Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold301
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: 1013018
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 32220 characters in sequence are not A, C, G, or T
File 1 of 4
Found at i:1253 original size:17 final size:19
Alignment explanation
Indices: 1231--1266 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1221 GATATTAGTC
1231 TAATT-AAT-TTTATTTTT
1 TAATTAAATATTTATTTTT
1248 TAATTAAATATTTATTTTT
1 TAATTAAATATTTATTTTT
1267 AGATAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 3 0.18
19 9 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TAATTAAATATTTATTTTT
Found at i:2167 original size:71 final size:72
Alignment explanation
Indices: 2050--2188 Score: 235
Period size: 71 Copynumber: 1.9 Consensus size: 72
2040 TCTCGGATTT
* *
2050 AAAAAAGGGATCATGCACAATAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAGGGATCACGCACAATAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
2115 CTTAAGG
66 CTTAAGG
* *
2122 AAAAAA-GGATCACGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAGGGATCACGCACAATAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
2186 CTT
66 CTT
2189 GAGTTTGAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 57 0.90
72 6 0.10
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (72 bp):
AAAAAAGGGATCACGCACAATAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
CTTAAGG
Found at i:5196 original size:19 final size:18
Alignment explanation
Indices: 5159--5195 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5149 ATTTTTAAAA
5159 TATAAATTTTAGAACTTT
1 TATAAATTTTAGAACTTT
5177 TATAAATATTTAGAA-TTT
1 TATAAAT-TTTAGAACTTT
5195 T
1 T
5196 TGAAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (18 bp):
TATAAATTTTAGAACTTT
Found at i:5206 original size:20 final size:19
Alignment explanation
Indices: 5159--5196 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5149 ATTTTTAAAA
*
5159 TATAAAT-TTTAGAACTTT
1 TATAAATATTTAGAATTTT
5177 TATAAATATTTAGAATTTT
1 TATAAATATTTAGAATTTT
5196 T
1 T
5197 GAAAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:7220 original size:21 final size:21
Alignment explanation
Indices: 7196--7238 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
7186 TTTTGCCTAA
*
7196 AATATGAATTGGATTGAATTG
1 AATATGAATTGGATTAAATTG
*
7217 AATATGAATTGTATTAAATTG
1 AATATGAATTGGATTAAATTG
7238 A
1 A
7239 GTTAAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.40
Consensus pattern (21 bp):
AATATGAATTGGATTAAATTG
Found at i:7987 original size:31 final size:31
Alignment explanation
Indices: 7943--8004 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
7933 TACTTAAATT
*
7943 TTAAGTTAAAAGATATTTAT-TAGATAAATAA
1 TTAAATTAAAAGATATTTATGT-GATAAATAA
* * *
7974 TTAAATTATAAGATTTTTGTGTGATAAATAA
1 TTAAATTAAAAGATATTTATGTGATAAATAA
8005 AATAAATGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (31 bp):
TTAAATTAAAAGATATTTATGTGATAAATAA
Found at i:8509 original size:22 final size:24
Alignment explanation
Indices: 8481--8524 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
8471 TATGACAAGA
8481 AATTAAG-TAGAAAAG-AAGTATG
1 AATTAAGTTAGAAAAGTAAGTATG
*
8503 AATTAAGTTGGAAAAGTAAGTA
1 AATTAAGTTAGAAAAGTAAGTA
8525 AACTTAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 7 0.37
24 5 0.26
ACGTcount: A:0.52, C:0.00, G:0.23, T:0.25
Consensus pattern (24 bp):
AATTAAGTTAGAAAAGTAAGTATG
Found at i:14777 original size:25 final size:25
Alignment explanation
Indices: 14742--14814 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 25
14732 TATTGACTTG
* *
14742 CATGAGC-TTCCTGA-ATATGGCTCT
1 CATGAGCTTTCC-GATACATGGCTCA
*
14766 TATGAGCTTTCCGATACATGGCTCA
1 CATGAGCTTTCCGATACATGGCTCA
* * *
14791 CATGAGCTTCCCGTTATATGGCTC
1 CATGAGCTTTCCGATACATGGCTC
14815 GAGAGAGTGC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
24 8 0.20
25 32 0.80
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.33
Consensus pattern (25 bp):
CATGAGCTTTCCGATACATGGCTCA
Found at i:17283 original size:49 final size:49
Alignment explanation
Indices: 17230--17359 Score: 215
Period size: 49 Copynumber: 2.7 Consensus size: 49
17220 ATTTGGTAGC
*
17230 AGGGTTTTGTTATTACCTTCCGTGAGTCTCCCCCTATGCATCTAGGAAA
1 AGGGTTTTGTTATTACCTTCCGTGAGCCTCCCCCTATGCATCTAGGAAA
17279 AGGGTTTTGTTATTACCTTCCGTGAGCCTCCCCCTATGCATCTAGGAAA
1 AGGGTTTTGTTATTACCTTCCGTGAGCCTCCCCCTATGCATCTAGGAAA
* * * *
17328 AGAGTTTTATTATTACCTTCCATAAGCCTCCC
1 AGGGTTTTGTTATTACCTTCCGTGAGCCTCCC
17360 ATCATACGTC
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 76 1.00
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.35
Consensus pattern (49 bp):
AGGGTTTTGTTATTACCTTCCGTGAGCCTCCCCCTATGCATCTAGGAAA
Found at i:24651 original size:30 final size:30
Alignment explanation
Indices: 24615--25001 Score: 497
Period size: 30 Copynumber: 12.8 Consensus size: 30
24605 ATGTATACAT
*
24615 ATACAAATAAATTCGGCAATGTATATCCAA
1 ATACAAATCAATTCGGCAATGTATATCCAA
* * * * *
24645 ATACAAATCAATTCAGAAATGAATATCTAT
1 ATACAAATCAATTCGGCAATGTATATCCAA
* *
24675 ATACAAATCAATTCGACAATGTATATCTAA
1 ATACAAATCAATTCGGCAATGTATATCCAA
* *
24705 ATACGAATCAATTCGACAATGTATATCCAA
1 ATACAAATCAATTCGGCAATGTATATCCAA
*
24735 ATACAAATCAATTCAGCAATGTATAT-CAA
1 ATACAAATCAATTCGGCAATGTATATCCAA
*
24764 TATACCAATCAATTCGGCAATGTATATCCAA
1 -ATACAAATCAATTCGGCAATGTATATCCAA
** * *
24795 ATACAAATCAATTCGATAATGTATATCTAT
1 ATACAAATCAATTCGGCAATGTATATCCAA
24825 ATACAAATCAATTCGGCAATGTATATCCAA
1 ATACAAATCAATTCGGCAATGTATATCCAA
* *
24855 ATACGAATCAATTTGGCAATGTATATCCAA
1 ATACAAATCAATTCGGCAATGTATATCCAA
* * *
24885 ATACAAATCAATTCGGCAATGTAGATCTAT
1 ATACAAATCAATTCGGCAATGTATATCCAA
* ** *
24915 ATACCAATCAATTCGGCAATGTATATATATGT
1 ATACAAATCAATTCGGCAATGTATATCCA--A
24947 ATACAAATCAATTCGGCAATGTATATCCAA
1 ATACAAATCAATTCGGCAATGTATATCCAA
* *
24977 ATACGAATTAATTCGGCAATGTATA
1 ATACAAATCAATTCGGCAATGTATA
25002 AAACATATAC
Statistics
Matches: 310, Mismatches: 43, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
29 3 0.01
30 277 0.89
31 3 0.01
32 27 0.09
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (30 bp):
ATACAAATCAATTCGGCAATGTATATCCAA
Found at i:26107 original size:20 final size:21
Alignment explanation
Indices: 26082--26123 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
26072 TGTTGAATTG
26082 TGTATT-TTGGAATGTT-CAAA
1 TGTATTCTT-GAATGTTACAAA
26102 TGTATTCTTGAATGTTACAAA
1 TGTATTCTTGAATGTTACAAA
26123 T
1 T
26124 TGGTACAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.45
Consensus pattern (21 bp):
TGTATTCTTGAATGTTACAAA
Found at i:32791 original size:19 final size:18
Alignment explanation
Indices: 32763--32798 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
32753 AAGTTACCTT
32763 CTTTGTTTCTGGTTTTGA
1 CTTTGTTTCTGGTTTTGA
*
32781 CTTTGGTTTCTGTTTTTG
1 CTTT-GTTTCTGGTTTTG
32799 TTTGTGGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.03, C:0.11, G:0.22, T:0.64
Consensus pattern (18 bp):
CTTTGTTTCTGGTTTTGA
Found at i:36966 original size:27 final size:27
Alignment explanation
Indices: 36935--37003 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
36925 AAAACATATT
36935 TATATTTTATAATAT-ATAAGTTGGTAAA
1 TATATTTTATAATATCATAAGTT--TAAA
* * *
36963 -ATATTTTTATATTTTCATTAGTTTAAA
1 TATA-TTTTATAATATCATAAGTTTAAA
36990 TATATTTTATAATA
1 TATATTTTATAATA
37004 CATTTATTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
27 15 0.45
28 12 0.36
29 6 0.18
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (27 bp):
TATATTTTATAATATCATAAGTTTAAA
Found at i:40968 original size:2 final size:2
Alignment explanation
Indices: 40916--40951 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
40906 TAATCTGTAC
*
40916 GA GA GA GA GA GA GA GA GA GG GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
40952 CTTGATGAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:44303 original size:44 final size:44
Alignment explanation
Indices: 44241--44941 Score: 188
Period size: 44 Copynumber: 16.2 Consensus size: 44
44231 GATAAGATCC
*
44241 AAGATT-TATGGTTCTAATCTGCTCCATTGCAACTTCAAGGAGAT
1 AAGATTAT-TGGTTCTAATCTGCTCCACTGCAACTTCAAGGAGAT
* * *
44285 AGGATTATTGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGAT
1 AAGATTATTGGTTCTAATCTGCTCCACTGCAACTTCAAGGAGAT
** * *
44329 AAGA-T-TTGCCATCTTCAGTCTGC-CTCGCTGCAACTTC-AGGAGGAT
1 AAGATTATTG-GTTC-T-AATCTGCTC-CACTGCAACTTCAAGGA-GAT
* * * *
44374 AAGA--CTT-GCT-TAGTCTGCTCCACTGCAACTTCAGGGAGAT
1 AAGATTATTGGTTCTAATCTGCTCCACTGCAACTTCAAGGAGAT
* * * * * *
44414 AAGACTA--GATGC-GATCTGCT-CTCTGCAACTT-TAGAGAGAT
1 AAGATTATTGGTTCTAATCTGCTCCACTGCAACTTCAAG-GAGAT
* * * * *
44454 AAGATCCA-AGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGAT
1 AAGAT-TATTGGTTCTAATCTGCTCCACTGCAACTTCAAGGAGAT
* * * * * *
44498 AGGATTATCGGCTT-TAACCTGCTCCACTGTAACTTCAGGGAAAT
1 AAGATTATTGG-TTCTAATCTGCTCCACTGCAACTTCAAGGAGAT
* ** * * *
44542 AATA-T-TTGCCATCTTCAGTTTGC-CTCGCTGCAACTTC-AGGAGGAT
1 AAGATTATTG-GTTC-T-AATCTGCTC-CACTGCAACTTCAAGGA-GAT
* * * * *
44587 AAGACTTGCTT-G-TATAGTTTGCTCCACTGCAACTTCAGGGAGAT
1 AAGA-TT-ATTGGTTCTAATCTGCTCCACTGCAACTTCAAGGAGAT
* * * * * *
44631 AAGACTA--GATGC-GATCTGCT-CTCTGCAACTT-TAGAGAGAT
1 AAGATTATTGGTTCTAATCTGCTCCACTGCAACTTCAAG-GAGAT
* * * * *
44671 AAGATCCA-AGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGAT
1 AAGAT-TATTGGTTCTAATCTGCTCCACTGCAACTTCAAGGAGAT
* * * * *
44715 AGGATTATTGGTTTTAATTTGCTCCACTGCAACTTTAGGGAGAT
1 AAGATTATTGGTTCTAATCTGCTCCACTGCAACTTCAAGGAGAT
** * *
44759 AAGA-T-TTGCCATCTTCAGTCTGC-CTCACTGCAACTTC-AGTAGGAT
1 AAGATTATTG-GTTC-T-AATCTGCTC-CACTGCAACTTCAAGGA-GAT
* * * *
44804 AAGA--CTTGCTTGCTTAGTCTGCTCCACTGCAACTTCAGGGAGAT
1 AAGATTATTGGTT-C-TAATCTGCTCCACTGCAACTTCAAGGAGAT
* * * * * *
44848 AAGACTA--GATGC-GATCTGCT-CTCTGCAACTTC-AGAAAGAT
1 AAGATTATTGGTTCTAATCTGCTCCACTGCAACTTCAAG-GAGAT
* ** *
44888 AAGATCT-TTGATT-TAATCCACTCCACTGCAACTTCAGGGAGAT
1 AAGAT-TATTGGTTCTAATCTGCTCCACTGCAACTTCAAGGAGAT
* *
44931 AGGATCATTGG
1 AAGATTATTGG
44942 CTTTCGATCT
Statistics
Matches: 480, Mismatches: 116, Indels: 123
0.67 0.16 0.17
Matches are distributed among these distances:
39 3 0.01
40 82 0.17
41 25 0.05
42 21 0.04
43 44 0.09
44 214 0.45
45 87 0.18
46 1 0.00
47 1 0.00
49 2 0.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (44 bp):
AAGATTATTGGTTCTAATCTGCTCCACTGCAACTTCAAGGAGAT
Found at i:44365 original size:45 final size:40
Alignment explanation
Indices: 44302--44931 Score: 234
Period size: 44 Copynumber: 14.7 Consensus size: 40
44292 TTGGTTTTAA
*
44302 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG----CTT-AG
*
44347 TCTGC-CTCGCTGCAACTTCA-GGAGGATAAGACTTGCTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCTTAG
* * **
44387 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTAG
* * * ** * *
44427 ATCTGCT-CTCTGCAACTTTAGAGAGATAAGATCCAAGGTTTTAA
1 -TCTGCTCCACTGCAACTTCAGGGAGATAAGA--C-TTG-CTTAG
* * * *
44471 TCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACT-T--GC-TTAG
* * * * *
44515 CCTGCTCCACTGTAACTTCAGGGAAATAATATTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG----CTT-AG
* *
44560 TTTGC-CTCGCTGCAACTTCA-GGAGGATAAGACTTGCTTGTATAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGC---T-TAG
* * * **
44604 TTTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTAG
* * * ** * *
44644 ATCTGCT-CTCTGCAACTTTAGAGAGATAAGATCCAAGGTTTTAA
1 -TCTGCTCCACTGCAACTTCAGGGAGATAAGA--C-TTG-CTTAG
* * * * *
44688 TCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA--CTT-G-CTTAG
* * *
44732 TTTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG----CTT-AG
*
44777 TCTGC-CTCACTGCAACTTCA-GTAGGATAAGACTTGCTTGCTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGA----CTTGCTTAG
* * **
44821 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTAG
* ** * *
44861 ATCTGCT-CTCTGCAACTTCAGAAAGATAAGATCTTTGATTTAA
1 -TCTGCTCCACTGCAACTTCAGGGAGATAAGA-C-TTG-CTTAG
**
44904 TCCACTCCACTGCAACTTCAGGGAGATA
1 TCTGCTCCACTGCAACTTCAGGGAGATA
44932 GGATCATTGG
Statistics
Matches: 442, Mismatches: 92, Indels: 104
0.69 0.14 0.16
Matches are distributed among these distances:
40 100 0.23
41 29 0.07
42 10 0.02
43 32 0.07
44 182 0.41
45 86 0.19
49 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (40 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTAG
Found at i:44703 original size:217 final size:216
Alignment explanation
Indices: 44171--44945 Score: 1162
Period size: 217 Copynumber: 3.6 Consensus size: 216
44161 CTTCAATCTA
* * * *
44171 CTCCTCTGCAACTTCAGGGAGATAAGGCTAGATGTGATCTGCTCTCTGCAACTTCATAAAGATAA
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAAAGATAA
* * * * *
44236 GATCCAAGATTTATGGTTCTAATCTGCTCCATTGCAACTTCAAGGAGATAGGATTATTGGTTTTA
66 GATCC---A---A-GGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTA
44301 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCGCTGCAACTTC
124 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCGCTGCAACTTC
44366 AGGAGGATAAGACTTGC---TTAGTCTG
189 AGGAGGATAAGACTTGCTTGTTAGTCTG
* *
44391 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTTAGAGAGATAA
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAAAGATAA
* *
44456 GATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAACCTGCT
66 GATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCT
* * * *
44521 CCACTGTAACTTCAGGGAAATAATATTTGCCATCTTCAGTTTGCCTCGCTGCAACTTCAGGAGGA
131 CCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCGCTGCAACTTCAGGAGGA
*
44586 TAAGACTTGCTTGTATAGTTTG
196 TAAGACTTGCTTGT-TAGTCTG
* *
44608 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTTAGAGAGATAA
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAAAGATAA
* *
44673 GATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGTTTTAATTTGCT
66 GATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCT
* * *
44738 CCACTGCAACTTTAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGTAGGA
131 CCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCGCTGCAACTTCAGGAGGA
44803 TAAGACTTGCTTGCTTAGTCTG
196 TAAGACTTGCTTG-TTAGTCTG
44825 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAAAGATAA
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAAAGATAA
*** * * *
44890 GAT-CTTTGATTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATCATTGGCTTT
66 GATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTT
44946 CGATCTGTTC
Statistics
Matches: 511, Mismatches: 39, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
213 122 0.24
214 1 0.00
216 47 0.09
217 276 0.54
218 1 0.00
220 64 0.13
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (216 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAAAGATAA
GATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCT
CCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCGCTGCAACTTCAGGAGGA
TAAGACTTGCTTGTTAGTCTG
Found at i:65942 original size:8 final size:8
Alignment explanation
Indices: 65901--65954 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
65891 GGATTAATAT
65901 TATTATAA
1 TATTATAA
*
65909 AATT-TAA
1 TATTATAA
*
65916 -AGTTAAAA
1 TA-TTATAA
65924 TA-TATATA
1 TATTATA-A
65932 TATTATAA
1 TATTATAA
65940 TATTATAA
1 TATTATAA
65948 TATTATA
1 TATTATA
65955 TCTTAATGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
6 1 0.03
7 8 0.21
8 24 0.63
9 5 0.13
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (8 bp):
TATTATAA
Found at i:66810 original size:41 final size:39
Alignment explanation
Indices: 66765--66873 Score: 114
Period size: 37 Copynumber: 2.8 Consensus size: 39
66755 ACTTCGAGTT
* **
66765 GATGAGACACTGGGTGTCAATTTACTACTTTGGATTAATTC
1 GATGAGACACTGGGTGTCAATTTA-TACTTCGG-TTAAGCC
* * *
66806 GATGAGGCACTGGGTGCCAA-TT-TACTTCGGTTTAGCC
1 GATGAGACACTGGGTGTCAATTTATACTTCGGTTAAGCC
*
66843 GATGAGACACTGGGTGTTAATTTATTACTTC
1 GATGAGACACTGGGTGTCAATTTA-TACTTC
66874 AAATTATCCG
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
37 21 0.38
38 9 0.16
40 8 0.14
41 18 0.32
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.35
Consensus pattern (39 bp):
GATGAGACACTGGGTGTCAATTTATACTTCGGTTAAGCC
Found at i:66885 original size:40 final size:40
Alignment explanation
Indices: 66765--66898 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 40
66755 ACTTCGAGTT
* * *
66765 GATGAGACACTGGGTGTCAATTTACTACTTTGGATTAATTC
1 GATGAGACACTGGGTGTCAATTTATTACTTCGGATT-ATCC
* * * *
66806 GATGAGGCACTGGGTGCCAA--T-TTACTTCGGTTTAGCC
1 GATGAGACACTGGGTGTCAATTTATTACTTCGGATTATCC
* **
66843 GATGAGACACTGGGTGTTAATTTATTACTTCAAATTATCC
1 GATGAGACACTGGGTGTCAATTTATTACTTCGGATTATCC
* *
66883 GATGAGGCACTAGGTG
1 GATGAGACACTGGGTG
66899 CCAAACTGGT
Statistics
Matches: 74, Mismatches: 16, Indels: 7
0.76 0.16 0.07
Matches are distributed among these distances:
37 19 0.26
38 9 0.12
39 2 0.03
40 26 0.35
41 18 0.24
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (40 bp):
GATGAGACACTGGGTGTCAATTTATTACTTCGGATTATCC
Found at i:89224 original size:21 final size:20
Alignment explanation
Indices: 89182--89241 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
89172 AGCTTATTTA
* **
89182 TATTTTAATTAATCATGTTT
1 TATTTTAATTAATCTTAATT
89202 TAGTTTTAATTAATCTTAATT
1 TA-TTTTAATTAATCTTAATT
* *
89223 TA-CTTAATTAAGCTTAATT
1 TATTTTAATTAATCTTAATT
89242 GTTAATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 15 0.44
20 2 0.06
21 17 0.50
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (20 bp):
TATTTTAATTAATCTTAATT
Found at i:90104 original size:14 final size:14
Alignment explanation
Indices: 90085--90113 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
90075 TAAAACAATG
90085 AAAATATTTTACAT
1 AAAATATTTTACAT
90099 AAAATATTTTACAT
1 AAAATATTTTACAT
90113 A
1 A
90114 CAAACAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAATATTTTACAT
Found at i:94465 original size:21 final size:21
Alignment explanation
Indices: 94441--94487 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
94431 AGATATTGTG
* *
94441 ATACCCAAAGTGGATATCGCT
1 ATACCCAAAATGGATACCGCT
*
94462 ATACCCAAAATGGATACCGTT
1 ATACCCAAAATGGATACCGCT
94483 ATACC
1 ATACC
94488 ACTGTAGGTG
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:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (21 bp):
ATACCCAAAATGGATACCGCT
Found at i:95522 original size:27 final size:27
Alignment explanation
Indices: 95492--95543 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
95482 GAACGCCAGT
*
95492 ACCCCTACGGCGCAGCGGAAAATTAGA
1 ACCCCTACGGCGCAGCAGAAAATTAGA
* *
95519 ACCCCTACTGCGTAGCAGAAAATTA
1 ACCCCTACGGCGCAGCAGAAAATTA
95544 AAACATTCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.35, C:0.29, G:0.21, T:0.15
Consensus pattern (27 bp):
ACCCCTACGGCGCAGCAGAAAATTAGA
Found at i:96597 original size:20 final size:20
Alignment explanation
Indices: 96546--96588 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
96536 CTCTTTCAAA
* *
96546 ATTTC-TTATTTTCATTTGC
1 ATTTCATTACTTTCAATTGC
96565 ATTTCATTACTTTCAATTGC
1 ATTTCATTACTTTCAATTGC
96585 ATTT
1 ATTT
96589 ACTTTCTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.21, C:0.16, G:0.05, T:0.58
Consensus pattern (20 bp):
ATTTCATTACTTTCAATTGC
Found at i:99316 original size:134 final size:134
Alignment explanation
Indices: 99076--99325 Score: 500
Period size: 134 Copynumber: 1.9 Consensus size: 134
99066 GTGTGTATTG
99076 GTATTTAAAAATGATATATTATATGCATGTGGTAAATATTATATGATGATTGTGTGGGTCTTGCC
1 GTATTTAAAAATGATATATTATATGCATGTGGTAAATATTATATGATGATTGTGTGGGTCTTGCC
99141 TTTGGGTGGTATATAGTTTATTGAAATGATTTTATGTGTATTTTAATCATTATATGATATATTTT
66 TTTGGGTGGTATATAGTTTATTGAAATGATTTTATGTGTATTTTAATCATTATATGATATATTTT
99206 ATGT
131 ATGT
99210 GTATTTAAAAATGATATATTATATGCATGTGGTAAATATTATATGATGATTGTGTGGGTCTTGCC
1 GTATTTAAAAATGATATATTATATGCATGTGGTAAATATTATATGATGATTGTGTGGGTCTTGCC
99275 TTTGGGTGGTATATAGTTTATTGAAATGATTTTATGTGTATTTTAATCATT
66 TTTGGGTGGTATATAGTTTATTGAAATGATTTTATGTGTATTTTAATCATT
99326 GTACATGTTG
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
134 116 1.00
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (134 bp):
GTATTTAAAAATGATATATTATATGCATGTGGTAAATATTATATGATGATTGTGTGGGTCTTGCC
TTTGGGTGGTATATAGTTTATTGAAATGATTTTATGTGTATTTTAATCATTATATGATATATTTT
ATGT
Found at i:103463 original size:37 final size:35
Alignment explanation
Indices: 103389--103460 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 35
103379 TAATAACAAA
*
103389 GAAAAATAAAAACAAAAAATATTTTTGGATTTTTT
1 GAAAAATAAAAAAAAAAAATATTTTTGGATTTTTT
103424 GAAAAATAAAAAAATAGAAAATATTTTTGGGATTTTT
1 GAAAAATAAAAAAA-A-AAAATATTTTT-GGATTTTT
103461 GAATTTTTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 13 0.39
36 1 0.03
37 11 0.33
38 8 0.24
ACGTcount: A:0.51, C:0.01, G:0.11, T:0.36
Consensus pattern (35 bp):
GAAAAATAAAAAAAAAAAATATTTTTGGATTTTTT
Found at i:106329 original size:57 final size:57
Alignment explanation
Indices: 106163--106355 Score: 235
Period size: 57 Copynumber: 3.4 Consensus size: 57
106153 TTATTGTTTG
* * ** *
106163 CATGCTATCATAAATTGAATTAAAGCTGTTGTTTGAGTGCGTCAAATTGAGCATTTC
1 CATGCTATCATAAATTGAATTAAAGTTGTTGTTTTAGTGTATCAAATTGAGCATTTT
* * * * * *
106220 CTTACTGTCTTAAATTGAA-TCAAGTTGTTGTTTTAGTGTTTCAAATTGAGCATTTT
1 CATGCTATCATAAATTGAATTAAAGTTGTTGTTTTAGTGTATCAAATTGAGCATTTT
* * *
106276 CATGCTGTCATAAATTGAATTAAAGTTGCTATTTTAGTGTATCAAATTGAGCATTTT
1 CATGCTATCATAAATTGAATTAAAGTTGTTGTTTTAGTGTATCAAATTGAGCATTTT
* *
106333 CATGCTATCTTAAATTAAATTAA
1 CATGCTATCATAAATTGAATTAA
106356 CCTAATGTTT
Statistics
Matches: 115, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
56 47 0.41
57 68 0.59
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.42
Consensus pattern (57 bp):
CATGCTATCATAAATTGAATTAAAGTTGTTGTTTTAGTGTATCAAATTGAGCATTTT
Found at i:106365 original size:113 final size:114
Alignment explanation
Indices: 106163--106414 Score: 292
Period size: 113 Copynumber: 2.2 Consensus size: 114
106153 TTATTGTTTG
* * * * * * *
106163 CATGCTATCATAAATTGAATTAAAGCTGTTGTTTGAGTGCGTCAAATTGAGCATTTCCTTACTGT
1 CATGCTGTCATAAATTGAATTAAAGTTGCTATTTGAGTGCATCAAATTGAGCATTTCCATACTAT
* ** ** * *
106228 CTTAAATTGAATCAAGTTGTTGTTTTAGTGTTTCAAATTGAGCATT-TT
66 CTTAAATTAAATCAACCTAATGTTTTAATGGTTCAAATTGAGCATTATT
* * * *
106276 CATGCTGTCATAAATTGAATTAAAGTTGCTATTTTAGTGTATCAAATTGAGCATTTTCATGCTAT
1 CATGCTGTCATAAATTGAATTAAAGTTGCTATTTGAGTGCATCAAATTGAGCATTTCCATACTAT
* *
106341 CTTAAATTAAATTAACCTAATGTTTTAATGGTTCAAATTGAGTATTATT
66 CTTAAATTAAATCAACCTAATGTTTTAATGGTTCAAATTGAGCATTATT
* *
106390 -ATGCTGTCCTAAATTAAATTAAAGT
1 CATGCTGTCATAAATTGAATTAAAGT
106415 GTTTCTTCAA
Statistics
Matches: 116, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
113 114 0.98
114 2 0.02
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (114 bp):
CATGCTGTCATAAATTGAATTAAAGTTGCTATTTGAGTGCATCAAATTGAGCATTTCCATACTAT
CTTAAATTAAATCAACCTAATGTTTTAATGGTTCAAATTGAGCATTATT
Found at i:106433 original size:56 final size:53
Alignment explanation
Indices: 106163--106450 Score: 179
Period size: 56 Copynumber: 5.1 Consensus size: 53
106153 TTATTGTTTG
* * * * *
106163 CATGCTATCATAAATTGAATTAAAGCTGTTGTTTGAGTGCGTCAAATTGAGCATTTC
1 CATGCTGTCATAAATTAAATTAAAG-TGTT-TTT-AATG-TTCAAATTGAGCATTTT
* * * * * *
106220 CTTACTGTCTTAAATTGAA-TCAAGTTGTTGTTTTAGTGTTTCAAATTGAGCATTTT
1 CATGCTGTCATAAATTAAATTAAAG-TG-T-TTTTAATG-TTCAAATTGAGCATTTT
* *
106276 CATGCTGTCATAAATTGAATTAAAGTTGCTATTTTAGTGTATCAAATTGAGCATTTT
1 CATGCTGTCATAAATTAAATTAAAG-TG-T-TTTTAATGT-TCAAATTGAGCATTTT
* * * *
106333 CATGCTATCTTAAATTAAATTAACCTAATG-TTTTAATGGTTCAAATTGAGTATTATT
1 CATGCTGTCATAAATTAAATTAA---AGTGTTTTTAAT-GTTCAAATTGAGCATT-TT
* * *
106390 -ATGCTGTCCTAAATTAAATTAAAGTGTTTCTTCAATGTCTCAAAGTAAGCATTATT
1 CATGCTGTCATAAATTAAATTAAAGTGTTT-TT-AATGT-TCAAATTGAGCATT-TT
106446 -ATGCT
1 CATGCT
106451 ATTGAAAAAT
Statistics
Matches: 191, Mismatches: 27, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
53 3 0.02
54 2 0.01
55 4 0.02
56 103 0.54
57 75 0.39
58 1 0.01
59 2 0.01
60 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (53 bp):
CATGCTGTCATAAATTAAATTAAAGTGTTTTTAATGTTCAAATTGAGCATTTT
Found at i:106461 original size:113 final size:113
Alignment explanation
Indices: 106248--106452 Score: 249
Period size: 113 Copynumber: 1.8 Consensus size: 113
106238 ATCAAGTTGT
* * * *
106248 TGTTTTAGTGTTTCAAATTGAGCATTTTCATGCTGTCATAAATTGAATTAAAGTTGCTATTTTAG
1 TGTTTTAATGGTTCAAATTGAGCATTTTCATGCTGTCATAAATTAAATTAAAGTTGCTATTTTAA
* * *
106313 TGTATCAAATTGAGCATTTTCATGCTATCTTAAATTAAATTAACCTAA
66 TGTATCAAAGTAAGCATTTTCATGCTATCTAAAATTAAATTAACCTAA
* *
106361 TGTTTTAATGGTTCAAATTGAGTATTATT-ATGCTGTCCTAAATTAAATTAAAG-TG-T-TTCTT
1 TGTTTTAATGGTTCAAATTGAGCATT-TTCATGCTGTCATAAATTAAATTAAAGTTGCTATT-TT
*
106422 CAATGTCTCAAAGTAAGCATTATT-ATGCTAT
64 -AATGTATCAAAGTAAGCATT-TTCATGCTAT
106453 TGAAAAATTG
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
110 2 0.03
111 3 0.04
112 25 0.32
113 47 0.59
114 2 0.03
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (113 bp):
TGTTTTAATGGTTCAAATTGAGCATTTTCATGCTGTCATAAATTAAATTAAAGTTGCTATTTTAA
TGTATCAAAGTAAGCATTTTCATGCTATCTAAAATTAAATTAACCTAA
Found at i:107306 original size:113 final size:113
Alignment explanation
Indices: 107105--107334 Score: 433
Period size: 113 Copynumber: 2.0 Consensus size: 113
107095 GAAAAGTAAG
*
107105 AATATTCATTATATTGATAAAGTACACTACATTCTCTTTTGGCTTATGTGCCTCCAATGTGATGA
1 AATATTCATTATATTGATAAAGTACACCACATTCTCTTTTGGCTTATGTGCCTCCAATGTGATGA
*
107170 AAATTATAAGGAAATCAATAGTAAAATCTTGTTAAATGGTTTTCTTGA
66 AAATTATAAGGAAATCAAGAGTAAAATCTTGTTAAATGGTTTTCTTGA
*
107218 AATATTCATTATATTGATAAAGTACACCACATTCTCTTTTGGCTTATGTGCCTCGAATGTGATGA
1 AATATTCATTATATTGATAAAGTACACCACATTCTCTTTTGGCTTATGTGCCTCCAATGTGATGA
107283 AAATTATAAGGAAATCAAGAGTAAAATCTTGTTAAATGGTTTTCTTGA
66 AAATTATAAGGAAATCAAGAGTAAAATCTTGTTAAATGGTTTTCTTGA
107331 AATA
1 AATA
107335 CATCAATAAT
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 114 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (113 bp):
AATATTCATTATATTGATAAAGTACACCACATTCTCTTTTGGCTTATGTGCCTCCAATGTGATGA
AAATTATAAGGAAATCAAGAGTAAAATCTTGTTAAATGGTTTTCTTGA
Found at i:133460 original size:16 final size:16
Alignment explanation
Indices: 133439--133472 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
133429 TTTCTTCCCC
133439 AACTAAAAGTATAAAG
1 AACTAAAAGTATAAAG
133455 AACTAAAAGTATAAAG
1 AACTAAAAGTATAAAG
133471 AA
1 AA
133473 ACCATAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (16 bp):
AACTAAAAGTATAAAG
Found at i:134392 original size:140 final size:140
Alignment explanation
Indices: 134140--134429 Score: 573
Period size: 140 Copynumber: 2.1 Consensus size: 140
134130 ATGAAATAAA
134140 GTACAAAGTGTTAGTGAAGGTATTGGATAATGGAGAAGGTCCAAAAAATAAATATATAAATAAAA
1 GTACAAAGTGTTAGTGAAGGTATTGGATAATGGAGAAGGTCCAAAAAATAAATATATAAATAAAA
134205 TAAAATATATATTATTATATTATGAGATATAAATTTGAGGTATTAACTAAATTGAGAAAAAGTGA
66 TAAAATATATATTATTATATTATGAGATATAAATTTGAGGTATTAACTAAATTGAGAAAAAGTGA
134270 AAAGTGATGG
131 AAAGTGATGG
134280 GTACAAAGTGTTAGTGAAGGTATTGGATAATGGAGAAGGTCCAAAAAATAAATATATAAATAAAA
1 GTACAAAGTGTTAGTGAAGGTATTGGATAATGGAGAAGGTCCAAAAAATAAATATATAAATAAAA
134345 TAAAATATATATTATTATATTATGAGATATAAATTTGAGGTATTAACTAAATTGAGAAAAAGTGA
66 TAAAATATATATTATTATATTATGAGATATAAATTTGAGGTATTAACTAAATTGAGAAAAAGTGA
134410 AAAGTGATGG
131 AAAGTGATGG
134420 GT-CAAAGTGT
1 GTACAAAGTGT
134430 GAATATTAAA
Statistics
Matches: 150, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
139 8 0.05
140 142 0.95
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (140 bp):
GTACAAAGTGTTAGTGAAGGTATTGGATAATGGAGAAGGTCCAAAAAATAAATATATAAATAAAA
TAAAATATATATTATTATATTATGAGATATAAATTTGAGGTATTAACTAAATTGAGAAAAAGTGA
AAAGTGATGG
Found at i:134739 original size:26 final size:29
Alignment explanation
Indices: 134691--134746 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 29
134681 GATGTTGGTG
134691 ATATTTTAAATAATATATATTAATAATAA
1 ATATTTTAAATAATATATATTAATAATAA
*
134720 ATATTTT-GATAATAT-T-TTAATAATAA
1 ATATTTTAAATAATATATATTAATAATAA
134746 A
1 A
134747 ATGATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 11 0.42
27 1 0.04
28 7 0.27
29 7 0.27
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (29 bp):
ATATTTTAAATAATATATATTAATAATAA
Found at i:142457 original size:16 final size:16
Alignment explanation
Indices: 142406--142448 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
142396 ATTAAAATGT
*
142406 ATAATATATAACATATAA
1 ATAATATTTAA-A-ATAA
*
142424 GTAATATTTAAAATAA
1 ATAATATTTAAAATAA
142440 ATAATATTT
1 ATAATATTT
142449 TATAAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 12 0.55
17 1 0.05
18 9 0.41
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
ATAATATTTAAAATAA
Found at i:143179 original size:44 final size:46
Alignment explanation
Indices: 143129--143227 Score: 130
Period size: 52 Copynumber: 2.1 Consensus size: 46
143119 TACAAGATAG
143129 AAAATTATTTT-AAG-ACATTTGGAAATTTAAAATGACATATATAT
1 AAAATTATTTTAAAGAACATTTGGAAATTTAAAATGACATATATAT
143173 AAAATTATTTTAAAAGAACTTAACATTTGGAAATTTAAAATGACATATATAT
1 AAAATTATTTT-AAAG-----AACATTTGGAAATTTAAAATGACATATATAT
143225 AAA
1 AAA
143228 TATATGATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
44 11 0.23
46 3 0.06
52 33 0.70
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.36
Consensus pattern (46 bp):
AAAATTATTTTAAAGAACATTTGGAAATTTAAAATGACATATATAT
Found at i:150782 original size:40 final size:40
Alignment explanation
Indices: 150711--150787 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
150701 CCTTTTTTTA
**
150711 TTTTTTAATTTTTTAAATCTTTTTTTTAAAAAGTAAAAGT
1 TTTTTTAATTTTTTAAATCTTTTTTAAAAAAAGTAAAAGT
*
150751 TTTTTTCAATTTTTTAAA-CTTTTTTAAAAAAATTAAA
1 TTTTTT-AATTTTTTAAATCTTTTTTAAAAAAAGTAAA
150788 TAATAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 22 0.67
41 11 0.33
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.56
Consensus pattern (40 bp):
TTTTTTAATTTTTTAAATCTTTTTTAAAAAAAGTAAAAGT
Found at i:157590 original size:180 final size:180
Alignment explanation
Indices: 157282--157641 Score: 630
Period size: 180 Copynumber: 2.0 Consensus size: 180
157272 TCATAGGGAC
* *
157282 ATTGTTTGAACCCGTTCTCCTTGAAGTATGTATCGATACGAGTATTCCATGCCCACGGTGCTTGC
1 ATTGTTTGAACCCGTTCTCCTTGAAGTATGTACCAATACGAGTATTCCATGCCCACGGTGCTTGC
*
157347 TTCAACCCGTAAAGTGCCTTATTCAATTTCAGCACCTTCTTCTCTTCTCTATTTTTCATGTACTC
66 TTCAACCAGTAAAGTGCCTTATTCAATTTCAGCACCTTCTTCTCTTCTCTATTTTTCATGTACTC
*
157412 GGGTGGTTGTTCGATGTAGACTTCTTCTTCGAGCACACCATTCAAGAATG
131 GGGTGGTTGTTCGATGTAGACTTCTTCTTCAAGCACACCATTCAAGAATG
* *
157462 ATTGTTTGAACCCGTTCTCCTTGAAGTATGTACCAATACGAGTATTCCATGCTCGCGGTGCTTGC
1 ATTGTTTGAACCCGTTCTCCTTGAAGTATGTACCAATACGAGTATTCCATGCCCACGGTGCTTGC
* * * *
157527 TTCAACCAGTAAAGTGCCTTCTTCAATTTCAGCACCTTTTTCTCTTTTCTATTTTTTATGTACTC
66 TTCAACCAGTAAAGTGCCTTATTCAATTTCAGCACCTTCTTCTCTTCTCTATTTTTCATGTACTC
157592 GGGTGGTTGTTCGATGTAGACTTCTTCTTCAAGCACACCATTCAAGAATG
131 GGGTGGTTGTTCGATGTAGACTTCTTCTTCAAGCACACCATTCAAGAATG
157642 CCGACTTGAC
Statistics
Matches: 170, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
180 170 1.00
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (180 bp):
ATTGTTTGAACCCGTTCTCCTTGAAGTATGTACCAATACGAGTATTCCATGCCCACGGTGCTTGC
TTCAACCAGTAAAGTGCCTTATTCAATTTCAGCACCTTCTTCTCTTCTCTATTTTTCATGTACTC
GGGTGGTTGTTCGATGTAGACTTCTTCTTCAAGCACACCATTCAAGAATG
Found at i:160516 original size:15 final size:15
Alignment explanation
Indices: 160496--160526 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
160486 AAAACAACAT
160496 AACTCTTAACCTTTC
1 AACTCTTAACCTTTC
*
160511 AACTCTTGACCTTTC
1 AACTCTTAACCTTTC
160526 A
1 A
160527 CTTACATAAC
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:0.26, C:0.32, G:0.03, T:0.39
Consensus pattern (15 bp):
AACTCTTAACCTTTC
Found at i:162621 original size:29 final size:29
Alignment explanation
Indices: 162579--162634 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
162569 AAATTTTGTT
* *
162579 CTTTTGTTTGATG-ATTGTGATACTATTCC
1 CTTTTGGTTAATGAATT-TGATACTATTCC
*
162608 CTTTTGGTTAATGAATTTGATTCTATT
1 CTTTTGGTTAATGAATTTGATACTATT
162635 TTATCCCCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.20, C:0.11, G:0.16, T:0.54
Consensus pattern (29 bp):
CTTTTGGTTAATGAATTTGATACTATTCC
Found at i:173222 original size:44 final size:43
Alignment explanation
Indices: 173141--173224 Score: 141
Period size: 43 Copynumber: 1.9 Consensus size: 43
173131 ATACAGAAAG
* *
173141 CTCACAAAAGGTCATGCTTTCAAGGAGCACGCAGAGTGAGCGA
1 CTCACAAAAGCTCATGCTCTCAAGGAGCACGCAGAGTGAGCGA
173184 CTCACAAAAGCTCATGCTCTCAAAGGAGCACGCAGAGTGAG
1 CTCACAAAAGCTCATGCTCTC-AAGGAGCACGCAGAGTGAG
173225 TCGTCTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 19 0.50
44 19 0.50
ACGTcount: A:0.33, C:0.25, G:0.26, T:0.15
Consensus pattern (43 bp):
CTCACAAAAGCTCATGCTCTCAAGGAGCACGCAGAGTGAGCGA
Found at i:173255 original size:42 final size:43
Alignment explanation
Indices: 173142--173256 Score: 112
Period size: 42 Copynumber: 2.7 Consensus size: 43
173132 TACAGAAAGC
* * * *
173142 TCACAAAAGGTCATGCTTTC-AAGGAGCACGCAGAGTGAGCGA
1 TCACAAAAGCTCATACTCTCAAAAGAGCACGCAGAGTGAGCGA
* *
173184 CTCACAAAAGCTCATGCTCTCAAAGGAGCACGCAGAGTGAGTCG-
1 -TCACAAAAGCTCATACTCTCAAAAGAGCACGCAGAGTGAG-CGA
*
173228 TC-TAAAAGCTCATACTCGT-AAAAGAGCAC
1 TCACAAAAGCTCATACTC-TCAAAAGAGCAC
173257 ATAGAAACAG
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
42 22 0.34
43 21 0.33
44 19 0.30
45 2 0.03
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.17
Consensus pattern (43 bp):
TCACAAAAGCTCATACTCTCAAAAGAGCACGCAGAGTGAGCGA
Found at i:182558 original size:21 final size:20
Alignment explanation
Indices: 182515--182564 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
182505 ATTATCAACT
182515 AATATCAAACAATTCATACCG
1 AATATCAAACAATTCATA-CG
182536 AATATCAAATCAAATTCAT-CG
1 AATATCAAA-C-AATTCATACG
*
182557 AATGTCAA
1 AATATCAA
182565 TGACATCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 18 0.69
22 1 0.04
23 7 0.27
ACGTcount: A:0.48, C:0.20, G:0.06, T:0.26
Consensus pattern (20 bp):
AATATCAAACAATTCATACG
Found at i:195361 original size:30 final size:30
Alignment explanation
Indices: 195327--195383 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
195317 AGTGTGGCCA
195327 GGCCATGTGACTCACACGGTCAGGAGAAAC
1 GGCCATGTGACTCACACGGTCAGGAGAAAC
195357 GGCCATGTGACTCACACGGTCAGGAGA
1 GGCCATGTGACTCACACGGTCAGGAGA
195384 CACGCCCGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.26, G:0.32, T:0.14
Consensus pattern (30 bp):
GGCCATGTGACTCACACGGTCAGGAGAAAC
Found at i:195557 original size:12 final size:12
Alignment explanation
Indices: 195540--195569 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
195530 CCTCACATGC
195540 CCATGTGCCAGG
1 CCATGTGCCAGG
*
195552 CCATGTGCTAGG
1 CCATGTGCCAGG
195564 CCATGT
1 CCATGT
195570 AACAGCCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (12 bp):
CCATGTGCCAGG
Found at i:198200 original size:20 final size:20
Alignment explanation
Indices: 198172--198209 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
198162 AACTATCATG
*
198172 TTTTCTTTATTTTATTAACC
1 TTTTATTTATTTTATTAACC
198192 TTTTATTTATTTTATTAA
1 TTTTATTTATTTTATTAA
198210 TAAAATAACA
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:0.08, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTATTTATTTTATTAACC
Found at i:203486 original size:12 final size:11
Alignment explanation
Indices: 203458--203500 Score: 77
Period size: 11 Copynumber: 3.8 Consensus size: 11
203448 ATATTTTTTT
203458 TATTTTTAAAA
1 TATTTTTAAAA
203469 TATTTTTAAAA
1 TATTTTTAAAA
203480 TATTTTTAAAA
1 TATTTTTAAAA
203491 TACTTTTTAA
1 TA-TTTTTAA
203501 TAGGGACTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 24 0.77
12 7 0.23
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:203915 original size:476 final size:476
Alignment explanation
Indices: 203023--203973 Score: 1877
Period size: 476 Copynumber: 2.0 Consensus size: 476
203013 GAAATTGTCA
203023 AATAGGGACTAAATTAAAAATTAGGAAATTATACATGGTGAAATTGTGAAATAAATAAAATATAG
1 AATAGGGACTAAATTAAAAATTAGGAAATTATACATGGTGAAATTGTGAAATAAATAAAATATAG
203088 GGCATGCTAGGGACCTAATTATAGTCGGCCATAGTGGGTTGTGGTGAAATTGCATAAATTTCCAT
66 GGCATGCTAGGGACCTAATTATAGTCGGCCATAGTGGGTTGTGGTGAAATTGCATAAATTTCCAT
203153 TTTTATGAGCTAGAGACTAAATTACAAAGAAATTAAAAGTATATGGGCAAAATCGTAATTTTGCA
131 TTTTATGAGCTAGAGACTAAATTACAAAGAAATTAAAAGTATATGGGCAAAATCGTAATTTTGCA
203218 AAAATATTTGGGTTAAATTGAATGAAATATATTTTGAATTGAGTTAAATTTATCTATTTAGGTCT
196 AAAATATTTGGGTTAAATTGAATGAAATATATTTTGAATTGAGTTAAATTTATCTATTTAGGTCT
203283 AGAGGTGTCCATGGGCTGGGCGGCCCGGCCCGGCCCGACGACCTGTCCTAAATATGTGAGGGTTC
261 AGAGGTGTCCATGGGCTGGGCGGCCCGGCCCGGCCCGACGACCTGTCCTAAATATGTGAGGGTTC
203348 GGGGTAAAATATAGGCCCAAAATATGGGTTTGGGCAAAAAAACTAAACAGGCTGGGCTCGGGCAC
326 GGGGTAAAATATAGGCCCAAAATATGGGTTTGGGCAAAAAAACTAAACAGGCTGGGCTCGGGCAC
203413 CACTTTTTTGCCCGGACCCGGCCCAGATATAATAAATATTTTTTTTATTTTTAAAATATTTTTAA
391 CACTTTTTTGCCCGGACCCGGCCCAGATATAATAAATATTTTTTTTATTTTTAAAATATTTTTAA
203478 AATATTTTTAAAATACTTTTT
456 AATATTTTTAAAATACTTTTT
203499 AATAGGGACTAAATTAAAAATTAGGAAATTATACATGGTGAAATTGTGAAATAAATAAAATATAG
1 AATAGGGACTAAATTAAAAATTAGGAAATTATACATGGTGAAATTGTGAAATAAATAAAATATAG
203564 GGCATGCTAGGGACCTAATTATAGTCGGCCATAGTGGGTTGTGGTGAAATTGCATAAATTTCCAT
66 GGCATGCTAGGGACCTAATTATAGTCGGCCATAGTGGGTTGTGGTGAAATTGCATAAATTTCCAT
203629 TTTTATGAGCTAGAGACTAAATTACAAAGAAATTAAAAGTATATGGGCAAAATCGTAATTTTGCA
131 TTTTATGAGCTAGAGACTAAATTACAAAGAAATTAAAAGTATATGGGCAAAATCGTAATTTTGCA
203694 AAAATATTTGGGTTAAATTGAATGAAATATATTTTGAATTGAGTTAAATTTATCTATTTAGGTCT
196 AAAATATTTGGGTTAAATTGAATGAAATATATTTTGAATTGAGTTAAATTTATCTATTTAGGTCT
203759 AGAGGTGTCCATGGGCTGGGCGGCCCGGCCCGGCCCGACGACCTGTCCTAAATATGTGAGGGTTC
261 AGAGGTGTCCATGGGCTGGGCGGCCCGGCCCGGCCCGACGACCTGTCCTAAATATGTGAGGGTTC
*
203824 -GGGTAAAAATATAGGCCCAAAATATGGGTTTGGGCAAAAAAACTAAACAGGCTGGGCTCGGGCC
326 GGGGT-AAAATATAGGCCCAAAATATGGGTTTGGGCAAAAAAACTAAACAGGCTGGGCTCGGGCA
203888 CCACTTTTTTGCCCGGACCCGGCCCAGATATAATAAATATTTTTTTTATTTTTAAAATATTTTTA
390 CCACTTTTTTGCCCGGACCCGGCCCAGATATAATAAATATTTTTTTTATTTTTAAAATATTTTTA
203953 AAATATTTTTAAAATACTTTT
455 AAATATTTTTAAAATACTTTT
203974 ATTTATTTTT
Statistics
Matches: 473, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
475 4 0.01
476 469 0.99
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (476 bp):
AATAGGGACTAAATTAAAAATTAGGAAATTATACATGGTGAAATTGTGAAATAAATAAAATATAG
GGCATGCTAGGGACCTAATTATAGTCGGCCATAGTGGGTTGTGGTGAAATTGCATAAATTTCCAT
TTTTATGAGCTAGAGACTAAATTACAAAGAAATTAAAAGTATATGGGCAAAATCGTAATTTTGCA
AAAATATTTGGGTTAAATTGAATGAAATATATTTTGAATTGAGTTAAATTTATCTATTTAGGTCT
AGAGGTGTCCATGGGCTGGGCGGCCCGGCCCGGCCCGACGACCTGTCCTAAATATGTGAGGGTTC
GGGGTAAAATATAGGCCCAAAATATGGGTTTGGGCAAAAAAACTAAACAGGCTGGGCTCGGGCAC
CACTTTTTTGCCCGGACCCGGCCCAGATATAATAAATATTTTTTTTATTTTTAAAATATTTTTAA
AATATTTTTAAAATACTTTTT
Found at i:203950 original size:11 final size:11
Alignment explanation
Indices: 203934--203974 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
203924 ATATTTTTTT
203934 TATTTTTAAAA
1 TATTTTTAAAA
203945 TATTTTTAAAA
1 TATTTTTAAAA
203956 TATTTTTAAAA
1 TATTTTTAAAA
*
203967 TACTTTTA
1 TATTTTTA
203975 TTTATTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:203983 original size:22 final size:21
Alignment explanation
Indices: 203922--203985 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
203912 CAGATATAAT
*
203922 AAATATTTTTTTTA-TTTTTA
1 AAATATTTTATTTATTTTTTA
**
203942 AAATATTTT-TAAAATATTTTTA
1 AAATATTTTAT-TTAT-TTTTTA
203964 AAATACTTTTATTTATTTTTTA
1 AAATA-TTTTATTTATTTTTTA
203986 TTTTTAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 1 0.03
20 10 0.29
22 17 0.49
23 6 0.17
24 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
AAATATTTTATTTATTTTTTA
Found at i:205731 original size:11 final size:11
Alignment explanation
Indices: 205715--205755 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
205705 ATATTTTTTT
205715 TATTTTTAAAA
1 TATTTTTAAAA
205726 TATTTTTAAAA
1 TATTTTTAAAA
205737 TATTTTTAAAA
1 TATTTTTAAAA
*
205748 TACTTTTA
1 TATTTTTA
205756 TTTATTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:205764 original size:22 final size:21
Alignment explanation
Indices: 205703--205766 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
205693 CAGATATAAT
*
205703 AAATATTTTTTTTA-TTTTTA
1 AAATATTTTATTTATTTTTTA
**
205723 AAATATTTT-TAAAATATTTTTA
1 AAATATTTTAT-TTAT-TTTTTA
205745 AAATACTTTTATTTATTTTTTA
1 AAATA-TTTTATTTATTTTTTA
205767 TTTTTAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 1 0.03
20 10 0.29
22 17 0.49
23 6 0.17
24 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
AAATATTTTATTTATTTTTTA
Found at i:206100 original size:21 final size:20
Alignment explanation
Indices: 206049--206101 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
206039 TGTGTAATTA
* * *
206049 AATTGTATTTATATGTTTTT
1 AATTGTATATATATGTTATG
*
206069 AATTGAAATATATATGTTATG
1 AATTG-TATATATATGTTATG
206090 AATTGTCATATA
1 AATTGT-ATATA
206102 AAATTACCGA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (20 bp):
AATTGTATATATATGTTATG
Found at i:206412 original size:25 final size:25
Alignment explanation
Indices: 206311--206412 Score: 91
Period size: 25 Copynumber: 4.1 Consensus size: 25
206301 AGAAAGCAAA
*
206311 ACTGATCTACAGCTCGAGTAAGCAT
1 ACTGATCTACAACTCGAGTAAGCAT
*
206336 ACTAATCTACAGA-TCGAGTAAGCAT
1 ACTGATCTACA-ACTCGAGTAAGCAT
* * * * * *
206361 ACTGATTTATAGCTTG-GGAGAGTAT
1 ACTGATCTACAACTCGAGTA-AGCAT
*
206386 ACTGATCTACAACTCGAGTGAGCAT
1 ACTGATCTACAACTCGAGTAAGCAT
206411 AC
1 AC
206413 CGATTCACAG
Statistics
Matches: 57, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
24 2 0.04
25 54 0.95
26 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (25 bp):
ACTGATCTACAACTCGAGTAAGCAT
Found at i:206426 original size:25 final size:25
Alignment explanation
Indices: 206267--206426 Score: 67
Period size: 25 Copynumber: 6.4 Consensus size: 25
206257 GCGGATACTC
* *
206267 CACAGCTCGTGTGAGCATACCGATT
1 CACAGCTCGAGTAAGCATACCGATT
* * * * * *
206292 TATAGCTCAAGAAAGCAAAACTGA-T
1 CACAGCTCGAGTAAGC-ATACCGATT
* *
206317 CTACAGCTCGAGTAAGCATA-CTAAT
1 C-ACAGCTCGAGTAAGCATACCGATT
* *
206342 CTACAGATCGAGTAAGCATACTGATT
1 C-ACAGCTCGAGTAAGCATACCGATT
* * * * * *
206368 TATAGCTTG-GGAGAGTATACTGA-T
1 CACAGCTCGAGTA-AGCATACCGATT
* *
206392 CTACAACTCGAGTGAGCATACCGATT
1 C-ACAGCTCGAGTAAGCATACCGATT
206418 CACAGCTCG
1 CACAGCTCG
206427 TATGAGTATA
Statistics
Matches: 93, Mismatches: 34, Indels: 16
0.65 0.24 0.11
Matches are distributed among these distances:
24 4 0.04
25 67 0.72
26 22 0.24
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (25 bp):
CACAGCTCGAGTAAGCATACCGATT
Found at i:211194 original size:21 final size:21
Alignment explanation
Indices: 211133--211194 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 21
211123 CTTTCTGTTT
* * *
211133 AGCTTTTTCGAGCTTCTGTTT
1 AGCTCTTTCGAGCTTCCGTTC
* * * * *
211154 AACTCATACGAGTTTTCGTTC
1 AGCTCTTTCGAGCTTCCGTTC
211175 AGCTCTTTCGAGCTTCCGTT
1 AGCTCTTTCGAGCTTCCGTT
211195 AACCCTTATG
Statistics
Matches: 28, Mismatches: 13, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (21 bp):
AGCTCTTTCGAGCTTCCGTTC
Found at i:211215 original size:41 final size:41
Alignment explanation
Indices: 211124--211250 Score: 137
Period size: 41 Copynumber: 3.1 Consensus size: 41
211114 CGTGTTTTAC
* * * * * * *
211124 TTTCTGTTTAGCTTTTTCGAGCTTCTGTTTAACTCATACGAG
1 TTTCCGTTCAGCTCTTTCGAGCTTCTG-TTAACCCTTATGGG
* *
211166 TTTTCGTTCAGCTCTTTCGAGCTTCCGTTAACCCTTATGGG
1 TTTCCGTTCAGCTCTTTCGAGCTTCTGTTAACCCTTATGGG
* * *
211207 TTTCCGTTCTGCTCTTACAAGCTTCTGTTAACCCTTATGGG
1 TTTCCGTTCAGCTCTTTCGAGCTTCTGTTAACCCTTATGGG
211248 TTT
1 TTT
211251 AGGTCTCATG
Statistics
Matches: 71, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
41 49 0.69
42 22 0.31
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (41 bp):
TTTCCGTTCAGCTCTTTCGAGCTTCTGTTAACCCTTATGGG
Found at i:213324 original size:20 final size:20
Alignment explanation
Indices: 213281--213322 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
213271 TAAAGAAAGT
213281 AAATGCAATGGAAAGTAATG
1 AAATGCAATGGAAAGTAATG
213301 AAATGCAAAT-GAAAGTAA-G
1 AAATGC-AATGGAAAGTAATG
213320 AAA
1 AAA
213323 ATTTGGAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 14 0.67
21 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.17
Consensus pattern (20 bp):
AAATGCAATGGAAAGTAATG
Found at i:213793 original size:15 final size:16
Alignment explanation
Indices: 213773--213802 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
213763 TGGTGCCTTG
213773 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
213788 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
213803 AGCATGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:213981 original size:32 final size:32
Alignment explanation
Indices: 213945--214006 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
213935 CCAACTAGAT
* *
213945 ATGGTTAGATTTGTGTAATTTAGATGGCCTTG
1 ATGGTTAGAGTTGTGTAATTTAGACGGCCTTG
*
213977 ATGGTTGGAGTTGTGTAATTTAGACGGCCT
1 ATGGTTAGAGTTGTGTAATTTAGACGGCCT
214007 GGCACACTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.21, C:0.08, G:0.31, T:0.40
Consensus pattern (32 bp):
ATGGTTAGAGTTGTGTAATTTAGACGGCCTTG
Found at i:216582 original size:25 final size:23
Alignment explanation
Indices: 216536--216701 Score: 109
Period size: 23 Copynumber: 7.1 Consensus size: 23
216526 AAAATAGTAA
* * *
216536 GTATACTTGGTTTTGTTCGGAGG
1 GTATAATTGGTTGTGTTTGGAGG
* *
216559 TTATATATATGGTTGTGTATGGAGG
1 GTATA-AT-TGGTTGTGTTTGGAGG
* *
216584 GTATACTTGGTTGGGTTTGGAGG
1 GTATAATTGGTTGTGTTTGGAGG
* ** *
216607 TTATAAATAAAGTTGTGTTTGAAGG
1 GTAT-AAT-TGGTTGTGTTTGGAGG
216632 GTATAATTGGTTGTG-TTGGAGG
1 GTATAATTGGTTGTGTTTGGAGG
** * *
216654 GTATGTTTAGTTGTGTTTGGAAG
1 GTATAATTGGTTGTGTTTGGAGG
* ** * *
216677 ATATGTTTGGTTATGTTTGGTGG
1 GTATAATTGGTTGTGTTTGGAGG
216700 GT
1 GT
216702 GATAGTTTTA
Statistics
Matches: 109, Mismatches: 29, Indels: 10
0.74 0.20 0.07
Matches are distributed among these distances:
22 18 0.17
23 52 0.48
24 7 0.06
25 32 0.29
ACGTcount: A:0.19, C:0.02, G:0.35, T:0.44
Consensus pattern (23 bp):
GTATAATTGGTTGTGTTTGGAGG
Found at i:216607 original size:48 final size:48
Alignment explanation
Indices: 216536--216653 Score: 148
Period size: 48 Copynumber: 2.5 Consensus size: 48
216526 AAAATAGTAA
* * * ** *
216536 GTATACTTGGTTTTGTTCGGAGGTTATATATATGGTTGTGTATGGAGG
1 GTATACTTGGTTGTGTTTGGAGGTTATAAATAAAGTTGTGTATGAAGG
* *
216584 GTATACTTGGTTGGGTTTGGAGGTTATAAATAAAGTTGTGTTTGAAGG
1 GTATACTTGGTTGTGTTTGGAGGTTATAAATAAAGTTGTGTATGAAGG
*
216632 GTATAATTGGTTGTG-TTGGAGG
1 GTATACTTGGTTGTGTTTGGAGG
216654 GTATGTTTAG
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
47 7 0.12
48 53 0.88
ACGTcount: A:0.21, C:0.03, G:0.35, T:0.42
Consensus pattern (48 bp):
GTATACTTGGTTGTGTTTGGAGGTTATAAATAAAGTTGTGTATGAAGG
Found at i:220896 original size:3 final size:3
Alignment explanation
Indices: 220888--220929 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
220878 ATAAGTAAAT
* *
220888 ATA ATA ATA ATA ATA GTA GTA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
220930 CAAAGATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:220972 original size:21 final size:23
Alignment explanation
Indices: 220935--220982 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
220925 TAATACAAAG
220935 ATAATGGTATAATATAA-T-AAT
1 ATAATGGTATAATATAAGTAAAT
*
220956 ATAATGGTAATGA-ATAAGTAAAT
1 ATAATGGT-ATAATATAAGTAAAT
220979 ATAA
1 ATAA
220983 AAAGAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 12 0.52
22 4 0.17
23 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.33
Consensus pattern (23 bp):
ATAATGGTATAATATAAGTAAAT
Found at i:222812 original size:51 final size:51
Alignment explanation
Indices: 222726--222937 Score: 201
Period size: 51 Copynumber: 4.2 Consensus size: 51
222716 CTTTAGTCTT
* * * * *
222726 TAACGCCAGAGAGATAAGATTCGCTGCCTTCAGCTTTAATCTACTCCGCTG
1 TAACGCCAGAGAAACAAGATTCGCTACCTTTAGCTTTAATCTGCTCCGCTG
* * * * *
222777 TAACGCCAGGGAAACAAGATTCTCTACCTTTAGCTTTAATATGTTCCACTG
1 TAACGCCAGAGAAACAAGATTCGCTACCTTTAGCTTTAATCTGCTCCGCTG
* *** * * *
222828 TAATGCCA-AGAAGATTGGATTCGCTGCCTTTAGCTTTAATCTGCTCTGCTA
1 TAACGCCAGAGAA-ACAAGATTCGCTACCTTTAGCTTTAATCTGCTCCGCTG
* * * * *
222879 TAACACCAGGGAAACAAGATTCTCTACCTTTAGCTTTAATCTGTTCCACTG
1 TAACGCCAGAGAAACAAGATTCGCTACCTTTAGCTTTAATCTGCTCCGCTG
*
222930 TAAGGCCA
1 TAACGCCA
222938 AGCAGATAGG
Statistics
Matches: 123, Mismatches: 36, Indels: 4
0.75 0.22 0.02
Matches are distributed among these distances:
50 3 0.02
51 117 0.95
52 3 0.02
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (51 bp):
TAACGCCAGAGAAACAAGATTCGCTACCTTTAGCTTTAATCTGCTCCGCTG
Found at i:222924 original size:102 final size:102
Alignment explanation
Indices: 222737--222970 Score: 369
Period size: 102 Copynumber: 2.3 Consensus size: 102
222727 AACGCCAGAG
* * *
222737 AGATAAGATTCGCTGCCTTCAGCTTTAATCTACTCCGCTGTAACGCCAGGGAAACAAGATTCTCT
1 AGATAGGATTCGCTGCCTTCAGCTTTAATCTACTCCGCTATAACACCAGGGAAACAAGATTCTCT
*
222802 ACCTTTAGCTTTAATATGTTCCACTGTAATGCCAAGA
66 ACCTTTAGCTTTAATATGTTCCACTGTAAGGCCAAGA
* * * *
222839 AGATTGGATTCGCTGCCTTTAGCTTTAATCTGCTCTGCTATAACACCAGGGAAACAAGATTCTCT
1 AGATAGGATTCGCTGCCTTCAGCTTTAATCTACTCCGCTATAACACCAGGGAAACAAGATTCTCT
* *
222904 ACCTTTAGCTTTAATCTGTTCCACTGTAAGGCCAAGC
66 ACCTTTAGCTTTAATATGTTCCACTGTAAGGCCAAGA
*
222941 AGATAGGATTCGCTGCCTTCATCTTTAATC
1 AGATAGGATTCGCTGCCTTCAGCTTTAATC
222971 CATTCCACTT
Statistics
Matches: 119, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
102 119 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.32
Consensus pattern (102 bp):
AGATAGGATTCGCTGCCTTCAGCTTTAATCTACTCCGCTATAACACCAGGGAAACAAGATTCTCT
ACCTTTAGCTTTAATATGTTCCACTGTAAGGCCAAGA
Found at i:222951 original size:51 final size:51
Alignment explanation
Indices: 222726--222979 Score: 190
Period size: 51 Copynumber: 5.0 Consensus size: 51
222716 CTTTAGTCTT
* * * ** *
222726 TAACGCC-AGAGAGATAAGATTCGCTGCCTTCAGCTTTAATCTACTCCGCTG
1 TAACGCCAAGA-AGATAGGATTCGCTACCTTTAGCTTTAATCTGTTCCACTG
* * * * *
222777 TAACGCCAGGGAA-ACAAGATTCTCTACCTTTAGCTTTAATATGTTCCACTG
1 TAACGCCA-AGAAGATAGGATTCGCTACCTTTAGCTTTAATCTGTTCCACTG
* * * * ** *
222828 TAATGCCAAGAAGATTGGATTCGCTGCCTTTAGCTTTAATCTGCTCTGCTA
1 TAACGCCAAGAAGATAGGATTCGCTACCTTTAGCTTTAATCTGTTCCACTG
* * * * *
222879 TAACACCAGGGAA-ACAAGATTCTCTACCTTTAGCTTTAATCTGTTCCACTG
1 TAACGCCA-AGAAGATAGGATTCGCTACCTTTAGCTTTAATCTGTTCCACTG
* * * * * **
222930 TAAGGCCAAGCAGATAGGATTCGCTGCCTTCATCTTTAATCCATTCCACT
1 TAACGCCAAGAAGATAGGATTCGCTACCTTTAGCTTTAATCTGTTCCACT
222980 TCAACTTTAA
Statistics
Matches: 153, Mismatches: 45, Indels: 10
0.74 0.22 0.05
Matches are distributed among these distances:
50 5 0.03
51 142 0.93
52 4 0.03
53 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (51 bp):
TAACGCCAAGAAGATAGGATTCGCTACCTTTAGCTTTAATCTGTTCCACTG
Found at i:223005 original size:21 final size:21
Alignment explanation
Indices: 222963--223005 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
222953 CTGCCTTCAT
*
222963 CTTTAATCCATTCCACTTCAA
1 CTTTAATCCATTCCACTGCAA
** *
222984 CTTTAATTTATTCCAGTGCAA
1 CTTTAATCCATTCCACTGCAA
223005 C
1 C
223006 GCTAGGGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.05, T:0.40
Consensus pattern (21 bp):
CTTTAATCCATTCCACTGCAA
Found at i:223074 original size:51 final size:51
Alignment explanation
Indices: 222984--223143 Score: 187
Period size: 51 Copynumber: 3.1 Consensus size: 51
222974 TCCACTTCAA
* * * * * *
222984 CTTTAATTTATTCCAGTGCAACGCTAGGGAAATATGATTCGCTACCTTTAG
1 CTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTACCTTTAG
* *
223035 CTTTAATCTGTTCCACTGCAACGCCAGAGAAACAAGATTCTCTACCTTTAG
1 CTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTACCTTTAG
* * * * *
223086 CTTTAATCTGTTCTACTGTAACGCCA-AGGAGATAGGATTCGCTACCTTCAG
1 CTTTAATCTGTTCCACTGCAACGCCAGA-GAAATAAGATTCGCTACCTTTAG
223137 CTTTAAT
1 CTTTAAT
223144 ACGCTCCACT
Statistics
Matches: 93, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
50 1 0.01
51 92 0.99
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (51 bp):
CTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTACCTTTAG
Found at i:223106 original size:174 final size:174
Alignment explanation
Indices: 222845--223248 Score: 583
Period size: 174 Copynumber: 2.3 Consensus size: 174
222835 AAGAAGATTG
* * ** ** * *
222845 GATTCGCTGCCTTTAGCTTTAATCTGCTCTGCTATAACACCAGGGAAACAAGATTCTCTACCTTT
1 GATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGAGAAACAAGATTCTCTACCTTT
* * * * *
222910 AGCTTTAATCTGTTCCACTGTAAGGCCAAGCAGATAGGATTCGCTGCCTTCATCTTTAATCCATT
66 AGCTTTAATCTGTTCCACTGTAACGCCAAGCAGATAGGATTCGCTACCTTCAGCTTTAATACACT
* *
222975 CCACTTCAACTTTAATTTATTCCAGTGCAACGCTAGGGAAATAT
131 CCACTTCAACTTTAATCTATTCCAGTGCAACGCTAGGGAAATAA
223019 GATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGAGAAACAAGATTCTCTACCTTT
1 GATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGAGAAACAAGATTCTCTACCTTT
* * *
223084 AGCTTTAATCTGTTCTACTGTAACGCCAAGGAGATAGGATTCGCTACCTTCAGCTTTAATACGCT
66 AGCTTTAATCTGTTCCACTGTAACGCCAAGCAGATAGGATTCGCTACCTTCAGCTTTAATACACT
* *
223149 CCACTTCATCTTTAATCTATTCTAGTGCAACGCTAGGGAAATAA
131 CCACTTCAACTTTAATCTATTCCAGTGCAACGCTAGGGAAATAA
* * * * *
223193 GATTCGCTATCTTTAGCTTTAATCTGTTCCACGGCAATGCCAAAGAAAAAAGATTC
1 GATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGAGAAACAAGATTC
223249 GCTGCCTACA
Statistics
Matches: 205, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
174 205 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (174 bp):
GATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGAGAAACAAGATTCTCTACCTTT
AGCTTTAATCTGTTCCACTGTAACGCCAAGCAGATAGGATTCGCTACCTTCAGCTTTAATACACT
CCACTTCAACTTTAATCTATTCCAGTGCAACGCTAGGGAAATAA
Found at i:224695 original size:88 final size:89
Alignment explanation
Indices: 224558--224754 Score: 369
Period size: 88 Copynumber: 2.2 Consensus size: 89
224548 CAAGGTGCCC
224558 TTTGCGAGTTTTCACCTTGGCCTCTTCTTTTTCTTTTTCTTCTTTCTTATTATTATTTTTTATAT
1 TTTGCGAGTTTTCACCTTGGCCTCTTCTTTTTCTTTTTCTTCTTTCTTATTATTATTTTTTATAT
224623 TA-TTTTTATGACTCAAAGCACCA
66 TATTTTTTATGACTCAAAGCACCA
224646 TTTGCGAGTTTTCACCTTGGCCTCTTCTTTTTCTTTTTCTTCTTTCTTATTATTATTTTTTATAT
1 TTTGCGAGTTTTCACCTTGGCCTCTTCTTTTTCTTTTTCTTCTTTCTTATTATTATTTTTTATAT
*
224711 TATTTTTTATGACTCAAAGCACCC
66 TATTTTTTATGACTCAAAGCACCA
*
224735 TTTGCGGGTTTTCACCTTGG
1 TTTGCGAGTTTTCACCTTGG
224755 TCTTTTTTTT
Statistics
Matches: 106, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
88 67 0.63
89 39 0.37
ACGTcount: A:0.15, C:0.20, G:0.10, T:0.55
Consensus pattern (89 bp):
TTTGCGAGTTTTCACCTTGGCCTCTTCTTTTTCTTTTTCTTCTTTCTTATTATTATTTTTTATAT
TATTTTTTATGACTCAAAGCACCA
Found at i:224713 original size:12 final size:12
Alignment explanation
Indices: 224696--224720 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
224686 TCTTTCTTAT
224696 TATTATTTTTTA
1 TATTATTTTTTA
224708 TATTATTTTTTA
1 TATTATTTTTTA
224720 T
1 T
224721 GACTCAAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTATTTTTTA
Found at i:224782 original size:46 final size:44
Alignment explanation
Indices: 224713--224842 Score: 154
Period size: 46 Copynumber: 2.9 Consensus size: 44
224703 TTTTATATTA
* * *
224713 TTTTTTATG-ACTCAAAGCACCCTTTGCGGGTTTTCACCTTGGTC
1 TTTTTTA-GAACTCAAAGCGCCCTTTACGGGTTTTCACCTTAGTC
* * *
224757 TTTTTTTTAGAACTTAAGGCGCCCTTTACCGGTTTTCACCTTAGTC
1 --TTTTTTAGAACTCAAAGCGCCCTTTACGGGTTTTCACCTTAGTC
* *
224803 TTTTTTAGAACTCAAAGCGCCCTTTACGAGTTTTCGCCTT
1 TTTTTTAGAACTCAAAGCGCCCTTTACGGGTTTTCACCTT
224843 TGTCCCTTCT
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
44 35 0.49
45 1 0.01
46 36 0.50
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.42
Consensus pattern (44 bp):
TTTTTTAGAACTCAAAGCGCCCTTTACGGGTTTTCACCTTAGTC
Found at i:225757 original size:11 final size:11
Alignment explanation
Indices: 225743--225785 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
225733 GGCCTCTCCT
*
225743 TTTTCTTTTCC
1 TTTTCTTTTTC
225754 TTTTCTTTTTC
1 TTTTCTTTTTC
*
225765 TTCTCTTTTTC
1 TTTTCTTTTTC
225776 TTTTCTTTTT
1 TTTTCTTTTT
225786 TCATCATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:225763 original size:17 final size:17
Alignment explanation
Indices: 225741--225784 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
225731 TTGGCCTCTC
225741 CTTTTTCTTTTCCTTTT
1 CTTTTTCTTTTCCTTTT
* *
225758 CTTTTTCTTCTCTTTTT
1 CTTTTTCTTTTCCTTTT
225775 C-TTTTCTTTT
1 CTTTTTCTTTT
225785 TTCATCATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (17 bp):
CTTTTTCTTTTCCTTTT
Found at i:225785 original size:6 final size:6
Alignment explanation
Indices: 225741--225785 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
225731 TTGGCCTCTC
* *
225741 CTTTTT C-TTTT CCTTTT CTTTTT C-TTCT CTTTTT C-TTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
225786 TCATCATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
5 14 0.42
6 19 0.58
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
CTTTTT
Found at i:225801 original size:22 final size:21
Alignment explanation
Indices: 225748--225805 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
225738 CTCCTTTTTC
*
225748 TTTTCCTTTTCTTTTTCTTCTCT
1 TTTT-CTTTTC-TTTTCTTCTCA
225771 TTTTCTTTTCTTTT-TTCATCA
1 TTTTCTTTTCTTTTCTTC-TCA
225792 TTTTCATTTT-TTTT
1 TTTTC-TTTTCTTTT
225806 AAATATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.09
21 15 0.47
22 10 0.31
23 4 0.12
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTCTTTTCTTTTCTTCTCA
Found at i:230784 original size:26 final size:26
Alignment explanation
Indices: 230727--230785 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
230717 AGCTTTTATA
*
230727 AACCCAATTAACCTAGCCCAAAATCT
1 AACCCAATTAACCTAGCCCAAAACCT
230753 AACCCAATTAACCTAGCCC-AAACCT
1 AACCCAATTAACCTAGCCCAAAACCT
230778 AAGCCCAA
1 AA-CCCAA
230786 CACCCTACCC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 7 0.23
26 24 0.77
ACGTcount: A:0.42, C:0.37, G:0.05, T:0.15
Consensus pattern (26 bp):
AACCCAATTAACCTAGCCCAAAACCT
Found at i:230792 original size:25 final size:25
Alignment explanation
Indices: 230727--230798 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 25
230717 AGCTTTTATA
* *
230727 AACCCAATTAACCTAGCCCAAAATCT
1 AACCCAATCAACCTAGCCC-AAACCT
*
230753 AACCCAATTAACCTAGCCCAAACCT
1 AACCCAATCAACCTAGCCCAAACCT
* *
230778 AAGCCCAA-CACCCTACCCCAA
1 AA-CCCAATCAACCTAGCCCAA
230799 CCGGCCTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
25 17 0.41
26 24 0.59
ACGTcount: A:0.40, C:0.42, G:0.04, T:0.14
Consensus pattern (25 bp):
AACCCAATCAACCTAGCCCAAACCT
Found at i:232126 original size:4 final size:4
Alignment explanation
Indices: 232119--232173 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
232109 TCATATATAT
232119 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
232167 ATAC ATA
1 ATAC ATA
232174 ATCCATTGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:237759 original size:8 final size:8
Alignment explanation
Indices: 237738--237788 Score: 63
Period size: 8 Copynumber: 6.6 Consensus size: 8
237728 TTTGAGTCCA
237738 AAAAAATG
1 AAAAAATG
*
237746 TGAAAAATG
1 -AAAAAATG
237755 AAAAAATG
1 AAAAAATG
237763 AAAAAATG
1 AAAAAATG
237771 --AAAATG
1 AAAAAATG
237777 -AAAAATG
1 AAAAAATG
237784 AAAAA
1 AAAAA
237789 GTAAAAATAG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
6 6 0.16
7 6 0.16
8 19 0.50
9 7 0.18
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (8 bp):
AAAAAATG
Found at i:237774 original size:14 final size:13
Alignment explanation
Indices: 237746--237787 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 13
237736 CAAAAAAATG
237746 TGAAAAATGAAAAAA
1 TGAAAAATG--AAAA
237761 TGAAAAAATGAAAA
1 TG-AAAAATGAAAA
237775 TGAAAAATGAAAA
1 TGAAAAATGAAAA
237788 AGTAAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 11 0.42
14 6 0.23
15 2 0.08
16 7 0.27
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
TGAAAAATGAAAA
Found at i:237794 original size:14 final size:13
Alignment explanation
Indices: 237747--237796 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 13
237737 AAAAAAATGT
237747 GAAAAATGAAAAAA
1 GAAAAATG-AAAAA
*
237761 TGAAAAAATGAAAAT
1 -G-AAAAATGAAAAA
237776 GAAAAATGAAAAA
1 GAAAAATGAAAAA
237789 GTAAAAAT
1 G-AAAAAT
237797 AGAGAGGCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 12 0.39
14 7 0.23
15 5 0.16
16 7 0.23
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
GAAAAATGAAAAA
Found at i:239169 original size:50 final size:50
Alignment explanation
Indices: 239111--239556 Score: 281
Period size: 50 Copynumber: 9.2 Consensus size: 50
239101 GCAGTGGAAC
* * *
239111 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGTAGTTAAAA
1 AGATTAAAGCCACATCGGCGAATCTTGCTTCCCAGACATTGAAGTTAAAA
* * * * * ** *
239161 AGATTAAAGCTACAACAGCGAATCTTAC-TCCCTAGGCGA-TGCAA-TGGAAT
1 AGATTAAAGCCACATCGGCGAATCTTGCTTCCC-AGAC-ATTG-AAGTTAAAA
*
239211 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCAGACATTGAAGTTAAAA
1 AGATTAAAGCCACATCGGCGAATCTTGCTTCCCAGACATTGAAGTTAAAA
* * * * * ** *
239261 AGATTAAAGCTACAACAGCGAATCTTAC-TCCCTAGGCGA-TGCAA-TGGAAT
1 AGATTAAAGCCACATCGGCGAATCTTGCTTCCC-AGAC-ATTG-AAGTTAAAA
*
239311 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCAGACATTGAAGTTAAAA
1 AGATTAAAGCCACATCGGCGAATCTTGCTTCCCAGACATTGAAGTTAAAA
* * * * * * ** *
239361 AGATTAAAGCTACAACAGCGAA---T-CTT--AAG-CAGTGCAGTGGAAC
1 AGATTAAAGCCACATCGGCGAATCTTGCTTCCCAGACATTGAAGTTAAAA
*
239404 AGATTAAAGCCACAAT-GGCGAATCTTGCTTCCCCGACATTGAAGTTAAAA
1 AGATTAAAGCCAC-ATCGGCGAATCTTGCTTCCCAGACATTGAAGTTAAAA
* * * * * * ** *
239454 AGATTAAAGCTACAACAGCGAA---T-CTT--AAG-CAGTGCAGTGGAAC
1 AGATTAAAGCCACATCGGCGAATCTTGCTTCCCAGACATTGAAGTTAAAA
*
239497 AGATTAAAGCCACAAT-GGCGAATCTTGCTTCCCCGACATTGCAA-TTAAAA
1 AGATTAAAGCCAC-ATCGGCGAATCTTGCTTCCCAGACATTG-AAGTTAAAA
239547 AGATTAAAGC
1 AGATTAAAGC
239557 TACAACAGCC
Statistics
Matches: 288, Mismatches: 78, Indels: 60
0.68 0.18 0.14
Matches are distributed among these distances:
43 52 0.18
44 5 0.02
46 8 0.03
47 8 0.03
49 17 0.06
50 184 0.64
51 14 0.05
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCCACATCGGCGAATCTTGCTTCCCAGACATTGAAGTTAAAA
Found at i:239258 original size:100 final size:99
Alignment explanation
Indices: 239085--239565 Score: 690
Period size: 100 Copynumber: 4.9 Consensus size: 99
239075 AATATTAGTT
239085 TTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
1 TTAC-TCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
*
239150 TGTAGTTAAAAAGATTAAAGCTACAACAGCGAATC
65 TGAAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* * *
239185 TTACTCCCTAGGCGATGCAATGGAATAGATTAAAGCCACATCGGTGAATCTTGCTTCCCAGACAT
1 TTACTCCC-AGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
239250 TGAAGTTAAAAAGATTAAAGCTACAACAGCGAATC
65 TGAAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* * *
239285 TTACTCCCTAGGCGATGCAATGGAATAGATTAAAGCCACATCGGTGAATCTTGCTTCCCAGACAT
1 TTACTCCC-AGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
239350 TGAAGTTAAAAAGATTAAAGCTACAACAGCGAATC
65 TGAAGTTAAAAAGATTAAAGCTACAACAGCGAATC
*
239385 TTA-----A-GC-AGTGCAGTGGAACAGATTAAAGCCACAAT-GGCGAATCTTGCTTCCCCGACA
1 TTACTCCCAGGCGA-TGCAGTGGAACAGATTAAAGCCAC-ATCGGTGAATCTTGCTTCCCCGACA
239442 TTGAAGTTAAAAAGATTAAAGCTACAACAGCGAATC
64 TTGAAGTTAAAAAGATTAAAGCTACAACAGCGAATC
*
239478 TTA-----A-GC-AGTGCAGTGGAACAGATTAAAGCCACAAT-GGCGAATCTTGCTTCCCCGACA
1 TTACTCCCAGGCGA-TGCAGTGGAACAGATTAAAGCCAC-ATCGGTGAATCTTGCTTCCCCGACA
239535 TTGCAA-TTAAAAAGATTAAAGCTACAACAGC
64 TTG-AAGTTAAAAAGATTAAAGCTACAACAGC
239566 CGACATTGCA
Statistics
Matches: 369, Mismatches: 8, Indels: 15
0.94 0.02 0.04
Matches are distributed among these distances:
92 1 0.00
93 165 0.45
94 5 0.01
99 4 0.01
100 194 0.53
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (99 bp):
TTACTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATT
GAAGTTAAAAAGATTAAAGCTACAACAGCGAATC
Found at i:239425 original size:43 final size:43
Alignment explanation
Indices: 239361--239522 Score: 144
Period size: 43 Copynumber: 3.6 Consensus size: 43
239351 GAAGTTAAAA
*
239361 AGATTAAAGCTACAACAGCGAATCTTAAGCAGTGCAGTGGAAC
1 AGATTAAAGCCACAACAGCGAATCTTAAGCAGTGCAGTGGAAC
** ** * * ** *
239404 AGATTAAAGCCACAATGGCGAATCTTGCTTCCCCGACATTGAAGTTAAAA
1 AGATTAAAGCCACAACAGCGAA---T-CTT--AAG-CAGTGCAGTGGAAC
*
239454 AGATTAAAGCTACAACAGCGAATCTTAAGCAGTGCAGTGGAAC
1 AGATTAAAGCCACAACAGCGAATCTTAAGCAGTGCAGTGGAAC
**
239497 AGATTAAAGCCACAATGGCGAATCTT
1 AGATTAAAGCCACAACAGCGAATCTT
239523 GCTTCCCCGA
Statistics
Matches: 89, Mismatches: 23, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
43 51 0.57
44 1 0.01
46 4 0.04
47 4 0.04
49 1 0.01
50 28 0.31
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (43 bp):
AGATTAAAGCCACAACAGCGAATCTTAAGCAGTGCAGTGGAAC
Found at i:239581 original size:36 final size:36
Alignment explanation
Indices: 239529--239601 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
239519 TCTTGCTTCC
239529 CCGACATTGCAATTAAAAAGATTAAAGCTACAACAG
1 CCGACATTGCAATTAAAAAGATTAAAGCTACAACAG
*
239565 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAG
1 CCGACATTGCAATTAAAAAGATTAAAGCTACAACAG
239601 C
1 C
239602 GAATCTTACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.45, C:0.21, G:0.15, T:0.19
Consensus pattern (36 bp):
CCGACATTGCAATTAAAAAGATTAAAGCTACAACAG
Found at i:239598 original size:129 final size:131
Alignment explanation
Indices: 239436--239701 Score: 412
Period size: 136 Copynumber: 2.0 Consensus size: 131
239426 TCTTGCTTCC
239436 CCGACATTGAAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTA-A-GCAGTGCAGTGGAACAG
1 CCGACATTGAAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACAGGCAGTGCAGTGGAACAG
*
239499 ATTAAAGCCACAAT-GGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTAAAGCTACAAC
66 ATTAAAGCCAC-ATCGGCGAATCTTACTTCCCCGACATTGCAATTAAAAAGATTAAAGCTACAAC
239563 AG
130 AG
* *
239565 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCTAGGCGGTGCAGTGG
1 CCGACATTGAAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTA----C-AGGCAGTGCAGTGG
* *
239630 AACAGATTAAAGCCACATCGGTGAATCTTACTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTA
61 AACAGATTAAAGCCACATCGGCGAATCTTACTTCCCCGACATTGCAATTAAAAAGATTAAAGCTA
239695 CAACAG
126 CAACAG
239701 C
1 C
239702 GAATCTTACT
Statistics
Matches: 124, Mismatches: 5, Indels: 9
0.90 0.04 0.07
Matches are distributed among these distances:
129 44 0.35
135 3 0.02
136 77 0.62
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (131 bp):
CCGACATTGAAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACAGGCAGTGCAGTGGAACAG
ATTAAAGCCACATCGGCGAATCTTACTTCCCCGACATTGCAATTAAAAAGATTAAAGCTACAACA
G
Found at i:239656 original size:50 final size:49
Alignment explanation
Indices: 239580--240049 Score: 287
Period size: 50 Copynumber: 9.6 Consensus size: 49
239570 ATTGCAGTTA
*
239580 AAAAGATTAAAGCTACAACAGCGAATCTTACTCCCTAGGCGGTGCAGTGG
1 AAAAGATTAAAGCCACAACAGCGAATCTTACTCCC-AGGCGGTGCAGTGG
* * * * * * ** **
239630 AACAGATTAAAGCCACATCGGTGAATCTTACTTCCCCGACATTGCAGTTA
1 AAAAGATTAAAGCCACAACAGCGAATCTTAC-TCCCAGGCGGTGCAGTGG
* *
239680 AAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCGGTGCAGTGG
1 AAAAGATTAAAGCCACAACAGCGAATCTTACT-CCCAGGCGGTGCAGTGG
* ** * * *
239730 AATAGATTAAAGCCACAATGGCGAATCTTGCTTCCC---C-G-ACA-TTG
1 AAAAGATTAAAGCCACAACAGCGAATCTTAC-TCCCAGGCGGTGCAGTGG
* * *
239774 --CA-ATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCGGTGCAGTGG
1 AAAAGATTAAAGCCACAACAGCGAATCTTACT-CCCAGGCGGTGCAGTGG
* ** * * * * ** **
239821 AATAGATTAAAGCCACAATGGCGAACCTTGCTTCCCCGACATTGCAGTTA
1 AAAAGATTAAAGCCACAACAGCGAATCTTAC-TCCCAGGCGGTGCAGTGG
* * * *
239871 AAAAGATTAAAGCTAGAACAGCGAATCTTACTTCTCAAGCGGTGCAGTGG
1 AAAAGATTAAAGCCACAACAGCGAATCTTAC-TCCCAGGCGGTGCAGTGG
* * * * * **** *
239921 AACAGATTAACGCCACAACGGTGAATCTTGCTTCCTC-GATATTGCAGT-T
1 AAAAGATTAAAGCCACAACAGCGAATCTTAC-TCC-CAGGCGGTGCAGTGG
* * *
239970 AGAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCGGTGTAATGG
1 A-AAAGATTAAAGCCACAACAGCGAATCTTAC-TCCCAGGCGGTGCAGTGG
* * *
240021 AACAGATTGAAGCTACAACAGCGAATCTT
1 AAAAGATTAAAGCCACAACAGCGAATCTT
240050 GCTTCCTCGA
Statistics
Matches: 308, Mismatches: 94, Indels: 36
0.70 0.21 0.08
Matches are distributed among these distances:
40 1 0.00
41 25 0.08
42 1 0.00
44 3 0.01
45 3 0.01
46 3 0.01
47 3 0.01
49 4 0.01
50 257 0.83
51 8 0.03
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (49 bp):
AAAAGATTAAAGCCACAACAGCGAATCTTACTCCCAGGCGGTGCAGTGG
Found at i:239738 original size:100 final size:100
Alignment explanation
Indices: 239565--240082 Score: 689
Period size: 100 Copynumber: 5.3 Consensus size: 100
239555 GCTACAACAG
* *
239565 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCTAGGCGGTGCAGTGG
1 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCGGTGCAGTGG
* *
239630 AACAGATTAAAGCCACATCGGTGAATCTTACTTCC
66 AACAGATTAAAGCCACATCGGCGAATCTTGCTTCC
239665 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCGGTGCAGTGG
1 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCGGTGCAGTGG
*
239730 AATAGATTAAAGCCACAAT-GGCGAATCTTGCTTCC
66 AACAGATTAAAGCCAC-ATCGGCGAATCTTGCTTCC
239765 CCGACATTGC--------A-ATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCGGTGCAGTGG
1 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCGGTGCAGTGG
* *
239821 AATAGATTAAAGCCACAAT-GGCGAACCTTGCTTCC
66 AACAGATTAAAGCCAC-ATCGGCGAATCTTGCTTCC
* * *
239856 CCGACATTGCAGTTAAAAAGATTAAAGCTAGAACAGCGAATCTTACTTCTCAAGCGGTGCAGTGG
1 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCGGTGCAGTGG
* * *
239921 AACAGATTAACGCCACAACGGTGAATCTTGCTTCC
66 AACAGATTAAAGCCACATCGGCGAATCTTGCTTCC
* * * * * * *
239956 TCGATATTGCAGTTAGAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCGGTGTAATGG
1 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCGGTGCAGTGG
* * * *
240021 AACAGATTGAAGCTACAACAGCGAATCTTGCTTCC
66 AACAGATTAAAGCCACATCGGCGAATCTTGCTTCC
* ** *
240056 TCGACATCACAGTTAAACAGATTAAAG
1 CCGACATTGCAGTTAAAAAGATTAAAG
240083 TTACGAGTTA
Statistics
Matches: 375, Mismatches: 32, Indels: 22
0.87 0.07 0.05
Matches are distributed among these distances:
91 89 0.24
92 1 0.00
99 2 0.01
100 281 0.75
101 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.23
Consensus pattern (100 bp):
CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCGGTGCAGTGG
AACAGATTAAAGCCACATCGGCGAATCTTGCTTCC
Found at i:239816 original size:191 final size:197
Alignment explanation
Indices: 239574--240082 Score: 690
Period size: 191 Copynumber: 2.6 Consensus size: 197
239564 GCCGACATTG
* *
239574 CAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCTAGGCGGTGCAGTGGAACAGATTA
1 CAGTTAGAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAGGCGGTGCAGTGGAACAGATTA
* *
239639 AAGCCACATCGGTGAATCTTACTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGA
66 AAGCCACATCGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGA
* *
239704 ATCTTACTCCCCAAGCGGTGCAGTGGAATAGATTAAAGCCACAATGGCGAATCTTGCTTCCCCG-
131 ATCTTACTCCCCAAGCGGTGCAGTGGAACAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGA
239768 A-
196 AT
* * *
239769 CA-TT-G-CA-ATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCGGTGCAGTGGAATAGATTA
1 CAGTTAGAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAGGCGGTGCAGTGGAACAGATTA
* *
239830 AAGCCACAAT-GGCGAACCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTAGAACAGCG
66 AAGCCAC-ATCGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCG
* * * * *
239894 AATCTTACTTCTCAAGCGGTGCAGTGGAACAGATTAACGCCACAACGGTGAATCTTGCTTCCTCG
130 AATCTTACTCCCCAAGCGGTGCAGTGGAACAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCG
239959 ATATT
195 A-A-T
* * *
239964 GCAGTTAGAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCGGTGTAATGGAACAGATT
1 -CAGTTAGAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAGGCGGTGCAGTGGAACAGATT
* * * * * ** *
240029 GAAGCTACAACAGCGAATCTTGCTTCCTCGACATCACAGTTAAACAGATTAAAG
65 AAAGCCACATCGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAG
240083 TTACGAGTTA
Statistics
Matches: 272, Mismatches: 31, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
191 166 0.61
192 3 0.01
193 1 0.00
194 2 0.01
195 2 0.01
196 2 0.01
197 2 0.01
198 1 0.00
199 2 0.01
200 91 0.33
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (197 bp):
CAGTTAGAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAGGCGGTGCAGTGGAACAGATTA
AAGCCACATCGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGA
ATCTTACTCCCCAAGCGGTGCAGTGGAACAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGA
AT
Found at i:240075 original size:50 final size:50
Alignment explanation
Indices: 239776--240082 Score: 217
Period size: 50 Copynumber: 6.1 Consensus size: 50
239766 CGACATTGCA
* * * ** ** *
239776 ATTAAAGCTACAACAGCGAATCTTAC-TCCCCAAGCGGTGCAGTGGAATAG
1 ATTAAAGCTACAACAGCGAATCTTGCTTCCTCGA-CATTGCAGTTAAACAG
* ** * * *
239826 ATTAAAGCCACAATGGCGAACCTTGCTTCCCCGACATTGCAGTTAAAAAG
1 ATTAAAGCTACAACAGCGAATCTTGCTTCCTCGACATTGCAGTTAAACAG
* * * ** **
239876 ATTAAAGCTAGAACAGCGAATCTTACTT-CTCAAGCGGTGCAGTGGAACAG
1 ATTAAAGCTACAACAGCGAATCTTGCTTCCTCGA-CATTGCAGTTAAACAG
* * * * *
239926 ATTAACGCCACAACGGTGAATCTTGCTTCCTCGATATTGCAGTTAGAA-AG
1 ATTAAAGCTACAACAGCGAATCTTGCTTCCTCGACATTGCAGTTA-AACAG
* * ** * * **
239976 ATTAAAGCTACAACAGCGAATCTTACTTCC-CAGGCGGTGTAATGGAACAG
1 ATTAAAGCTACAACAGCGAATCTTGCTTCCTC-GACATTGCAGTTAAACAG
* **
240026 ATTGAAGCTACAACAGCGAATCTTGCTTCCTCGACATCACAGTTAAACAG
1 ATTAAAGCTACAACAGCGAATCTTGCTTCCTCGACATTGCAGTTAAACAG
240076 ATTAAAG
1 ATTAAAG
240083 TTACGAGTTA
Statistics
Matches: 189, Mismatches: 61, Indels: 14
0.72 0.23 0.05
Matches are distributed among these distances:
49 6 0.03
50 170 0.90
51 13 0.07
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (50 bp):
ATTAAAGCTACAACAGCGAATCTTGCTTCCTCGACATTGCAGTTAAACAG
Found at i:240612 original size:13 final size:13
Alignment explanation
Indices: 240594--240618 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
240584 AACATATTGT
240594 ATTTTTATTTTAG
1 ATTTTTATTTTAG
240607 ATTTTTATTTTA
1 ATTTTTATTTTA
240619 TTTTCCTTTT
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:0.04, T:0.72
Consensus pattern (13 bp):
ATTTTTATTTTAG
Found at i:241577 original size:4 final size:4
Alignment explanation
Indices: 241576--241666 Score: 164
Period size: 4 Copynumber: 22.8 Consensus size: 4
241566 TCATATATAT
* *
241576 ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATAT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
241624 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
241667 ATCCATTGTT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 83 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:243085 original size:3 final size:3
Alignment explanation
Indices: 243077--243118 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
243067 ATAAGTAAAT
* *
243077 ATA ATA ATA ATA ATA GTA GTA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
243119 CAAAGATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:243161 original size:21 final size:23
Alignment explanation
Indices: 243124--243171 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
243114 TAATACAAAG
243124 ATAATGGTATAATATAA-T-AAT
1 ATAATGGTATAATATAAGTAAAT
*
243145 ATAATGGTAATGA-ATAAGTAAAT
1 ATAATGGT-ATAATATAAGTAAAT
243168 ATAA
1 ATAA
243172 AAAGAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 12 0.52
22 4 0.17
23 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.33
Consensus pattern (23 bp):
ATAATGGTATAATATAAGTAAAT
Found at i:251036 original size:22 final size:21
Alignment explanation
Indices: 251011--251063 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 21
251001 GAAATTGGTT
251011 ATATATATTGCACTTAT-ATATA
1 ATATATATTG--CTTATAATATA
251033 ATATAT-TGTGCTTATAGATATA
1 ATATATAT-TGCTTATA-ATATA
251055 ATATATATT
1 ATATATATT
251064 ATTAGATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
20 5 0.19
21 1 0.04
22 20 0.74
23 1 0.04
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.47
Consensus pattern (21 bp):
ATATATATTGCTTATAATATA
Found at i:251038 original size:20 final size:21
Alignment explanation
Indices: 251013--251060 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
251003 AATTGGTTAT
251013 ATATATTGCACTTAT-ATATA
1 ATATATTGCACTTATAATATA
**
251033 ATATATTGTGCTTATAGATATA
1 ATATATTGCACTTATA-ATATA
251055 ATATAT
1 ATATAT
251061 ATTATTAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.54
22 11 0.46
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (21 bp):
ATATATTGCACTTATAATATA
Found at i:254453 original size:22 final size:22
Alignment explanation
Indices: 254428--254478 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
254418 CATCAAAATG
254428 TATATACAAATATAATATTTAT
1 TATATACAAATATAATATTTAT
*
254450 TATATACGAATATAATATTTAT
1 TATATACAAATATAATATTTAT
254472 TATATAC
1 TATATAC
254479 CTATGTTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (22 bp):
TATATACAAATATAATATTTAT
Found at i:260565 original size:132 final size:131
Alignment explanation
Indices: 260429--260692 Score: 449
Period size: 132 Copynumber: 2.0 Consensus size: 131
260419 AATAACAGCC
*
260429 ACAATAACTGCAACACTCTTTTCAACCACAACCTGAAATGGTTCGTCC-GACTCAACCTGCTTCA
1 ACAATAACTGCAACACCCTTTTCAACCACAACCTGAAATGGTTCG-CCTGACTCAACCTGCTTCA
* *
260493 CCTGTGCGTACTACGACTCCCCATAAGGTTGATCCTATTCGAGAAATTCAAAAAAGAGGTGTCAA
65 CCT-TGCCTACTACGACTCCCCATAAGGTTGATCCTATTCGAGAAATTCAAAAAAGAGGCGTCAA
260558 GGA
129 GGA
260561 ACAATAACTGCAACACCCTTTTCAACCACAACCTGAAATGGTTCGCCTGACTCAACCTGCTTCAC
1 ACAATAACTGCAACACCCTTTTCAACCACAACCTGAAATGGTTCGCCTGACTCAACCTGCTTCAC
* * *
260626 CTTGCCTACTATGACTCCTCATAAGGTTGATCCTATTTGAGAAATTCAAAAAAGAGGCGTCAAGG
66 CTTGCCTACTACGACTCCCCATAAGGTTGATCCTATTCGAGAAATTCAAAAAAGAGGCGTCAAGG
260691 A
131 A
260692 A
1 A
260693 TTTATTGGTG
Statistics
Matches: 125, Mismatches: 6, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
131 62 0.50
132 63 0.50
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (131 bp):
ACAATAACTGCAACACCCTTTTCAACCACAACCTGAAATGGTTCGCCTGACTCAACCTGCTTCAC
CTTGCCTACTACGACTCCCCATAAGGTTGATCCTATTCGAGAAATTCAAAAAAGAGGCGTCAAGG
A
Found at i:265024 original size:41 final size:39
Alignment explanation
Indices: 264979--265109 Score: 131
Period size: 40 Copynumber: 3.3 Consensus size: 39
264969 CGACTTCGAG
264979 TCGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAAT
1 TCGATGAGACACTGGGTGTCAATTTA-TACTTCGGATT-AT
* * * * * *
265020 TCGATGAGGCACTGGGTGCCAA-TT-TACGTCAGTTTAG
1 TCGATGAGACACTGGGTGTCAATTTATACTTCGGATTAT
* *
265057 TCGATGAGACACTAGGTGTCAATTTATTACTTCGAATTAT
1 TCGATGAGACACTGGGTGTCAATTTA-TACTTCGGATTAT
* *
265097 TTGATGAGGCACT
1 TCGATGAGACACT
265110 AAGTGCCAAA
Statistics
Matches: 71, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
37 20 0.28
38 10 0.14
40 21 0.30
41 20 0.28
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.34
Consensus pattern (39 bp):
TCGATGAGACACTGGGTGTCAATTTATACTTCGGATTAT
Found at i:265080 original size:37 final size:38
Alignment explanation
Indices: 264977--265082 Score: 115
Period size: 37 Copynumber: 2.7 Consensus size: 38
264967 TTCGACTTCG
* *
264977 AGTCGATGAGACACTGGGTGTCAATTTACTACTTCGGATTA
1 AGTCGATGAGACACTGGGTGTCAA-TT--TACGTCAGATTA
* * * *
265018 ATTCGATGAGGCACTGGGTGCCAATTTACGTCAG-TTT
1 AGTCGATGAGACACTGGGTGTCAATTTACGTCAGATTA
*
265055 AGTCGATGAGACACTAGGTGTCAATTTA
1 AGTCGATGAGACACTGGGTGTCAATTTA
265083 TTACTTCGAA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
37 26 0.47
38 6 0.11
40 2 0.04
41 21 0.38
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.31
Consensus pattern (38 bp):
AGTCGATGAGACACTGGGTGTCAATTTACGTCAGATTA
Found at i:265258 original size:14 final size:14
Alignment explanation
Indices: 265239--265282 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
265229 AATGGAAGTG
265239 AAATAGTGAATTGA
1 AAATAGTGAATTGA
265253 AAATA--GAATGTG-
1 AAATAGTGAAT-TGA
265265 AAATAGTGAATTGA
1 AAATAGTGAATTGA
265279 AAAT
1 AAAT
265283 TGGAATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 9 0.35
13 4 0.15
14 13 0.50
ACGTcount: A:0.52, C:0.00, G:0.20, T:0.27
Consensus pattern (14 bp):
AAATAGTGAATTGA
Found at i:265266 original size:26 final size:25
Alignment explanation
Indices: 265228--265282 Score: 92
Period size: 26 Copynumber: 2.2 Consensus size: 25
265218 ATGGTATGAG
*
265228 AAATGGAAGTGAAATAGTGAATTGA
1 AAATAGAAGTGAAATAGTGAATTGA
265253 AAATAGAATGTGAAATAGTGAATTGA
1 AAATAGAA-GTGAAATAGTGAATTGA
265279 AAAT
1 AAAT
265283 TGGAATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 7 0.25
26 21 0.75
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.25
Consensus pattern (25 bp):
AAATAGAAGTGAAATAGTGAATTGA
Found at i:265279 original size:13 final size:13
Alignment explanation
Indices: 265237--265280 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
265227 GAAATGGAAG
265237 TGAAATAGTGAAT
1 TGAAATAGTGAAT
265250 TGAAA-A-TAGAAT
1 TGAAATAGT-GAAT
265262 GTGAAATAGTGAAT
1 -TGAAATAGTGAAT
265276 TGAAA
1 TGAAA
265281 ATTGGAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
11 1 0.04
12 5 0.19
13 15 0.56
14 5 0.19
15 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (13 bp):
TGAAATAGTGAAT
Found at i:267720 original size:39 final size:40
Alignment explanation
Indices: 267610--267765 Score: 115
Period size: 39 Copynumber: 3.9 Consensus size: 40
267600 CTTACGCAAC
* * * * *
267610 ATACTAAAATTTCTAAAGGTATACCAAAATATCTGA-A-GAA
1 ATACCAAAATCTCTAATGG-ATACCAAAATTTCTAACACG-A
* * * *
267650 ATATCAAAATTTCTAAAGGGGTACCAAAATTTCTAACACG-
1 ATACCAAAATCTCT-AATGGATACCAAAATTTCTAACACGA
* *
267690 TTACCAAAATCTCTAATGGATACCAAAATTTCCT-A-ATGA
1 ATACCAAAATCTCTAATGGATACCAAAATTT-CTAACACGA
* * *
267729 ATGCCAAAATCTCTAATGGATACCTACATTTCTAACA
1 ATACCAAAATCTCTAATGGATACCAAAATTTCTAACA
267766 TATACCTACA
Statistics
Matches: 93, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
38 4 0.04
39 44 0.47
40 39 0.42
41 5 0.05
42 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.29
Consensus pattern (40 bp):
ATACCAAAATCTCTAATGGATACCAAAATTTCTAACACGA
Found at i:267727 original size:20 final size:19
Alignment explanation
Indices: 267691--267752 Score: 88
Period size: 19 Copynumber: 3.2 Consensus size: 19
267681 TCTAACACGT
267691 TACCAAAATCTCTAATGGA
1 TACCAAAATCTCTAATGGA
* *
267710 TACCAAAATTTCCTAATGAA
1 TACCAAAATCT-CTAATGGA
*
267730 TGCCAAAATCTCTAATGGA
1 TACCAAAATCTCTAATGGA
267749 TACC
1 TACC
267753 TACATTTCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
19 20 0.56
20 16 0.44
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (19 bp):
TACCAAAATCTCTAATGGA
Found at i:267762 original size:19 final size:19
Alignment explanation
Indices: 267610--267763 Score: 103
Period size: 20 Copynumber: 7.8 Consensus size: 19
267600 CTTACGCAAC
* *
267610 ATACTAAAATTTCTAAAGG
1 ATACCAAAATTTCTAATGG
* *
267629 TATACCAAAATATCTGAA-GAA
1 -ATACCAAAATTTCT-AATG-G
* *
267650 ATATCAAAATTTCTAAAGGG
1 ATACCAAAATTTCT-AATGG
* **
267670 GTACCAAAATTTCTAACACG
1 ATACCAAAATTTCTAA-TGG
* *
267690 TTACCAAAATCTCTAATGG
1 ATACCAAAATTTCTAATGG
*
267709 ATACCAAAATTTCCTAATGA
1 ATACCAAAATTT-CTAATGG
* *
267729 ATGCCAAAATCTCTAATGG
1 ATACCAAAATTTCTAATGG
* *
267748 ATACCTACATTTCTAA
1 ATACCAAAATTTCTAA
267764 CATATACCTA
Statistics
Matches: 104, Mismatches: 25, Indels: 11
0.74 0.18 0.08
Matches are distributed among these distances:
19 31 0.30
20 70 0.67
21 3 0.03
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (19 bp):
ATACCAAAATTTCTAATGG
Found at i:268926 original size:20 final size:20
Alignment explanation
Indices: 268903--268947 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
268893 TGCATTATAG
*
268903 ATTTTAGTA-TTAGTTAAAA
1 ATTTTAGTATTTAATTAAAA
*
268922 AATTTAGTATTTAATTAAAA
1 ATTTTAGTATTTAATTAAAA
268942 ATTTTA
1 ATTTTA
268948 AAAATTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (20 bp):
ATTTTAGTATTTAATTAAAA
Found at i:271492 original size:13 final size:13
Alignment explanation
Indices: 271474--271499 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
271464 AACTTAGCCG
271474 TTCCTTCTGTTTC
1 TTCCTTCTGTTTC
271487 TTCCTTCTGTTTC
1 TTCCTTCTGTTTC
271500 AGTTTAGCTG
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:0.00, C:0.31, G:0.08, T:0.62
Consensus pattern (13 bp):
TTCCTTCTGTTTC
Found at i:275342 original size:18 final size:17
Alignment explanation
Indices: 275314--275348 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
275304 AATTATAAGA
*
275314 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
275331 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
275349 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:275621 original size:16 final size:16
Alignment explanation
Indices: 275585--275634 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
275575 GATTTCCTAT
*
275585 TACACCTCTAATCC-A
1 TACACCTCAAATCCAA
*
275600 -ACACCTCCAATCCAA
1 TACACCTCAAATCCAA
*
275615 TACACCTCAAATCTAA
1 TACACCTCAAATCCAA
275631 TACA
1 TACA
275635 GCGAACCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.40
15 1 0.03
16 17 0.57
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.22
Consensus pattern (16 bp):
TACACCTCAAATCCAA
Found at i:276255 original size:21 final size:21
Alignment explanation
Indices: 276222--276278 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
276212 ATTTTTTTAA
* *
276222 ATTAAACCCTGAACCTTGAAC
1 ATTAAATCTTGAACCTTGAAC
* * *
276243 ATTAAATCTTGAACATTTACC
1 ATTAAATCTTGAACCTTGAAC
*
276264 CTTAAATCTTGAACC
1 ATTAAATCTTGAACC
276279 CTAAATATTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.37, C:0.25, G:0.07, T:0.32
Consensus pattern (21 bp):
ATTAAATCTTGAACCTTGAAC
Found at i:277295 original size:41 final size:41
Alignment explanation
Indices: 277250--277380 Score: 110
Period size: 41 Copynumber: 3.1 Consensus size: 41
277240 AAAATATAAT
277250 TAATATATTTTTTCATGTGAATTTTAAATATTTTATTGAAA
1 TAATATATTTTTTCATGTGAATTTTAAATATTTTATTGAAA
* * * ** *
277291 TAATAT-TTTAATT-AAGAT-CATTTT-TTTATTTAATAAAATT-AAT
1 TAATATATTT-TTTCATG-TGAATTTTAAATATTT--T---ATTGAAA
277334 TAATATATTTTTTCATGTGAATTTTAAATATTTTATTGAAA
1 TAATATATTTTTTCATGTGAATTTTAAATATTTTATTGAAA
277375 TAATAT
1 TAATAT
277381 TTTAATTAAG
Statistics
Matches: 66, Mismatches: 12, Indels: 24
0.65 0.12 0.24
Matches are distributed among these distances:
39 5 0.08
40 13 0.20
41 18 0.27
43 12 0.18
44 13 0.20
45 5 0.08
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.53
Consensus pattern (41 bp):
TAATATATTTTTTCATGTGAATTTTAAATATTTTATTGAAA
Found at i:277298 original size:39 final size:39
Alignment explanation
Indices: 277254--277383 Score: 97
Period size: 39 Copynumber: 3.2 Consensus size: 39
277244 TATAATTAAT
277254 ATATTTTTTCATGTGAATTTTAAATATTTTATTGAAATA
1 ATATTTTTTCATGTGAATTTTAAATATTTTATTGAAATA
* * ** *
277293 ATATTTTAATT-AAGAT-CATTTT-TTTATTTAATAAAATT-AATTAA
1 ATATTTT--TTCATG-TGAATTTTAAATATTT--T---ATTGAAAT-A
277337 TATATTTTTTCATGTGAATTTTAAATATTTTATTGAAATA
1 -ATATTTTTTCATGTGAATTTTAAATATTTTATTGAAATA
277377 ATATTTT
1 ATATTTT
277384 AATTAAGATC
Statistics
Matches: 67, Mismatches: 10, Indels: 28
0.64 0.10 0.27
Matches are distributed among these distances:
39 19 0.28
40 11 0.16
41 7 0.10
43 7 0.10
44 11 0.16
45 12 0.18
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (39 bp):
ATATTTTTTCATGTGAATTTTAAATATTTTATTGAAATA
Found at i:277341 original size:84 final size:85
Alignment explanation
Indices: 277228--277399 Score: 337
Period size: 84 Copynumber: 2.0 Consensus size: 85
277218 TGGAATATTA
277228 TTTTTATTTAATAAAATATAATTAATATATTTTTTCATGTGAATTTTAAATATTTTATTGAAATA
1 TTTTTATTTAATAAAATATAATTAATATATTTTTTCATGTGAATTTTAAATATTTTATTGAAATA
277293 ATATTTTAATTAAGATCATT
66 ATATTTTAATTAAGATCATT
277313 TTTTTATTTAATAAAAT-TAATTAATATATTTTTTCATGTGAATTTTAAATATTTTATTGAAATA
1 TTTTTATTTAATAAAATATAATTAATATATTTTTTCATGTGAATTTTAAATATTTTATTGAAATA
277377 ATATTTTAATTAAGATCATT
66 ATATTTTAATTAAGATCATT
277397 TTT
1 TTT
277400 AAGTAATAAA
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
84 70 0.80
85 17 0.20
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (85 bp):
TTTTTATTTAATAAAATATAATTAATATATTTTTTCATGTGAATTTTAAATATTTTATTGAAATA
ATATTTTAATTAAGATCATT
Found at i:283212 original size:14 final size:14
Alignment explanation
Indices: 283193--283220 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
283183 CATATTGACT
283193 CCTAATCTAAATCA
1 CCTAATCTAAATCA
283207 CCTAATCTAAATCA
1 CCTAATCTAAATCA
283221 TTATTCAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.29
Consensus pattern (14 bp):
CCTAATCTAAATCA
Found at i:287271 original size:24 final size:24
Alignment explanation
Indices: 287244--287295 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
287234 AATCAAAGTC
* *
287244 AAATATATTATGTTAATAAATGCT
1 AAATATATTATATTAATAAATACT
*
287268 AAATATATTATATTCATAAATACT
1 AAATATATTATATTAATAAATACT
287292 AAAT
1 AAAT
287296 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATATATTATATTAATAAATACT
Found at i:291685 original size:24 final size:24
Alignment explanation
Indices: 291643--291694 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
291633 AATCAAAGTC
** *
291643 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
291667 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
291691 AAAT
1 AAAT
291695 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Done.