Multiple sequence alignment - TraesCS6A01G181900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G181900 chr6A 100.000 3175 0 0 921 4095 209266652 209269826 0.000000e+00 5864
1 TraesCS6A01G181900 chr6A 100.000 582 0 0 1 582 209265732 209266313 0.000000e+00 1075
2 TraesCS6A01G181900 chr6A 93.156 263 17 1 1 263 140091904 140091643 6.420000e-103 385
3 TraesCS6A01G181900 chr6A 91.255 263 22 1 1 263 605361277 605361016 1.400000e-94 357
4 TraesCS6A01G181900 chr6B 97.941 3109 56 6 921 4024 278539501 278542606 0.000000e+00 5380
5 TraesCS6A01G181900 chr6B 92.832 279 5 5 265 535 278539096 278539367 1.380000e-104 390
6 TraesCS6A01G181900 chr6B 89.015 264 27 2 3833 4095 704702377 704702639 3.950000e-85 326
7 TraesCS6A01G181900 chr6D 97.291 3175 71 9 927 4095 155541694 155544859 0.000000e+00 5373
8 TraesCS6A01G181900 chr6D 97.516 322 4 1 265 582 155541265 155541586 7.740000e-152 547
9 TraesCS6A01G181900 chr6D 91.635 263 21 1 1 263 47202241 47201980 3.010000e-96 363
10 TraesCS6A01G181900 chr6D 89.015 264 28 1 3833 4095 3832123 3831860 3.950000e-85 326
11 TraesCS6A01G181900 chr6D 89.015 264 28 1 3833 4095 430311402 430311665 3.950000e-85 326
12 TraesCS6A01G181900 chr7D 76.593 1773 370 33 1337 3085 484361992 484363743 0.000000e+00 933
13 TraesCS6A01G181900 chr7B 76.637 1772 365 34 1337 3085 511062677 511064422 0.000000e+00 933
14 TraesCS6A01G181900 chr7A 76.209 1799 373 40 1313 3085 552679371 552681140 0.000000e+00 900
15 TraesCS6A01G181900 chr4A 92.015 263 19 2 1 263 729733128 729733388 6.470000e-98 368
16 TraesCS6A01G181900 chr4A 91.255 263 21 2 1 263 598465587 598465327 1.400000e-94 357
17 TraesCS6A01G181900 chr4A 88.258 264 29 2 3833 4095 630904003 630903741 8.540000e-82 315
18 TraesCS6A01G181900 chr2B 91.603 262 21 1 1 262 483784368 483784628 1.080000e-95 361
19 TraesCS6A01G181900 chr5B 91.255 263 22 1 1 263 528708975 528709236 1.400000e-94 357
20 TraesCS6A01G181900 chr5B 88.258 264 30 1 3833 4095 426623175 426622912 8.540000e-82 315
21 TraesCS6A01G181900 chr2A 91.255 263 22 1 1 263 713668452 713668713 1.400000e-94 357
22 TraesCS6A01G181900 chr1A 91.221 262 22 1 1 262 392482586 392482846 5.030000e-94 355
23 TraesCS6A01G181900 chr1A 89.015 264 28 1 3833 4095 531692676 531692939 3.950000e-85 326
24 TraesCS6A01G181900 chr3D 89.773 264 26 1 3833 4095 144777732 144777469 1.820000e-88 337


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G181900 chr6A 209265732 209269826 4094 False 3469.5 5864 100.0000 1 4095 2 chr6A.!!$F1 4094
1 TraesCS6A01G181900 chr6B 278539096 278542606 3510 False 2885.0 5380 95.3865 265 4024 2 chr6B.!!$F2 3759
2 TraesCS6A01G181900 chr6D 155541265 155544859 3594 False 2960.0 5373 97.4035 265 4095 2 chr6D.!!$F2 3830
3 TraesCS6A01G181900 chr7D 484361992 484363743 1751 False 933.0 933 76.5930 1337 3085 1 chr7D.!!$F1 1748
4 TraesCS6A01G181900 chr7B 511062677 511064422 1745 False 933.0 933 76.6370 1337 3085 1 chr7B.!!$F1 1748
5 TraesCS6A01G181900 chr7A 552679371 552681140 1769 False 900.0 900 76.2090 1313 3085 1 chr7A.!!$F1 1772

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
40 41 0.034896 AACGACGAACCCAGCAGAAT 59.965 50.000 0.00 0.00 0.00 2.40 F
135 136 0.036732 TCCGCTGTGAGCCAAAATCT 59.963 50.000 0.00 0.00 38.18 2.40 F
136 137 0.169672 CCGCTGTGAGCCAAAATCTG 59.830 55.000 0.00 0.00 38.18 2.90 F
1553 1571 0.179023 GGAGGATACGGACGACTCCT 60.179 60.000 15.74 15.74 43.37 3.69 F
2131 2155 1.227263 CTATGGGAAGGCCGTCACG 60.227 63.158 20.72 0.13 33.83 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1076 1091 1.269621 ACAACAACCCGACTCTCTTCG 60.270 52.381 0.00 0.0 38.80 3.79 R
2131 2155 1.134670 AGGCGAGCAAGTGTAAGATCC 60.135 52.381 0.00 0.0 0.00 3.36 R
2349 2373 2.503765 TCCATCACCTTTGCCGATTCTA 59.496 45.455 0.00 0.0 0.00 2.10 R
2914 2938 1.301716 GGCACGGAGCTTGAAGTGA 60.302 57.895 13.46 0.0 44.79 3.41 R
4039 4071 0.326264 AAGCGATGGCCAAGAGAAGT 59.674 50.000 10.96 0.0 41.24 3.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.752412 CGCAGCAGAATCTGAATCAAA 57.248 42.857 15.38 0.00 36.19 2.69
23 24 3.423571 CGCAGCAGAATCTGAATCAAAC 58.576 45.455 15.38 0.00 36.19 2.93
24 25 3.423571 GCAGCAGAATCTGAATCAAACG 58.576 45.455 15.38 0.00 36.19 3.60
25 26 3.125829 GCAGCAGAATCTGAATCAAACGA 59.874 43.478 15.38 0.00 36.19 3.85
26 27 4.645956 CAGCAGAATCTGAATCAAACGAC 58.354 43.478 15.38 0.00 36.19 4.34
27 28 3.369147 AGCAGAATCTGAATCAAACGACG 59.631 43.478 15.38 0.00 32.44 5.12
28 29 3.367932 GCAGAATCTGAATCAAACGACGA 59.632 43.478 15.38 0.00 32.44 4.20
29 30 4.143115 GCAGAATCTGAATCAAACGACGAA 60.143 41.667 15.38 0.00 32.44 3.85
30 31 5.308927 CAGAATCTGAATCAAACGACGAAC 58.691 41.667 3.77 0.00 32.44 3.95
31 32 4.389077 AGAATCTGAATCAAACGACGAACC 59.611 41.667 0.00 0.00 0.00 3.62
32 33 2.409975 TCTGAATCAAACGACGAACCC 58.590 47.619 0.00 0.00 0.00 4.11
33 34 2.139917 CTGAATCAAACGACGAACCCA 58.860 47.619 0.00 0.00 0.00 4.51
34 35 2.139917 TGAATCAAACGACGAACCCAG 58.860 47.619 0.00 0.00 0.00 4.45
35 36 0.872388 AATCAAACGACGAACCCAGC 59.128 50.000 0.00 0.00 0.00 4.85
36 37 0.250124 ATCAAACGACGAACCCAGCA 60.250 50.000 0.00 0.00 0.00 4.41
37 38 0.878523 TCAAACGACGAACCCAGCAG 60.879 55.000 0.00 0.00 0.00 4.24
38 39 0.878523 CAAACGACGAACCCAGCAGA 60.879 55.000 0.00 0.00 0.00 4.26
39 40 0.179067 AAACGACGAACCCAGCAGAA 60.179 50.000 0.00 0.00 0.00 3.02
40 41 0.034896 AACGACGAACCCAGCAGAAT 59.965 50.000 0.00 0.00 0.00 2.40
41 42 0.389948 ACGACGAACCCAGCAGAATC 60.390 55.000 0.00 0.00 0.00 2.52
42 43 1.084370 CGACGAACCCAGCAGAATCC 61.084 60.000 0.00 0.00 0.00 3.01
43 44 1.079127 ACGAACCCAGCAGAATCCG 60.079 57.895 0.00 0.00 0.00 4.18
44 45 1.218047 CGAACCCAGCAGAATCCGA 59.782 57.895 0.00 0.00 0.00 4.55
45 46 0.179073 CGAACCCAGCAGAATCCGAT 60.179 55.000 0.00 0.00 0.00 4.18
46 47 1.743772 CGAACCCAGCAGAATCCGATT 60.744 52.381 0.00 0.00 0.00 3.34
47 48 2.369394 GAACCCAGCAGAATCCGATTT 58.631 47.619 0.00 0.00 0.00 2.17
48 49 2.514458 ACCCAGCAGAATCCGATTTT 57.486 45.000 0.00 0.00 0.00 1.82
49 50 3.644966 ACCCAGCAGAATCCGATTTTA 57.355 42.857 0.00 0.00 0.00 1.52
50 51 3.545703 ACCCAGCAGAATCCGATTTTAG 58.454 45.455 0.00 0.00 0.00 1.85
51 52 3.199946 ACCCAGCAGAATCCGATTTTAGA 59.800 43.478 0.00 0.00 0.00 2.10
52 53 4.199310 CCCAGCAGAATCCGATTTTAGAA 58.801 43.478 0.00 0.00 0.00 2.10
53 54 4.640201 CCCAGCAGAATCCGATTTTAGAAA 59.360 41.667 0.00 0.00 0.00 2.52
54 55 5.300286 CCCAGCAGAATCCGATTTTAGAAAT 59.700 40.000 0.00 0.00 0.00 2.17
55 56 6.433766 CCAGCAGAATCCGATTTTAGAAATC 58.566 40.000 0.00 3.84 0.00 2.17
56 57 6.433766 CAGCAGAATCCGATTTTAGAAATCC 58.566 40.000 7.58 0.00 0.00 3.01
57 58 5.237344 AGCAGAATCCGATTTTAGAAATCCG 59.763 40.000 7.58 2.69 0.00 4.18
58 59 5.444122 CAGAATCCGATTTTAGAAATCCGC 58.556 41.667 7.58 0.00 0.00 5.54
59 60 5.237344 CAGAATCCGATTTTAGAAATCCGCT 59.763 40.000 7.58 0.00 0.00 5.52
60 61 5.237344 AGAATCCGATTTTAGAAATCCGCTG 59.763 40.000 7.58 0.00 0.00 5.18
61 62 2.612212 TCCGATTTTAGAAATCCGCTGC 59.388 45.455 7.58 0.00 0.00 5.25
62 63 2.287009 CCGATTTTAGAAATCCGCTGCC 60.287 50.000 7.58 0.00 0.00 4.85
63 64 2.354510 CGATTTTAGAAATCCGCTGCCA 59.645 45.455 7.58 0.00 0.00 4.92
64 65 3.181501 CGATTTTAGAAATCCGCTGCCAA 60.182 43.478 7.58 0.00 0.00 4.52
65 66 4.674101 CGATTTTAGAAATCCGCTGCCAAA 60.674 41.667 7.58 0.00 0.00 3.28
66 67 4.592485 TTTTAGAAATCCGCTGCCAAAA 57.408 36.364 0.00 0.00 0.00 2.44
67 68 4.799564 TTTAGAAATCCGCTGCCAAAAT 57.200 36.364 0.00 0.00 0.00 1.82
68 69 4.799564 TTAGAAATCCGCTGCCAAAATT 57.200 36.364 0.00 0.00 0.00 1.82
69 70 3.683365 AGAAATCCGCTGCCAAAATTT 57.317 38.095 0.00 0.00 0.00 1.82
70 71 4.799564 AGAAATCCGCTGCCAAAATTTA 57.200 36.364 0.00 0.00 0.00 1.40
71 72 5.146010 AGAAATCCGCTGCCAAAATTTAA 57.854 34.783 0.00 0.00 0.00 1.52
72 73 5.546526 AGAAATCCGCTGCCAAAATTTAAA 58.453 33.333 0.00 0.00 0.00 1.52
73 74 5.408299 AGAAATCCGCTGCCAAAATTTAAAC 59.592 36.000 0.00 0.00 0.00 2.01
74 75 3.033368 TCCGCTGCCAAAATTTAAACC 57.967 42.857 0.00 0.00 0.00 3.27
75 76 2.365617 TCCGCTGCCAAAATTTAAACCA 59.634 40.909 0.00 0.00 0.00 3.67
76 77 3.134458 CCGCTGCCAAAATTTAAACCAA 58.866 40.909 0.00 0.00 0.00 3.67
77 78 3.561725 CCGCTGCCAAAATTTAAACCAAA 59.438 39.130 0.00 0.00 0.00 3.28
78 79 4.035675 CCGCTGCCAAAATTTAAACCAAAA 59.964 37.500 0.00 0.00 0.00 2.44
79 80 5.204101 CGCTGCCAAAATTTAAACCAAAAG 58.796 37.500 0.00 0.00 0.00 2.27
80 81 4.975502 GCTGCCAAAATTTAAACCAAAAGC 59.024 37.500 0.00 0.00 0.00 3.51
81 82 5.162000 TGCCAAAATTTAAACCAAAAGCG 57.838 34.783 0.00 0.00 0.00 4.68
82 83 4.035675 TGCCAAAATTTAAACCAAAAGCGG 59.964 37.500 0.00 0.00 0.00 5.52
83 84 4.273724 GCCAAAATTTAAACCAAAAGCGGA 59.726 37.500 0.00 0.00 0.00 5.54
84 85 5.220873 GCCAAAATTTAAACCAAAAGCGGAA 60.221 36.000 0.00 0.00 0.00 4.30
85 86 6.426327 CCAAAATTTAAACCAAAAGCGGAAG 58.574 36.000 0.00 0.00 0.00 3.46
97 98 2.125912 CGGAAGCAGACCAGGACG 60.126 66.667 0.00 0.00 0.00 4.79
98 99 2.932234 CGGAAGCAGACCAGGACGT 61.932 63.158 0.00 0.00 0.00 4.34
99 100 1.374758 GGAAGCAGACCAGGACGTG 60.375 63.158 0.00 0.00 0.00 4.49
100 101 2.029844 GAAGCAGACCAGGACGTGC 61.030 63.158 0.00 0.00 36.10 5.34
101 102 2.919856 AGCAGACCAGGACGTGCT 60.920 61.111 2.68 2.68 41.47 4.40
102 103 2.031163 GCAGACCAGGACGTGCTT 59.969 61.111 6.93 0.00 32.97 3.91
103 104 1.598130 GCAGACCAGGACGTGCTTT 60.598 57.895 6.93 0.00 32.97 3.51
104 105 1.166531 GCAGACCAGGACGTGCTTTT 61.167 55.000 6.93 0.00 32.97 2.27
105 106 0.868406 CAGACCAGGACGTGCTTTTC 59.132 55.000 6.93 6.71 0.00 2.29
106 107 0.468226 AGACCAGGACGTGCTTTTCA 59.532 50.000 6.93 0.00 0.00 2.69
107 108 1.134220 AGACCAGGACGTGCTTTTCAA 60.134 47.619 6.93 0.00 0.00 2.69
108 109 1.673920 GACCAGGACGTGCTTTTCAAA 59.326 47.619 6.93 0.00 0.00 2.69
109 110 2.096248 ACCAGGACGTGCTTTTCAAAA 58.904 42.857 6.93 0.00 0.00 2.44
110 111 2.693074 ACCAGGACGTGCTTTTCAAAAT 59.307 40.909 6.93 0.00 0.00 1.82
111 112 3.243401 ACCAGGACGTGCTTTTCAAAATC 60.243 43.478 6.93 0.00 0.00 2.17
112 113 3.004734 CCAGGACGTGCTTTTCAAAATCT 59.995 43.478 6.93 0.00 0.00 2.40
113 114 3.976942 CAGGACGTGCTTTTCAAAATCTG 59.023 43.478 6.93 0.00 0.00 2.90
114 115 3.882888 AGGACGTGCTTTTCAAAATCTGA 59.117 39.130 2.68 0.00 0.00 3.27
115 116 4.520492 AGGACGTGCTTTTCAAAATCTGAT 59.480 37.500 2.68 0.00 32.78 2.90
116 117 5.010012 AGGACGTGCTTTTCAAAATCTGATT 59.990 36.000 2.68 0.00 32.78 2.57
117 118 5.343325 GGACGTGCTTTTCAAAATCTGATTC 59.657 40.000 2.92 0.00 32.78 2.52
118 119 5.222631 ACGTGCTTTTCAAAATCTGATTCC 58.777 37.500 2.92 0.00 32.78 3.01
119 120 4.321745 CGTGCTTTTCAAAATCTGATTCCG 59.678 41.667 2.92 0.00 32.78 4.30
120 121 4.090498 GTGCTTTTCAAAATCTGATTCCGC 59.910 41.667 2.92 0.68 32.78 5.54
121 122 4.022068 TGCTTTTCAAAATCTGATTCCGCT 60.022 37.500 2.92 0.00 32.78 5.52
122 123 4.325472 GCTTTTCAAAATCTGATTCCGCTG 59.675 41.667 2.92 0.27 32.78 5.18
123 124 5.452078 TTTTCAAAATCTGATTCCGCTGT 57.548 34.783 2.92 0.00 32.78 4.40
124 125 4.424061 TTCAAAATCTGATTCCGCTGTG 57.576 40.909 2.92 0.00 32.78 3.66
125 126 3.673902 TCAAAATCTGATTCCGCTGTGA 58.326 40.909 2.92 0.00 0.00 3.58
126 127 3.686241 TCAAAATCTGATTCCGCTGTGAG 59.314 43.478 2.92 0.00 0.00 3.51
127 128 1.661341 AATCTGATTCCGCTGTGAGC 58.339 50.000 0.00 0.00 38.02 4.26
128 129 0.179062 ATCTGATTCCGCTGTGAGCC 60.179 55.000 0.00 0.00 38.18 4.70
129 130 1.078918 CTGATTCCGCTGTGAGCCA 60.079 57.895 0.00 0.00 38.18 4.75
130 131 0.674581 CTGATTCCGCTGTGAGCCAA 60.675 55.000 0.00 0.00 38.18 4.52
131 132 0.250684 TGATTCCGCTGTGAGCCAAA 60.251 50.000 0.00 0.00 38.18 3.28
132 133 0.881118 GATTCCGCTGTGAGCCAAAA 59.119 50.000 0.00 0.00 38.18 2.44
133 134 1.474077 GATTCCGCTGTGAGCCAAAAT 59.526 47.619 0.00 0.00 38.18 1.82
134 135 0.881118 TTCCGCTGTGAGCCAAAATC 59.119 50.000 0.00 0.00 38.18 2.17
135 136 0.036732 TCCGCTGTGAGCCAAAATCT 59.963 50.000 0.00 0.00 38.18 2.40
136 137 0.169672 CCGCTGTGAGCCAAAATCTG 59.830 55.000 0.00 0.00 38.18 2.90
137 138 1.159285 CGCTGTGAGCCAAAATCTGA 58.841 50.000 0.00 0.00 38.18 3.27
138 139 1.536766 CGCTGTGAGCCAAAATCTGAA 59.463 47.619 0.00 0.00 38.18 3.02
139 140 2.030893 CGCTGTGAGCCAAAATCTGAAA 60.031 45.455 0.00 0.00 38.18 2.69
140 141 3.550639 CGCTGTGAGCCAAAATCTGAAAA 60.551 43.478 0.00 0.00 38.18 2.29
141 142 4.370917 GCTGTGAGCCAAAATCTGAAAAA 58.629 39.130 0.00 0.00 34.48 1.94
162 163 4.708726 AAACTGTATCAGCTGATTTGCC 57.291 40.909 32.94 18.52 36.05 4.52
163 164 3.354948 ACTGTATCAGCTGATTTGCCA 57.645 42.857 32.94 21.52 36.05 4.92
164 165 3.689347 ACTGTATCAGCTGATTTGCCAA 58.311 40.909 32.94 12.45 36.05 4.52
165 166 4.081406 ACTGTATCAGCTGATTTGCCAAA 58.919 39.130 32.94 11.68 36.05 3.28
166 167 4.708421 ACTGTATCAGCTGATTTGCCAAAT 59.292 37.500 32.94 10.16 36.05 2.32
167 168 5.001237 TGTATCAGCTGATTTGCCAAATG 57.999 39.130 32.94 0.00 36.05 2.32
168 169 4.705991 TGTATCAGCTGATTTGCCAAATGA 59.294 37.500 32.94 9.39 36.05 2.57
169 170 3.581024 TCAGCTGATTTGCCAAATGAC 57.419 42.857 13.74 0.00 0.00 3.06
170 171 2.231964 TCAGCTGATTTGCCAAATGACC 59.768 45.455 13.74 0.00 0.00 4.02
171 172 2.232941 CAGCTGATTTGCCAAATGACCT 59.767 45.455 8.42 0.00 0.00 3.85
172 173 3.444742 CAGCTGATTTGCCAAATGACCTA 59.555 43.478 8.42 0.00 0.00 3.08
173 174 3.445096 AGCTGATTTGCCAAATGACCTAC 59.555 43.478 7.53 0.00 0.00 3.18
174 175 3.193267 GCTGATTTGCCAAATGACCTACA 59.807 43.478 7.53 0.00 0.00 2.74
175 176 4.142093 GCTGATTTGCCAAATGACCTACAT 60.142 41.667 7.53 0.00 41.45 2.29
176 177 5.581126 TGATTTGCCAAATGACCTACATC 57.419 39.130 7.53 0.00 38.38 3.06
177 178 5.263599 TGATTTGCCAAATGACCTACATCT 58.736 37.500 7.53 0.00 38.38 2.90
178 179 5.716228 TGATTTGCCAAATGACCTACATCTT 59.284 36.000 7.53 0.00 38.38 2.40
179 180 6.211184 TGATTTGCCAAATGACCTACATCTTT 59.789 34.615 7.53 0.00 38.38 2.52
180 181 6.418057 TTTGCCAAATGACCTACATCTTTT 57.582 33.333 0.00 0.00 38.38 2.27
181 182 6.418057 TTGCCAAATGACCTACATCTTTTT 57.582 33.333 0.00 0.00 38.38 1.94
182 183 6.024552 TGCCAAATGACCTACATCTTTTTC 57.975 37.500 0.00 0.00 38.38 2.29
183 184 5.538053 TGCCAAATGACCTACATCTTTTTCA 59.462 36.000 0.00 0.00 38.38 2.69
184 185 5.863935 GCCAAATGACCTACATCTTTTTCAC 59.136 40.000 0.00 0.00 38.38 3.18
185 186 6.516527 GCCAAATGACCTACATCTTTTTCACA 60.517 38.462 0.00 0.00 38.38 3.58
186 187 7.605449 CCAAATGACCTACATCTTTTTCACAT 58.395 34.615 0.00 0.00 38.38 3.21
187 188 7.756722 CCAAATGACCTACATCTTTTTCACATC 59.243 37.037 0.00 0.00 38.38 3.06
188 189 8.298854 CAAATGACCTACATCTTTTTCACATCA 58.701 33.333 0.00 0.00 38.38 3.07
189 190 7.621428 ATGACCTACATCTTTTTCACATCAG 57.379 36.000 0.00 0.00 33.46 2.90
190 191 6.768483 TGACCTACATCTTTTTCACATCAGA 58.232 36.000 0.00 0.00 0.00 3.27
191 192 7.397221 TGACCTACATCTTTTTCACATCAGAT 58.603 34.615 0.00 0.00 0.00 2.90
192 193 7.884877 TGACCTACATCTTTTTCACATCAGATT 59.115 33.333 0.00 0.00 0.00 2.40
193 194 8.641498 ACCTACATCTTTTTCACATCAGATTT 57.359 30.769 0.00 0.00 0.00 2.17
194 195 9.082313 ACCTACATCTTTTTCACATCAGATTTT 57.918 29.630 0.00 0.00 0.00 1.82
195 196 9.565213 CCTACATCTTTTTCACATCAGATTTTC 57.435 33.333 0.00 0.00 0.00 2.29
196 197 9.565213 CTACATCTTTTTCACATCAGATTTTCC 57.435 33.333 0.00 0.00 0.00 3.13
197 198 7.954835 ACATCTTTTTCACATCAGATTTTCCA 58.045 30.769 0.00 0.00 0.00 3.53
198 199 7.869429 ACATCTTTTTCACATCAGATTTTCCAC 59.131 33.333 0.00 0.00 0.00 4.02
199 200 7.345422 TCTTTTTCACATCAGATTTTCCACA 57.655 32.000 0.00 0.00 0.00 4.17
200 201 7.428020 TCTTTTTCACATCAGATTTTCCACAG 58.572 34.615 0.00 0.00 0.00 3.66
201 202 4.771590 TTCACATCAGATTTTCCACAGC 57.228 40.909 0.00 0.00 0.00 4.40
202 203 4.025040 TCACATCAGATTTTCCACAGCT 57.975 40.909 0.00 0.00 0.00 4.24
203 204 3.754850 TCACATCAGATTTTCCACAGCTG 59.245 43.478 13.48 13.48 0.00 4.24
204 205 3.504906 CACATCAGATTTTCCACAGCTGT 59.495 43.478 15.25 15.25 0.00 4.40
205 206 4.022589 CACATCAGATTTTCCACAGCTGTT 60.023 41.667 18.94 0.15 0.00 3.16
206 207 4.586001 ACATCAGATTTTCCACAGCTGTTT 59.414 37.500 18.94 0.00 0.00 2.83
207 208 5.069516 ACATCAGATTTTCCACAGCTGTTTT 59.930 36.000 18.94 0.00 0.00 2.43
208 209 5.596836 TCAGATTTTCCACAGCTGTTTTT 57.403 34.783 18.94 0.00 0.00 1.94
209 210 5.591099 TCAGATTTTCCACAGCTGTTTTTC 58.409 37.500 18.94 8.57 0.00 2.29
210 211 4.746611 CAGATTTTCCACAGCTGTTTTTCC 59.253 41.667 18.94 3.55 0.00 3.13
211 212 4.405358 AGATTTTCCACAGCTGTTTTTCCA 59.595 37.500 18.94 0.00 0.00 3.53
212 213 3.518634 TTTCCACAGCTGTTTTTCCAC 57.481 42.857 18.94 0.00 0.00 4.02
213 214 2.136298 TCCACAGCTGTTTTTCCACA 57.864 45.000 18.94 0.00 0.00 4.17
214 215 2.023673 TCCACAGCTGTTTTTCCACAG 58.976 47.619 18.94 1.97 46.15 3.66
249 250 9.677567 TTACAACTGATTTTAGAAATTCACAGC 57.322 29.630 0.00 0.00 0.00 4.40
250 251 7.147976 ACAACTGATTTTAGAAATTCACAGCC 58.852 34.615 0.00 0.00 0.00 4.85
251 252 5.942872 ACTGATTTTAGAAATTCACAGCCG 58.057 37.500 0.00 0.00 0.00 5.52
252 253 5.705441 ACTGATTTTAGAAATTCACAGCCGA 59.295 36.000 0.00 0.00 0.00 5.54
253 254 6.206634 ACTGATTTTAGAAATTCACAGCCGAA 59.793 34.615 0.00 0.00 0.00 4.30
254 255 6.378582 TGATTTTAGAAATTCACAGCCGAAC 58.621 36.000 0.00 0.00 0.00 3.95
255 256 4.759516 TTTAGAAATTCACAGCCGAACC 57.240 40.909 0.00 0.00 0.00 3.62
256 257 2.270352 AGAAATTCACAGCCGAACCA 57.730 45.000 0.00 0.00 0.00 3.67
257 258 2.582052 AGAAATTCACAGCCGAACCAA 58.418 42.857 0.00 0.00 0.00 3.67
258 259 2.955660 AGAAATTCACAGCCGAACCAAA 59.044 40.909 0.00 0.00 0.00 3.28
259 260 2.793278 AATTCACAGCCGAACCAAAC 57.207 45.000 0.00 0.00 0.00 2.93
260 261 1.686355 ATTCACAGCCGAACCAAACA 58.314 45.000 0.00 0.00 0.00 2.83
261 262 1.021202 TTCACAGCCGAACCAAACAG 58.979 50.000 0.00 0.00 0.00 3.16
262 263 0.817634 TCACAGCCGAACCAAACAGG 60.818 55.000 0.00 0.00 45.67 4.00
298 299 1.193644 GCATGTGCAATGTATGTGCG 58.806 50.000 0.00 0.00 45.27 5.34
488 493 4.394729 GCCGATTATTCAATTCCCACCTA 58.605 43.478 0.00 0.00 0.00 3.08
554 563 0.251832 TCCTCCCTCCTGTCACAGAC 60.252 60.000 6.30 0.00 32.44 3.51
967 982 2.440539 TGGTCGTGCTCTTCTTCTTC 57.559 50.000 0.00 0.00 0.00 2.87
1043 1058 3.749609 GGAGGTAAGCGATAGAGAGAGAC 59.250 52.174 0.00 0.00 39.76 3.36
1161 1176 2.069273 CCTGATGGTGTGTTCTTCGAC 58.931 52.381 0.00 0.00 0.00 4.20
1162 1177 2.547855 CCTGATGGTGTGTTCTTCGACA 60.548 50.000 0.00 0.00 0.00 4.35
1553 1571 0.179023 GGAGGATACGGACGACTCCT 60.179 60.000 15.74 15.74 43.37 3.69
2131 2155 1.227263 CTATGGGAAGGCCGTCACG 60.227 63.158 20.72 0.13 33.83 4.35
2349 2373 3.439857 TGCTGGTCTTAAGGCTTTCAT 57.560 42.857 4.45 0.00 0.00 2.57
2356 2380 6.049149 TGGTCTTAAGGCTTTCATAGAATCG 58.951 40.000 4.45 0.00 0.00 3.34
2443 2467 1.341285 TGCCTTATCAACTGCAGCCAT 60.341 47.619 15.27 5.73 0.00 4.40
2671 2695 3.078837 TGGGCTTCTTCCGTTGATAAAC 58.921 45.455 0.00 0.00 0.00 2.01
2685 2709 5.622914 CGTTGATAAACTCTTCCGAGGGTAA 60.623 44.000 0.00 0.00 41.71 2.85
2914 2938 4.722700 AGCCTGGCGTCCGCAAAT 62.723 61.111 13.96 0.00 44.11 2.32
2931 2955 1.160137 AATCACTTCAAGCTCCGTGC 58.840 50.000 0.00 0.00 43.29 5.34
3315 3342 3.395054 TCACAGATCACTCCTCAGGAT 57.605 47.619 0.00 0.00 0.00 3.24
3831 3863 9.030301 GTATGTGTTTGTTTTGCAAGTTCTATT 57.970 29.630 0.00 0.00 38.47 1.73
3841 3873 9.118236 GTTTTGCAAGTTCTATTCTTGTACATC 57.882 33.333 0.00 0.00 42.67 3.06
3963 3995 6.617782 TGAAATTTGAGGGGCATATTTTGA 57.382 33.333 0.00 0.00 37.97 2.69
4039 4071 4.281435 TGTCTTGTACAATTCCAGTCCGTA 59.719 41.667 9.13 0.00 34.29 4.02
4049 4081 2.168496 TCCAGTCCGTACTTCTCTTGG 58.832 52.381 0.00 0.00 31.97 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.042361 GATTCAGATTCTGCTGCGCG 60.042 55.000 8.89 0.00 35.86 6.86
1 2 1.012086 TGATTCAGATTCTGCTGCGC 58.988 50.000 8.89 0.00 35.86 6.09
2 3 3.423571 GTTTGATTCAGATTCTGCTGCG 58.576 45.455 8.89 0.00 35.86 5.18
3 4 3.125829 TCGTTTGATTCAGATTCTGCTGC 59.874 43.478 8.89 0.00 35.86 5.25
4 5 4.645956 GTCGTTTGATTCAGATTCTGCTG 58.354 43.478 8.89 0.00 37.24 4.41
5 6 3.369147 CGTCGTTTGATTCAGATTCTGCT 59.631 43.478 8.89 0.00 0.00 4.24
6 7 3.367932 TCGTCGTTTGATTCAGATTCTGC 59.632 43.478 8.89 0.00 0.00 4.26
7 8 5.308927 GTTCGTCGTTTGATTCAGATTCTG 58.691 41.667 7.38 7.38 0.00 3.02
8 9 4.389077 GGTTCGTCGTTTGATTCAGATTCT 59.611 41.667 0.00 0.00 0.00 2.40
9 10 4.435651 GGGTTCGTCGTTTGATTCAGATTC 60.436 45.833 0.00 0.00 0.00 2.52
10 11 3.435671 GGGTTCGTCGTTTGATTCAGATT 59.564 43.478 0.00 0.00 0.00 2.40
11 12 3.000727 GGGTTCGTCGTTTGATTCAGAT 58.999 45.455 0.00 0.00 0.00 2.90
12 13 2.224090 TGGGTTCGTCGTTTGATTCAGA 60.224 45.455 0.00 0.00 0.00 3.27
13 14 2.139917 TGGGTTCGTCGTTTGATTCAG 58.860 47.619 0.00 0.00 0.00 3.02
14 15 2.139917 CTGGGTTCGTCGTTTGATTCA 58.860 47.619 0.00 0.00 0.00 2.57
15 16 1.136057 GCTGGGTTCGTCGTTTGATTC 60.136 52.381 0.00 0.00 0.00 2.52
16 17 0.872388 GCTGGGTTCGTCGTTTGATT 59.128 50.000 0.00 0.00 0.00 2.57
17 18 0.250124 TGCTGGGTTCGTCGTTTGAT 60.250 50.000 0.00 0.00 0.00 2.57
18 19 0.878523 CTGCTGGGTTCGTCGTTTGA 60.879 55.000 0.00 0.00 0.00 2.69
19 20 0.878523 TCTGCTGGGTTCGTCGTTTG 60.879 55.000 0.00 0.00 0.00 2.93
20 21 0.179067 TTCTGCTGGGTTCGTCGTTT 60.179 50.000 0.00 0.00 0.00 3.60
21 22 0.034896 ATTCTGCTGGGTTCGTCGTT 59.965 50.000 0.00 0.00 0.00 3.85
22 23 0.389948 GATTCTGCTGGGTTCGTCGT 60.390 55.000 0.00 0.00 0.00 4.34
23 24 1.084370 GGATTCTGCTGGGTTCGTCG 61.084 60.000 0.00 0.00 0.00 5.12
24 25 1.084370 CGGATTCTGCTGGGTTCGTC 61.084 60.000 0.00 0.00 0.00 4.20
25 26 1.079127 CGGATTCTGCTGGGTTCGT 60.079 57.895 0.00 0.00 0.00 3.85
26 27 0.179073 ATCGGATTCTGCTGGGTTCG 60.179 55.000 0.00 0.00 0.00 3.95
27 28 2.044123 AATCGGATTCTGCTGGGTTC 57.956 50.000 0.00 0.00 0.00 3.62
28 29 2.514458 AAATCGGATTCTGCTGGGTT 57.486 45.000 3.28 0.00 0.00 4.11
29 30 2.514458 AAAATCGGATTCTGCTGGGT 57.486 45.000 3.28 0.00 0.00 4.51
30 31 3.808728 TCTAAAATCGGATTCTGCTGGG 58.191 45.455 3.28 0.00 0.00 4.45
31 32 5.818136 TTTCTAAAATCGGATTCTGCTGG 57.182 39.130 3.28 0.00 0.00 4.85
32 33 6.433766 GGATTTCTAAAATCGGATTCTGCTG 58.566 40.000 3.28 0.00 0.00 4.41
33 34 5.237344 CGGATTTCTAAAATCGGATTCTGCT 59.763 40.000 3.28 0.00 31.17 4.24
34 35 5.444122 CGGATTTCTAAAATCGGATTCTGC 58.556 41.667 3.28 0.00 31.17 4.26
35 36 5.237344 AGCGGATTTCTAAAATCGGATTCTG 59.763 40.000 18.50 0.00 31.17 3.02
36 37 5.237344 CAGCGGATTTCTAAAATCGGATTCT 59.763 40.000 18.50 0.00 31.17 2.40
37 38 5.444122 CAGCGGATTTCTAAAATCGGATTC 58.556 41.667 18.50 6.24 31.17 2.52
38 39 4.261197 GCAGCGGATTTCTAAAATCGGATT 60.261 41.667 18.50 0.00 31.17 3.01
39 40 3.251004 GCAGCGGATTTCTAAAATCGGAT 59.749 43.478 18.50 12.32 31.17 4.18
40 41 2.612212 GCAGCGGATTTCTAAAATCGGA 59.388 45.455 18.50 0.00 31.17 4.55
41 42 2.287009 GGCAGCGGATTTCTAAAATCGG 60.287 50.000 12.85 12.85 0.00 4.18
42 43 2.354510 TGGCAGCGGATTTCTAAAATCG 59.645 45.455 6.38 4.08 0.00 3.34
43 44 4.370364 TTGGCAGCGGATTTCTAAAATC 57.630 40.909 4.23 4.23 0.00 2.17
44 45 4.799564 TTTGGCAGCGGATTTCTAAAAT 57.200 36.364 0.00 0.00 0.00 1.82
45 46 4.592485 TTTTGGCAGCGGATTTCTAAAA 57.408 36.364 0.00 0.00 0.00 1.52
46 47 4.799564 ATTTTGGCAGCGGATTTCTAAA 57.200 36.364 0.00 0.00 0.00 1.85
47 48 4.799564 AATTTTGGCAGCGGATTTCTAA 57.200 36.364 0.00 0.00 0.00 2.10
48 49 4.799564 AAATTTTGGCAGCGGATTTCTA 57.200 36.364 0.00 0.00 0.00 2.10
49 50 3.683365 AAATTTTGGCAGCGGATTTCT 57.317 38.095 0.00 0.00 0.00 2.52
50 51 5.390461 GGTTTAAATTTTGGCAGCGGATTTC 60.390 40.000 0.00 0.00 0.00 2.17
51 52 4.454161 GGTTTAAATTTTGGCAGCGGATTT 59.546 37.500 0.00 0.00 0.00 2.17
52 53 4.000325 GGTTTAAATTTTGGCAGCGGATT 59.000 39.130 0.00 0.00 0.00 3.01
53 54 3.007398 TGGTTTAAATTTTGGCAGCGGAT 59.993 39.130 0.00 0.00 0.00 4.18
54 55 2.365617 TGGTTTAAATTTTGGCAGCGGA 59.634 40.909 0.00 0.00 0.00 5.54
55 56 2.760374 TGGTTTAAATTTTGGCAGCGG 58.240 42.857 0.00 0.00 0.00 5.52
56 57 4.802876 TTTGGTTTAAATTTTGGCAGCG 57.197 36.364 0.00 0.00 0.00 5.18
57 58 4.975502 GCTTTTGGTTTAAATTTTGGCAGC 59.024 37.500 0.00 0.00 0.00 5.25
58 59 5.204101 CGCTTTTGGTTTAAATTTTGGCAG 58.796 37.500 0.00 0.00 0.00 4.85
59 60 4.035675 CCGCTTTTGGTTTAAATTTTGGCA 59.964 37.500 0.00 0.00 0.00 4.92
60 61 4.273724 TCCGCTTTTGGTTTAAATTTTGGC 59.726 37.500 0.00 0.00 0.00 4.52
61 62 5.993106 TCCGCTTTTGGTTTAAATTTTGG 57.007 34.783 0.00 0.00 0.00 3.28
62 63 5.906838 GCTTCCGCTTTTGGTTTAAATTTTG 59.093 36.000 0.00 0.00 0.00 2.44
63 64 5.586643 TGCTTCCGCTTTTGGTTTAAATTTT 59.413 32.000 0.00 0.00 36.97 1.82
64 65 5.119694 TGCTTCCGCTTTTGGTTTAAATTT 58.880 33.333 0.00 0.00 36.97 1.82
65 66 4.698575 TGCTTCCGCTTTTGGTTTAAATT 58.301 34.783 0.00 0.00 36.97 1.82
66 67 4.038642 TCTGCTTCCGCTTTTGGTTTAAAT 59.961 37.500 0.00 0.00 36.97 1.40
67 68 3.381908 TCTGCTTCCGCTTTTGGTTTAAA 59.618 39.130 0.00 0.00 36.97 1.52
68 69 2.952978 TCTGCTTCCGCTTTTGGTTTAA 59.047 40.909 0.00 0.00 36.97 1.52
69 70 2.292292 GTCTGCTTCCGCTTTTGGTTTA 59.708 45.455 0.00 0.00 36.97 2.01
70 71 1.067060 GTCTGCTTCCGCTTTTGGTTT 59.933 47.619 0.00 0.00 36.97 3.27
71 72 0.668535 GTCTGCTTCCGCTTTTGGTT 59.331 50.000 0.00 0.00 36.97 3.67
72 73 1.172812 GGTCTGCTTCCGCTTTTGGT 61.173 55.000 0.00 0.00 36.97 3.67
73 74 1.172180 TGGTCTGCTTCCGCTTTTGG 61.172 55.000 0.00 0.00 36.97 3.28
74 75 0.239347 CTGGTCTGCTTCCGCTTTTG 59.761 55.000 0.00 0.00 36.97 2.44
75 76 0.890996 CCTGGTCTGCTTCCGCTTTT 60.891 55.000 0.00 0.00 36.97 2.27
76 77 1.302832 CCTGGTCTGCTTCCGCTTT 60.303 57.895 0.00 0.00 36.97 3.51
77 78 2.217038 TCCTGGTCTGCTTCCGCTT 61.217 57.895 0.00 0.00 36.97 4.68
78 79 2.604686 TCCTGGTCTGCTTCCGCT 60.605 61.111 0.00 0.00 36.97 5.52
79 80 2.435059 GTCCTGGTCTGCTTCCGC 60.435 66.667 0.00 0.00 0.00 5.54
80 81 2.125912 CGTCCTGGTCTGCTTCCG 60.126 66.667 0.00 0.00 0.00 4.30
81 82 1.374758 CACGTCCTGGTCTGCTTCC 60.375 63.158 0.00 0.00 0.00 3.46
82 83 2.029844 GCACGTCCTGGTCTGCTTC 61.030 63.158 0.00 0.00 0.00 3.86
83 84 2.031163 GCACGTCCTGGTCTGCTT 59.969 61.111 0.00 0.00 0.00 3.91
84 85 2.044806 AAAGCACGTCCTGGTCTGCT 62.045 55.000 10.34 10.34 41.83 4.24
85 86 1.166531 AAAAGCACGTCCTGGTCTGC 61.167 55.000 0.00 0.77 0.00 4.26
86 87 0.868406 GAAAAGCACGTCCTGGTCTG 59.132 55.000 0.00 0.00 0.00 3.51
87 88 0.468226 TGAAAAGCACGTCCTGGTCT 59.532 50.000 0.00 0.00 0.00 3.85
88 89 1.305201 TTGAAAAGCACGTCCTGGTC 58.695 50.000 0.00 0.00 0.00 4.02
89 90 1.757682 TTTGAAAAGCACGTCCTGGT 58.242 45.000 0.00 0.00 0.00 4.00
90 91 2.861462 TTTTGAAAAGCACGTCCTGG 57.139 45.000 0.00 0.00 0.00 4.45
91 92 3.976942 CAGATTTTGAAAAGCACGTCCTG 59.023 43.478 8.71 0.00 0.00 3.86
92 93 3.882888 TCAGATTTTGAAAAGCACGTCCT 59.117 39.130 8.71 0.00 31.34 3.85
93 94 4.223320 TCAGATTTTGAAAAGCACGTCC 57.777 40.909 8.71 0.00 31.34 4.79
94 95 5.343325 GGAATCAGATTTTGAAAAGCACGTC 59.657 40.000 8.71 0.46 39.77 4.34
95 96 5.222631 GGAATCAGATTTTGAAAAGCACGT 58.777 37.500 8.71 0.00 39.77 4.49
96 97 4.321745 CGGAATCAGATTTTGAAAAGCACG 59.678 41.667 8.71 0.00 39.77 5.34
97 98 4.090498 GCGGAATCAGATTTTGAAAAGCAC 59.910 41.667 8.71 0.00 39.77 4.40
98 99 4.022068 AGCGGAATCAGATTTTGAAAAGCA 60.022 37.500 8.71 0.00 39.77 3.91
99 100 4.325472 CAGCGGAATCAGATTTTGAAAAGC 59.675 41.667 0.00 0.00 39.77 3.51
100 101 5.344128 CACAGCGGAATCAGATTTTGAAAAG 59.656 40.000 0.00 0.00 39.77 2.27
101 102 5.009510 TCACAGCGGAATCAGATTTTGAAAA 59.990 36.000 0.00 0.00 39.77 2.29
102 103 4.518590 TCACAGCGGAATCAGATTTTGAAA 59.481 37.500 0.00 0.00 39.77 2.69
103 104 4.071423 TCACAGCGGAATCAGATTTTGAA 58.929 39.130 0.00 0.00 39.77 2.69
104 105 3.673902 TCACAGCGGAATCAGATTTTGA 58.326 40.909 0.00 0.00 40.85 2.69
105 106 3.730061 GCTCACAGCGGAATCAGATTTTG 60.730 47.826 0.00 0.00 0.00 2.44
106 107 2.421424 GCTCACAGCGGAATCAGATTTT 59.579 45.455 0.00 0.00 0.00 1.82
107 108 2.012673 GCTCACAGCGGAATCAGATTT 58.987 47.619 0.00 0.00 0.00 2.17
108 109 1.661341 GCTCACAGCGGAATCAGATT 58.339 50.000 0.00 0.00 0.00 2.40
109 110 0.179062 GGCTCACAGCGGAATCAGAT 60.179 55.000 0.00 0.00 43.62 2.90
110 111 1.219124 GGCTCACAGCGGAATCAGA 59.781 57.895 0.00 0.00 43.62 3.27
111 112 0.674581 TTGGCTCACAGCGGAATCAG 60.675 55.000 0.00 0.00 43.62 2.90
112 113 0.250684 TTTGGCTCACAGCGGAATCA 60.251 50.000 0.00 0.00 43.62 2.57
113 114 0.881118 TTTTGGCTCACAGCGGAATC 59.119 50.000 0.00 0.00 43.62 2.52
114 115 1.474077 GATTTTGGCTCACAGCGGAAT 59.526 47.619 0.00 0.00 43.62 3.01
115 116 0.881118 GATTTTGGCTCACAGCGGAA 59.119 50.000 0.00 0.00 43.62 4.30
116 117 0.036732 AGATTTTGGCTCACAGCGGA 59.963 50.000 0.00 0.00 43.62 5.54
117 118 0.169672 CAGATTTTGGCTCACAGCGG 59.830 55.000 0.00 0.00 43.62 5.52
118 119 1.159285 TCAGATTTTGGCTCACAGCG 58.841 50.000 0.00 0.00 43.62 5.18
119 120 3.648339 TTTCAGATTTTGGCTCACAGC 57.352 42.857 0.00 0.00 41.46 4.40
139 140 5.010922 TGGCAAATCAGCTGATACAGTTTTT 59.989 36.000 28.92 15.57 33.73 1.94
140 141 4.523943 TGGCAAATCAGCTGATACAGTTTT 59.476 37.500 28.92 16.28 33.73 2.43
141 142 4.081406 TGGCAAATCAGCTGATACAGTTT 58.919 39.130 28.92 17.00 33.73 2.66
142 143 3.689347 TGGCAAATCAGCTGATACAGTT 58.311 40.909 28.92 16.68 33.73 3.16
143 144 3.354948 TGGCAAATCAGCTGATACAGT 57.645 42.857 28.92 11.25 33.73 3.55
144 145 4.707030 TTTGGCAAATCAGCTGATACAG 57.293 40.909 28.92 20.87 33.73 2.74
145 146 4.705991 TCATTTGGCAAATCAGCTGATACA 59.294 37.500 28.92 20.87 33.73 2.29
146 147 5.039333 GTCATTTGGCAAATCAGCTGATAC 58.961 41.667 28.92 20.04 33.73 2.24
147 148 4.098349 GGTCATTTGGCAAATCAGCTGATA 59.902 41.667 28.92 12.40 33.73 2.15
148 149 3.118884 GGTCATTTGGCAAATCAGCTGAT 60.119 43.478 23.75 23.75 36.07 2.90
149 150 2.231964 GGTCATTTGGCAAATCAGCTGA 59.768 45.455 22.02 20.79 34.17 4.26
150 151 2.232941 AGGTCATTTGGCAAATCAGCTG 59.767 45.455 24.50 14.57 28.34 4.24
151 152 2.532843 AGGTCATTTGGCAAATCAGCT 58.467 42.857 20.61 20.61 34.17 4.24
152 153 3.193267 TGTAGGTCATTTGGCAAATCAGC 59.807 43.478 22.02 19.31 0.00 4.26
153 154 5.359009 AGATGTAGGTCATTTGGCAAATCAG 59.641 40.000 22.02 12.54 36.83 2.90
154 155 5.263599 AGATGTAGGTCATTTGGCAAATCA 58.736 37.500 22.02 15.74 36.83 2.57
155 156 5.841957 AGATGTAGGTCATTTGGCAAATC 57.158 39.130 22.02 12.16 36.83 2.17
156 157 6.610075 AAAGATGTAGGTCATTTGGCAAAT 57.390 33.333 19.39 19.39 36.83 2.32
157 158 6.418057 AAAAGATGTAGGTCATTTGGCAAA 57.582 33.333 16.01 16.01 36.83 3.68
158 159 6.041409 TGAAAAAGATGTAGGTCATTTGGCAA 59.959 34.615 0.00 0.00 36.83 4.52
159 160 5.538053 TGAAAAAGATGTAGGTCATTTGGCA 59.462 36.000 0.00 0.00 36.83 4.92
160 161 5.863935 GTGAAAAAGATGTAGGTCATTTGGC 59.136 40.000 0.00 0.00 36.83 4.52
161 162 6.980593 TGTGAAAAAGATGTAGGTCATTTGG 58.019 36.000 0.00 0.00 36.83 3.28
162 163 8.298854 TGATGTGAAAAAGATGTAGGTCATTTG 58.701 33.333 0.00 0.00 36.83 2.32
163 164 8.408043 TGATGTGAAAAAGATGTAGGTCATTT 57.592 30.769 0.00 0.00 36.83 2.32
164 165 7.884877 TCTGATGTGAAAAAGATGTAGGTCATT 59.115 33.333 0.00 0.00 36.83 2.57
165 166 7.397221 TCTGATGTGAAAAAGATGTAGGTCAT 58.603 34.615 0.00 0.00 39.77 3.06
166 167 6.768483 TCTGATGTGAAAAAGATGTAGGTCA 58.232 36.000 0.00 0.00 0.00 4.02
167 168 7.856145 ATCTGATGTGAAAAAGATGTAGGTC 57.144 36.000 0.00 0.00 0.00 3.85
168 169 8.641498 AAATCTGATGTGAAAAAGATGTAGGT 57.359 30.769 0.00 0.00 29.93 3.08
169 170 9.565213 GAAAATCTGATGTGAAAAAGATGTAGG 57.435 33.333 0.00 0.00 29.93 3.18
170 171 9.565213 GGAAAATCTGATGTGAAAAAGATGTAG 57.435 33.333 0.00 0.00 29.93 2.74
171 172 9.076781 TGGAAAATCTGATGTGAAAAAGATGTA 57.923 29.630 0.00 0.00 29.93 2.29
172 173 7.869429 GTGGAAAATCTGATGTGAAAAAGATGT 59.131 33.333 0.00 0.00 29.93 3.06
173 174 7.868922 TGTGGAAAATCTGATGTGAAAAAGATG 59.131 33.333 0.00 0.00 29.93 2.90
174 175 7.954835 TGTGGAAAATCTGATGTGAAAAAGAT 58.045 30.769 0.00 0.00 0.00 2.40
175 176 7.345422 TGTGGAAAATCTGATGTGAAAAAGA 57.655 32.000 0.00 0.00 0.00 2.52
176 177 6.145048 GCTGTGGAAAATCTGATGTGAAAAAG 59.855 38.462 0.00 0.00 0.00 2.27
177 178 5.984926 GCTGTGGAAAATCTGATGTGAAAAA 59.015 36.000 0.00 0.00 0.00 1.94
178 179 5.302568 AGCTGTGGAAAATCTGATGTGAAAA 59.697 36.000 0.00 0.00 0.00 2.29
179 180 4.828939 AGCTGTGGAAAATCTGATGTGAAA 59.171 37.500 0.00 0.00 0.00 2.69
180 181 4.216902 CAGCTGTGGAAAATCTGATGTGAA 59.783 41.667 5.25 0.00 0.00 3.18
181 182 3.754850 CAGCTGTGGAAAATCTGATGTGA 59.245 43.478 5.25 0.00 0.00 3.58
182 183 3.504906 ACAGCTGTGGAAAATCTGATGTG 59.495 43.478 20.97 0.00 32.73 3.21
183 184 3.759581 ACAGCTGTGGAAAATCTGATGT 58.240 40.909 20.97 0.00 0.00 3.06
184 185 4.778534 AACAGCTGTGGAAAATCTGATG 57.221 40.909 22.49 0.00 0.00 3.07
185 186 5.796424 AAAACAGCTGTGGAAAATCTGAT 57.204 34.783 22.49 0.00 0.00 2.90
186 187 5.451798 GGAAAAACAGCTGTGGAAAATCTGA 60.452 40.000 22.49 0.00 0.00 3.27
187 188 4.746611 GGAAAAACAGCTGTGGAAAATCTG 59.253 41.667 22.49 0.00 0.00 2.90
188 189 4.405358 TGGAAAAACAGCTGTGGAAAATCT 59.595 37.500 22.49 0.00 0.00 2.40
189 190 4.507756 GTGGAAAAACAGCTGTGGAAAATC 59.492 41.667 22.49 12.62 0.00 2.17
190 191 4.081198 TGTGGAAAAACAGCTGTGGAAAAT 60.081 37.500 22.49 0.00 0.00 1.82
191 192 3.259374 TGTGGAAAAACAGCTGTGGAAAA 59.741 39.130 22.49 1.99 0.00 2.29
192 193 2.828520 TGTGGAAAAACAGCTGTGGAAA 59.171 40.909 22.49 1.38 0.00 3.13
193 194 2.426738 CTGTGGAAAAACAGCTGTGGAA 59.573 45.455 22.49 0.21 41.05 3.53
194 195 2.023673 CTGTGGAAAAACAGCTGTGGA 58.976 47.619 22.49 0.00 41.05 4.02
195 196 2.497107 CTGTGGAAAAACAGCTGTGG 57.503 50.000 22.49 0.00 41.05 4.17
223 224 9.677567 GCTGTGAATTTCTAAAATCAGTTGTAA 57.322 29.630 0.00 0.00 29.13 2.41
224 225 8.296713 GGCTGTGAATTTCTAAAATCAGTTGTA 58.703 33.333 0.00 0.00 29.13 2.41
225 226 7.147976 GGCTGTGAATTTCTAAAATCAGTTGT 58.852 34.615 0.00 0.00 29.13 3.32
226 227 6.306356 CGGCTGTGAATTTCTAAAATCAGTTG 59.694 38.462 0.00 0.00 29.13 3.16
227 228 6.206634 TCGGCTGTGAATTTCTAAAATCAGTT 59.793 34.615 0.00 0.00 29.13 3.16
228 229 5.705441 TCGGCTGTGAATTTCTAAAATCAGT 59.295 36.000 0.00 0.00 29.13 3.41
229 230 6.182039 TCGGCTGTGAATTTCTAAAATCAG 57.818 37.500 0.00 0.00 29.13 2.90
230 231 6.378582 GTTCGGCTGTGAATTTCTAAAATCA 58.621 36.000 0.00 0.00 0.00 2.57
231 232 5.800438 GGTTCGGCTGTGAATTTCTAAAATC 59.200 40.000 0.00 0.00 0.00 2.17
232 233 5.242838 TGGTTCGGCTGTGAATTTCTAAAAT 59.757 36.000 0.00 0.00 0.00 1.82
233 234 4.580995 TGGTTCGGCTGTGAATTTCTAAAA 59.419 37.500 0.00 0.00 0.00 1.52
234 235 4.138290 TGGTTCGGCTGTGAATTTCTAAA 58.862 39.130 0.00 0.00 0.00 1.85
235 236 3.745799 TGGTTCGGCTGTGAATTTCTAA 58.254 40.909 0.00 0.00 0.00 2.10
236 237 3.410631 TGGTTCGGCTGTGAATTTCTA 57.589 42.857 0.00 0.00 0.00 2.10
237 238 2.270352 TGGTTCGGCTGTGAATTTCT 57.730 45.000 0.00 0.00 0.00 2.52
238 239 3.049912 GTTTGGTTCGGCTGTGAATTTC 58.950 45.455 0.00 0.00 0.00 2.17
239 240 2.428890 TGTTTGGTTCGGCTGTGAATTT 59.571 40.909 0.00 0.00 0.00 1.82
240 241 2.028130 TGTTTGGTTCGGCTGTGAATT 58.972 42.857 0.00 0.00 0.00 2.17
241 242 1.608590 CTGTTTGGTTCGGCTGTGAAT 59.391 47.619 0.00 0.00 0.00 2.57
242 243 1.021202 CTGTTTGGTTCGGCTGTGAA 58.979 50.000 0.00 0.00 0.00 3.18
243 244 0.817634 CCTGTTTGGTTCGGCTGTGA 60.818 55.000 0.00 0.00 0.00 3.58
244 245 1.654220 CCTGTTTGGTTCGGCTGTG 59.346 57.895 0.00 0.00 0.00 3.66
245 246 2.193536 GCCTGTTTGGTTCGGCTGT 61.194 57.895 0.00 0.00 39.42 4.40
246 247 1.733402 TTGCCTGTTTGGTTCGGCTG 61.733 55.000 0.00 0.00 42.90 4.85
247 248 1.454847 TTGCCTGTTTGGTTCGGCT 60.455 52.632 0.00 0.00 42.90 5.52
248 249 1.007387 CTTGCCTGTTTGGTTCGGC 60.007 57.895 0.00 0.00 42.78 5.54
249 250 0.310854 GTCTTGCCTGTTTGGTTCGG 59.689 55.000 0.00 0.00 38.35 4.30
250 251 0.041312 CGTCTTGCCTGTTTGGTTCG 60.041 55.000 0.00 0.00 38.35 3.95
251 252 1.305201 TCGTCTTGCCTGTTTGGTTC 58.695 50.000 0.00 0.00 38.35 3.62
252 253 1.676006 CTTCGTCTTGCCTGTTTGGTT 59.324 47.619 0.00 0.00 38.35 3.67
253 254 1.134220 TCTTCGTCTTGCCTGTTTGGT 60.134 47.619 0.00 0.00 38.35 3.67
254 255 1.264288 GTCTTCGTCTTGCCTGTTTGG 59.736 52.381 0.00 0.00 39.35 3.28
255 256 1.070577 CGTCTTCGTCTTGCCTGTTTG 60.071 52.381 0.00 0.00 0.00 2.93
256 257 1.217882 CGTCTTCGTCTTGCCTGTTT 58.782 50.000 0.00 0.00 0.00 2.83
257 258 1.222115 GCGTCTTCGTCTTGCCTGTT 61.222 55.000 0.00 0.00 39.49 3.16
258 259 1.664965 GCGTCTTCGTCTTGCCTGT 60.665 57.895 0.00 0.00 39.49 4.00
259 260 2.720758 CGCGTCTTCGTCTTGCCTG 61.721 63.158 0.00 0.00 39.49 4.85
260 261 2.430921 CGCGTCTTCGTCTTGCCT 60.431 61.111 0.00 0.00 39.49 4.75
261 262 2.733593 ACGCGTCTTCGTCTTGCC 60.734 61.111 5.58 0.00 38.44 4.52
262 263 2.465920 CACGCGTCTTCGTCTTGC 59.534 61.111 9.86 0.00 41.21 4.01
263 264 1.617755 ATGCACGCGTCTTCGTCTTG 61.618 55.000 9.86 0.00 41.21 3.02
298 299 1.080093 TGGATCACTCGTTCGTGCC 60.080 57.895 0.00 0.00 34.92 5.01
340 345 0.475906 GATGGAGTGGAGGGGATTGG 59.524 60.000 0.00 0.00 0.00 3.16
554 563 0.933700 AGGAGAGGGGAGAGGAGAAG 59.066 60.000 0.00 0.00 0.00 2.85
943 955 2.447244 AGAAGAGCACGACCAAGAAG 57.553 50.000 0.00 0.00 0.00 2.85
1066 1081 1.900486 GACTCTCTTCGGGGGAAAAGA 59.100 52.381 0.00 0.00 0.00 2.52
1067 1082 1.404315 CGACTCTCTTCGGGGGAAAAG 60.404 57.143 0.00 0.00 35.26 2.27
1076 1091 1.269621 ACAACAACCCGACTCTCTTCG 60.270 52.381 0.00 0.00 38.80 3.79
1161 1176 1.996786 GCACCCGCCATCTGATTGTG 61.997 60.000 0.00 0.00 0.00 3.33
1162 1177 1.750399 GCACCCGCCATCTGATTGT 60.750 57.895 0.00 0.00 0.00 2.71
1163 1178 3.113745 GCACCCGCCATCTGATTG 58.886 61.111 0.00 0.00 0.00 2.67
1765 1789 2.029073 CCAGCGTCGGTCACAAGT 59.971 61.111 0.00 0.00 0.00 3.16
2131 2155 1.134670 AGGCGAGCAAGTGTAAGATCC 60.135 52.381 0.00 0.00 0.00 3.36
2349 2373 2.503765 TCCATCACCTTTGCCGATTCTA 59.496 45.455 0.00 0.00 0.00 2.10
2356 2380 1.970640 AGGTTTTCCATCACCTTTGCC 59.029 47.619 0.00 0.00 40.85 4.52
2443 2467 2.834549 CAAGGAGAGAGCCCTGAACTTA 59.165 50.000 0.00 0.00 33.55 2.24
2853 2877 4.201990 CCATGCAGTTAGAAAGATCAAGCC 60.202 45.833 0.00 0.00 0.00 4.35
2914 2938 1.301716 GGCACGGAGCTTGAAGTGA 60.302 57.895 13.46 0.00 44.79 3.41
2931 2955 2.037136 CAGCCAAACAGCGAGAGGG 61.037 63.158 0.00 0.00 38.01 4.30
3166 3193 2.126071 GACGGTTGCGCTGCTAGA 60.126 61.111 9.73 0.00 0.00 2.43
3167 3194 1.565156 TTTGACGGTTGCGCTGCTAG 61.565 55.000 9.73 0.00 0.00 3.42
3225 3252 3.565307 TGAACAAAGTTCAGAAGCCCAT 58.435 40.909 8.39 0.00 0.00 4.00
3963 3995 8.074613 CAAATATGGATGCCATTCTTGGATAT 57.925 34.615 4.03 0.00 46.92 1.63
4032 4064 0.896226 GGCCAAGAGAAGTACGGACT 59.104 55.000 0.00 0.00 37.59 3.85
4035 4067 1.802880 CGATGGCCAAGAGAAGTACGG 60.803 57.143 10.96 0.00 0.00 4.02
4039 4071 0.326264 AAGCGATGGCCAAGAGAAGT 59.674 50.000 10.96 0.00 41.24 3.01
4049 4081 3.698029 ATCATGTGTTAAAGCGATGGC 57.302 42.857 0.00 0.00 40.37 4.40


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.