924 AA-A-ATA
1 AATATATA
*
304930 AATATTTA
1 AATATATA
304938 AAT
1 AAT
304941 TTAAAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
6 5 0.17
7 8 0.28
8 16 0.55
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AATATATA
Found at i:308668 original size:23 final size:24
Alignment explanation
Indices: 308626--308682 Score: 75
Period size: 23 Copynumber: 2.4 Consensus size: 24
308616 TTAAAATTTA
308626 TATAATATAAATTATTAATAT-AT
1 TATAATATAAATTATTAATATAAT
308649 TA-AATATATAATT-TTAAATATAAT
1 TATAATATA-AATTATT-AATATAAT
308673 TATAATATAA
1 TATAATATAA
308683 TAAAATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 8 0.27
23 11 0.37
24 5 0.17
25 6 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TATAATATAAATTATTAATATAAT
Found at i:308671 original size:12 final size:11
Alignment explanation
Indices: 308626--308683 Score: 55
Period size: 11 Copynumber: 5.0 Consensus size: 11
308616 TTAAAATTTA
308626 TATAATATAAAT
1 TATAATAT-AAT
308638 TATTAATAT-AT
1 TA-TAATATAAT
*
308649 TAAATATATAAT
1 TATA-ATATAAT
*
308661 TTTAAATATAAT
1 TAT-AATATAAT
308673 TATAATATAAT
1 TATAATATAAT
308684 AAAATATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
10 1 0.03
11 16 0.42
12 14 0.37
13 7 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TATAATATAAT
Found at i:308685 original size:14 final size:13
Alignment explanation
Indices: 308626--308681 Score: 59
Period size: 12 Copynumber: 4.7 Consensus size: 13
308616 TTAAAATTTA
308626 TATAATATA-AAT
1 TATAATATATAAT
*
308638 TATTA-ATAT-AT
1 TATAATATATAAT
308649 TA-AATATATAAT
1 TATAATATATAAT
*
308661 TTTAA-ATATAAT
1 TATAATATATAAT
308673 TATAATATA
1 TATAATATA
308682 ATAAAATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
10 1 0.03
11 11 0.31
12 18 0.51
13 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATAATATATAAT
Found at i:308689 original size:35 final size:38
Alignment explanation
Indices: 308620--308705 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 38
308610 TATTTTTTAA
*
308620 AATTTATATAATATAAATTATTAATATATTAAATATAT
1 AATTTATATAATATAAATTATTAATATATAAAATATAT
308658 AATTT-TA-AATAT-AATTA-TAATATAATAAAATATAT
1 AATTTATATAATATAAATTATTAATAT-ATAAAATATAT
308693 AAATATTATATAA
1 -AAT-TTATATAA
308706 ATGAACCAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
34 6 0.14
35 15 0.36
36 8 0.19
37 4 0.10
38 7 0.17
39 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (38 bp):
AATTTATATAATATAAATTATTAATATATAAAATATAT
Found at i:309407 original size:50 final size:50
Alignment explanation
Indices: 309328--309520 Score: 282
Period size: 50 Copynumber: 3.9 Consensus size: 50
309318 GGTGACTATC
* * *
309328 CTTCACCGACCTTT-AGCAATAAAGAGAGGTGGTCATAATTGTTGACGATT
1 CTTCACCAACCTTTGA-CAATAAAGGGAGGTGGCCATAATTGTTGACGATT
*
309378 CTTCACCAACCTTTGACAATAAAGGGAGGTGACCATAATTGTTGACGATT
1 CTTCACCAACCTTTGACAATAAAGGGAGGTGGCCATAATTGTTGACGATT
* *
309428 CTTCACCAACCTTTGACAATAGAA-GGAGGTGGTCATAATTGTTGATGATT
1 CTTCACCAACCTTTGACAATA-AAGGGAGGTGGCCATAATTGTTGACGATT
* *
309478 CTTCATCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTT
1 CTTCACCAACCTTTGACAATAAAGGGAGGTGGCCATAATTGTT
309521 TGACTCTAAG
Statistics
Matches: 130, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
49 1 0.01
50 126 0.97
51 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (50 bp):
CTTCACCAACCTTTGACAATAAAGGGAGGTGGCCATAATTGTTGACGATT
Found at i:313990 original size:50 final size:50
Alignment explanation
Indices: 313921--314126 Score: 335
Period size: 50 Copynumber: 4.1 Consensus size: 50
313911 AGTTGTTGCC
* *
313921 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* *
313971 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGGGAGGTGACCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
314021 ATTGTTGACGATTCTTTACCAACCTTTGACAATAGATG-GAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-GAGAGGTGGCCATA
314071 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
314121 ATTGTT
1 ATTGTT
314127 TGACTCTAAG
Statistics
Matches: 146, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
50 145 0.99
51 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.30
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:315215 original size:21 final size:21
Alignment explanation
Indices: 315187--315262 Score: 63
Period size: 21 Copynumber: 3.7 Consensus size: 21
315177 TACTCTATCT
315187 AAAT-TATTATTTAATAATTAA
1 AAATATATTATTTAATAA-TAA
* *
315208 AAA-ATATTTTTTAATTATAA
1 AAATATATTATTTAATAATAA
*
315228 AAATATATAAATATTAAT-ATAA
1 AAATATAT-TAT-TTAATAATAA
315250 AAATA-ATT-TTTAA
1 AAATATATTATTTAA
315263 AATTTTTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
18 4 0.09
19 1 0.02
20 6 0.13
21 20 0.43
22 10 0.22
23 5 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATATATTATTTAATAATAA
Found at i:316353 original size:18 final size:18
Alignment explanation
Indices: 316332--316367 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
316322 CTTTGAAGGG
316332 TTTTTACTCTTTTATTTT
1 TTTTTACTCTTTTATTTT
* *
316350 TTTTTATTTTTTTATTTT
1 TTTTTACTCTTTTATTTT
316368 GTTCTATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTACTCTTTTATTTT
Found at i:319055 original size:26 final size:28
Alignment explanation
Indices: 319012--319066 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
319002 TGATCGATTT
**
319012 AGTTAATTTAATCTA-TTTAA-ATTAAA
1 AGTTAATTTAATAAATTTTAATATTAAA
319038 AGTTAATTTAATAAATTTTAATATTAAA
1 AGTTAATTTAATAAATTTTAATATTAAA
319066 A
1 A
319067 TCGATTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 13 0.52
27 5 0.20
28 7 0.28
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (28 bp):
AGTTAATTTAATAAATTTTAATATTAAA
Found at i:320360 original size:24 final size:25
Alignment explanation
Indices: 320310--320361 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
320300 ATAAGATAAA
*
320310 TTTAAATTTTAATATTTATAATTTT
1 TTTAAATTTTAAGATTTATAATTTT
* *
320335 TTTAAATTTTTAGA-TTGTAATTTT
1 TTTAAATTTTAAGATTTATAATTTT
320359 TTT
1 TTT
320362 TGAGTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (25 bp):
TTTAAATTTTAAGATTTATAATTTT
Found at i:321481 original size:22 final size:21
Alignment explanation
Indices: 321453--321494 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
321443 AGATATGAAT
321453 AAATAAT-TCAAATATGAAATAA
1 AAATAATAT-AAATAT-AAATAA
321475 AAATAATATAAATATAAATA
1 AAATAATATAAATATAAATA
321495 TAATATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 13 0.68
23 1 0.05
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (21 bp):
AAATAATATAAATATAAATAA
Found at i:321488 original size:6 final size:6
Alignment explanation
Indices: 321462--321507 Score: 55
Period size: 6 Copynumber: 8.2 Consensus size: 6
321452 TAAATAATTC
321462 AAATAT GAAATA- AAA-AT -AATAT AAATAT AAATAT -AATAT AAATAT
1 AAATAT -AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
321507 A
1 A
321508 TGATATGTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
4 3 0.09
5 10 0.29
6 17 0.49
7 5 0.14
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (6 bp):
AAATAT
Found at i:321497 original size:17 final size:16
Alignment explanation
Indices: 321463--321507 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
321453 AAATAATTCA
321463 AATATGAAATA-AAAAT
1 AATAT-AAATATAAAAT
321479 AATATAAATATAAATAT
1 AATATAAATATAAA-AT
321496 AATATAAATATA
1 AATATAAATATA
321508 TGATATGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.19
16 8 0.30
17 14 0.52
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (16 bp):
AATATAAATATAAAAT
Found at i:323337 original size:13 final size:13
Alignment explanation
Indices: 323321--323345 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
323311 AGATAACATA
323321 TATTTTAAAAATG
1 TATTTTAAAAATG
323334 TATTTTAAAAAT
1 TATTTTAAAAAT
323346 AAAATATATA
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:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TATTTTAAAAATG
Found at i:324239 original size:18 final size:17
Alignment explanation
Indices: 324211--324244 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
324201 GTAAAATAAT
324211 ATTAATTTAATTAATTA
1 ATTAATTTAATTAATTA
324228 ATTAATTTTAATTAATT
1 ATTAA-TTTAATTAATT
324245 TACATAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTAATTTAATTAATTA
Found at i:324494 original size:25 final size:25
Alignment explanation
Indices: 324453--324503 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
324443 TCTATAAGAA
* *
324453 AAAAAAATTCTTACTTTTTT-ATTT
1 AAAAAAATACATACTTTTTTAATTT
324477 AAAAAAATACATATCTTTTTTAATTT
1 AAAAAAATACATA-CTTTTTTAATTT
324503 A
1 A
324504 TTATTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 11 0.48
25 7 0.30
26 5 0.22
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (25 bp):
AAAAAAATACATACTTTTTTAATTT
Found at i:324988 original size:2 final size:2
Alignment explanation
Indices: 324981--325009 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
324971 AAAACTATTC
324981 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 A
325010 CCTAAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:325670 original size:2 final size:2
Alignment explanation
Indices: 325663--325688 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
325653 TAACACTTTC
325663 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
325689 TTGTTATGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:326451 original size:16 final size:18
Alignment explanation
Indices: 326413--326454 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
326403 TACTTGTTTG
326413 ATTTTCTATCTCTTAATTA
1 ATTTT-TATCTCTTAATTA
*
326432 ATTTTTATCT-TT-ATTT
1 ATTTTTATCTCTTAATTA
326448 ATTTTTA
1 ATTTTTA
326455 ATTAAAGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 10 0.45
17 2 0.09
18 5 0.23
19 5 0.23
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTATCTCTTAATTA
Found at i:330938 original size:13 final size:13
Alignment explanation
Indices: 330920--330944 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
330910 TTGTAAATTG
330920 TAATATTTGGCTA
1 TAATATTTGGCTA
330933 TAATATTTGGCT
1 TAATATTTGGCT
330945 TACATTTCTC
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:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (13 bp):
TAATATTTGGCTA
Found at i:331636 original size:2 final size:2
Alignment explanation
Indices: 331629--331656 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
331619 ATGTTTTGTC
331629 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
331657 GAGAAACTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:335291 original size:25 final size:24
Alignment explanation
Indices: 335256--335305 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
335246 TTTTTAATCA
335256 TTTTATATATATAAAAATTTATAT
1 TTTTATATATATAAAAATTTATAT
**
335280 TTTTATATTATATTTAAATTTATAT
1 TTTTATA-TATATAAAAATTTATAT
335305 T
1 T
335306 AAATAATACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTATATATATAAAAATTTATAT
Found at i:335629 original size:2 final size:2
Alignment explanation
Indices: 335584--335612 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
335574 GTACATGATC
335584 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 A
335613 ATCTAAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:336377 original size:2 final size:2
Alignment explanation
Indices: 336370--336398 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
336360 ATCATTATGA
336370 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 A
336399 CACACGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:336694 original size:2 final size:2
Alignment explanation
Indices: 336687--336718 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
336677 TTCAACATGA
336687 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
336719 GAGTTTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:336881 original size:2 final size:2
Alignment explanation
Indices: 336874--336899 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
336864 AGTGTATTAA
336874 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
336900 GTTAGTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:338027 original size:15 final size:15
Alignment explanation
Indices: 338007--338047 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
337997 TTTTTAATTT
*
338007 TTTTTTCAATTCAAA
1 TTTTTTCAATGCAAA
338022 TTTTTTCTAATGCAAA
1 TTTTTTC-AATGCAAA
338038 TTTCTTTCAA
1 TTT-TTTCAA
338048 CAATAACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 7 0.30
16 12 0.52
17 4 0.17
ACGTcount: A:0.29, C:0.15, G:0.02, T:0.54
Consensus pattern (15 bp):
TTTTTTCAATGCAAA
Found at i:339228 original size:20 final size:18
Alignment explanation
Indices: 339178--339228 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
339168 TCTACTTGAT
*
339178 AAAATGAAAAAAAAATGA
1 AAAATAAAAAAAAAATGA
*
339196 AAATTAAAGAAAAAAAGTGA
1 AAAATAAA-AAAAAAA-TGA
339216 AAAGATAAAAAAA
1 AAA-ATAAAAAAA
339229 TATTTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 6 0.22
19 7 0.26
20 10 0.37
21 4 0.15
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (18 bp):
AAAATAAAAAAAAAATGA
Found at i:339430 original size:54 final size:54
Alignment explanation
Indices: 339201--339717 Score: 367
Period size: 54 Copynumber: 9.7 Consensus size: 54
339191 AATGAAAATT
*
339201 AAAG-AAAAAAAGTGAAAAGATAAAAA-AATATTTTTTTATTGATATGATTAG-CTGA
1 AAAGAAAAAAAAGTGAAAAGATAAAAATAA-A--TTTTTATTGATATGATTGGTC-GA
* * * *
339256 AAATAAGAAAAAGTG-AAAGAT-AAAA-AAATTTTCATTGATATGATTGGTCAA
1 AAAGAAAAAAAAGTGAAAAGATAAAAATAAATTTTTATTGATATGATTGGTCGA
* * *
339307 AAAG-AAAAAAAGTGAAAAGATAAAAAATTATATTTTTTTTATTGGTATGATTGGTTGA
1 AAAGAAAAAAAAGTGAAAAGAT-AAAAA-TA-A--ATTTTTATTGATATGATTGGTCGA
* * *
339365 AAAGAAGAAAAAGTGAAAAGATAAAAATAAATTTTTATTAATATAATTGGTCGA
1 AAAGAAAAAAAAGTGAAAAGATAAAAATAAATTTTTATTGATATGATTGGTCGA
* * * * * * *
339419 AATGAAAAAAAAATGAAAAGATAAAAAATATATTTTTTATTGACATGATTAGTTGG
1 AAAGAAAAAAAAGTGAAAAGAT-AAAAATA-AATTTTTATTGATATGATTGGTCGA
** * * * *
339475 AGCGAAGAAAAAGTGAAAA-A-ATAAA-AAATATTTATTGA-ATGATTGGTCTA
1 AAAGAAAAAAAAGTGAAAAGATAAAAATAAATTTTTATTGATATGATTGGTCGA
* * ** * * *
339525 AAAG-AAAAAAA-TGAAGAGAAAAAAATATTTTTTTATTGGTATAATTGGTTGGA
1 AAAGAAAAAAAAGTGAAAAGATAAAAATAAATTTTTATTGATATGATTGG-TCGA
* *
339578 AAA-AAGAAAAAGTGAAAAAATAAAAATAAA--TTTATTGATATGATTGGTCGA
1 AAAGAAAAAAAAGTGAAAAGATAAAAATAAATTTTTATTGATATGATTGGTCGA
* * ** *
339629 AAAG-AAAAAAA-T-AAAGAAATAAAAA-AATATTTTTTATTGGTACCATTGGTCGG
1 AAAGAAAAAAAAGTGAAA-AGATAAAAATAA-A-TTTTTATTGATATGATTGGTCGA
* *
339682 AAAG-AAGAAAAGATAAAAAGA-ATAAAATAAATTTTT
1 AAAGAAAAAAAAG-TGAAAAGATA-AAAATAAATTTTT
339718 TTCTATCAAT
Statistics
Matches: 364, Mismatches: 67, Indels: 63
0.74 0.14 0.13
Matches are distributed among these distances:
48 5 0.01
49 12 0.03
50 34 0.09
51 58 0.16
52 24 0.07
53 47 0.13
54 63 0.17
55 26 0.07
56 49 0.13
57 2 0.01
58 28 0.08
59 16 0.04
ACGTcount: A:0.53, C:0.02, G:0.16, T:0.29
Consensus pattern (54 bp):
AAAGAAAAAAAAGTGAAAAGATAAAAATAAATTTTTATTGATATGATTGGTCGA
Found at i:339446 original size:219 final size:208
Alignment explanation
Indices: 339205--339667 Score: 596
Period size: 219 Copynumber: 2.2 Consensus size: 208
339195 AAAATTAAAG
* * *
339205 AAAAAAAGTGAAAAGATAAAAAAATATTTTTTTATTGATATGATTAGCTGAAAATAAGAAAAAGT
1 AAAAAAAATGAAAAGATAAAAAAATATTTTTTTATTGACATGATTAGCTGAAAAGAAGAAAAAGT
* *
339270 G-AAAGATAAAAAA-ATTTTCATTGATATGATTGGTCAAAAAGAAAAAAAGTGAAAAGATAAAAA
66 GAAAAAATAAAAAATA-TTT-ATTGA-ATGATTGGTCAAAAAGAAAAAAA-TG--AAGAGAAAAA
* *
339333 ATTATATTTTTTTTATTGGTATGATTGGTT-GAAAAGAAGAAAAAGTGAAAAGATAAAAATAAAT
125 A--ATA-TTTTTTTATTGGTATAATTGGTTGGAAAA-AAGAAAAAGTGAAAAAATAAAAATAAA-
339397 TTTTATTAATATAATTGGTCGAAATGA
185 -TTTATTAATATAATTGGTCGAAA--A
* * **
339424 AAAAAAAATGAAAAGAT-AAAAAATATATTTTTTATTGACATGATTAGTTGGAGCGAAGAAAAAG
1 AAAAAAAATGAAAAGATAAAAAAATAT-TTTTTTATTGACATGATTAGCTGAAAAGAAGAAAAAG
*
339488 TGAAAAAATAAAAAATATTTATTGAATGATTGGTCTAAAAGAAAAAAATGAAGAGAAAAAAATAT
65 TGAAAAAATAAAAAATATTTATTGAATGATTGGTCAAAAAGAAAAAAATGAAGAGAAAAAAATAT
*
339553 TTTTTTATTGGTATAATTGGTTGGAAAAAAGAAAAAGTGAAAAAATAAAAATAAATTTATTGATA
130 TTTTTTATTGGTATAATTGGTTGGAAAAAAGAAAAAGTGAAAAAATAAAAATAAATTTATTAATA
*
339618 TGATTGGTCGAAAA
195 TAATTGGTCGAAAA
* *
339632 GAAAAAAAT-AAAGAAATAAAAAAATA-TTTTTTATTG
1 AAAAAAAATGAAA-AGATAAAAAAATATTTTTTTATTG
339668 GTACCATTGG
Statistics
Matches: 222, Mismatches: 16, Indels: 24
0.85 0.06 0.09
Matches are distributed among these distances:
207 13 0.06
208 12 0.05
209 8 0.04
210 21 0.09
212 48 0.22
213 8 0.04
215 10 0.05
217 2 0.01
218 31 0.14
219 54 0.24
220 14 0.06
221 1 0.00
ACGTcount: A:0.53, C:0.02, G:0.15, T:0.30
Consensus pattern (208 bp):
AAAAAAAATGAAAAGATAAAAAAATATTTTTTTATTGACATGATTAGCTGAAAAGAAGAAAAAGT
GAAAAAATAAAAAATATTTATTGAATGATTGGTCAAAAAGAAAAAAATGAAGAGAAAAAAATATT
TTTTTATTGGTATAATTGGTTGGAAAAAAGAAAAAGTGAAAAAATAAAAATAAATTTATTAATAT
AATTGGTCGAAAA
Found at i:339686 original size:102 final size:105
Alignment explanation
Indices: 339201--339715 Score: 500
Period size: 102 Copynumber: 4.8 Consensus size: 105
339191 AATGAAAATT
* * * * *
339201 AAAGAAAAAAAGTGAAAAGATAAAAAA-ATATTTTTTTATTGATATGATTAGCTGAAAATAAGAA
1 AAAGAAAAAAA-TGAAAAGATAAAAAATATATTTTTTTATTGGTATGATTGGTTG--GAGAAGAA
* * *
339265 AAAGTG-AAAGATAAAAA-AATTTTCATTGATATGATTGGTCAA
63 AAAGTGAAAAAATAAAAATAAATTT-ATTGATATGATTGGTCGA
*
339307 AAAGAAAAAAAGTGAAAAGATAAAAAATTATATTTTTTTTATTGGTATGATTGGTTGAAAAGAAG
1 AAAGAAAAAAA-TGAAAAGATAAAAAA-TATA-TTTTTTTATTGGTATGATTGGTTG--GAGAAG
* * *
339372 AAAAAGTGAAAAGATAAAAATAAATTTTTATTAATATAATTGGTCGA
61 AAAAAGTGAAAAAATAAAAATAAA--TTTATTGATATGATTGGTCGA
* ** *
339419 AATGAAAAAAAAATGAAAAGATAAAAAATATA-TTTTTTATTGACATGATTAGTTGGAGCGAAGA
1 AA--AGAAAAAAATGAAAAGATAAAAAATATATTTTTTTATTGGTATGATTGGTTGGA--GAAGA
* *
339483 AAAAGTGAAAAAATAAAAA-ATATTTATTGA-ATGATTGGTCTA
62 AAAAGTGAAAAAATAAAAATAAATTTATTGATATGATTGGTCGA
* * *
339525 AAAGAAAAAAATG--AAGAGAAAAAA-ATATTTTTTTATTGGTATAATTGGTTGGAAAAAAGAAA
1 AAAGAAAAAAATGAAAAGATAAAAAATATATTTTTTTATTGGTATGATTGGTTGG--AGAAGAAA
339587 AAGTGAAAAAATAAAAATAAATTTATTGATATGATTGGTCGA
64 AAGTGAAAAAATAAAAATAAATTTATTGATATGATTGGTCGA
* ** *
339629 AAAGAAAAAAAT-AAAGAAATAAAAAA-ATA-TTTTTTATTGGTACCATTGGTCGGA-AAGAAGA
1 AAAGAAAAAAATGAAA-AGATAAAAAATATATTTTTTTATTGGTATGATTGGTTGGAGAAG-A-A
*
339690 AAAGATAAAAAGAAT-AAAATAAATTT
63 AAAG-TGAAAA-AATAAAAATAAATTT
339716 TTTTCTATCA
Statistics
Matches: 353, Mismatches: 33, Indels: 47
0.82 0.08 0.11
Matches are distributed among these distances:
101 3 0.01
102 56 0.16
103 12 0.03
104 39 0.11
105 38 0.11
106 53 0.15
107 7 0.02
108 4 0.01
109 38 0.11
110 54 0.15
111 2 0.01
112 21 0.06
113 18 0.05
114 8 0.02
ACGTcount: A:0.53, C:0.02, G:0.16, T:0.29
Consensus pattern (105 bp):
AAAGAAAAAAATGAAAAGATAAAAAATATATTTTTTTATTGGTATGATTGGTTGGAGAAGAAAAA
GTGAAAAAATAAAAATAAATTTATTGATATGATTGGTCGA
Found at i:339813 original size:18 final size:20
Alignment explanation
Indices: 339790--339831 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 20
339780 TTATATCTTT
339790 TAAAAATT-AAAATAA-AAA
1 TAAAAATTAAAAATAATAAA
339808 TAAAAATTAGAAAATAATAAA
1 TAAAAATTA-AAAATAATAAA
339829 TAA
1 TAA
339832 TTTTATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
20 7 0.33
21 6 0.29
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (20 bp):
TAAAAATTAAAAATAATAAA
Found at i:339901 original size:17 final size:17
Alignment explanation
Indices: 339881--339915 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
339871 TTTTAATTTT
339881 TTTAATTTATAATA-AAA
1 TTTAATTT-TAATACAAA
339898 TTTAATTTTAATACAAA
1 TTTAATTTTAATACAAA
339915 T
1 T
339916 ATAAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAATTTTAATACAAA
Done.