Multiple sequence alignment - TraesCS6B01G395400

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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 TraesCS6B01G395400 chr6B 100.000 2507 0 0 1 2507 670602537 670600031 0.000000e+00 4630.0
1 TraesCS6B01G395400 chr6B 82.640 2068 284 47 343 2373 15249511 15247482 0.000000e+00 1760.0
2 TraesCS6B01G395400 chr6B 83.609 1269 151 31 1134 2373 53075844 53074604 0.000000e+00 1138.0
3 TraesCS6B01G395400 chr6B 80.031 1297 226 21 249 1528 53077240 53075960 0.000000e+00 929.0
4 TraesCS6B01G395400 chr6B 81.605 1109 185 14 714 1812 16255614 16256713 0.000000e+00 900.0
5 TraesCS6B01G395400 chr6B 78.302 1272 235 30 263 1509 15744168 15742913 0.000000e+00 782.0
6 TraesCS6B01G395400 chr6B 77.689 1246 237 26 249 1485 670592778 670591565 0.000000e+00 723.0
7 TraesCS6B01G395400 chr6B 77.055 1046 213 22 450 1479 27065867 27064833 6.010000e-161 577.0
8 TraesCS6B01G395400 chr6B 83.022 589 86 7 235 819 16338711 16339289 2.860000e-144 521.0
9 TraesCS6B01G395400 chr6B 85.550 436 53 7 1946 2372 65157422 65156988 4.920000e-122 448.0
10 TraesCS6B01G395400 chr6B 94.444 36 2 0 2311 2346 49416320 49416285 3.480000e-04 56.5
11 TraesCS6B01G395400 chr2B 81.271 2077 312 48 342 2373 89494606 89496650 0.000000e+00 1609.0
12 TraesCS6B01G395400 chr2B 80.720 1416 235 22 621 2018 709487505 709486110 0.000000e+00 1068.0
13 TraesCS6B01G395400 chr2B 83.668 398 47 13 235 617 709514976 709514582 2.370000e-95 359.0
14 TraesCS6B01G395400 chr2B 77.917 240 30 16 2124 2344 800418759 800418524 7.280000e-26 128.0
15 TraesCS6B01G395400 chr2B 88.889 99 8 3 1847 1942 800554973 800554875 4.380000e-23 119.0
16 TraesCS6B01G395400 chr2B 87.500 88 9 2 2287 2372 709251472 709251385 1.590000e-17 100.0
17 TraesCS6B01G395400 chr6D 82.310 1628 253 24 410 2018 8578870 8577259 0.000000e+00 1378.0
18 TraesCS6B01G395400 chr6D 79.096 1172 235 9 342 1508 8397165 8395999 0.000000e+00 798.0
19 TraesCS6B01G395400 chr6D 77.323 1173 243 17 334 1489 16775767 16774601 0.000000e+00 671.0
20 TraesCS6B01G395400 chr6D 81.076 502 65 18 1899 2373 34019219 34019717 8.470000e-100 374.0
21 TraesCS6B01G395400 chr6D 78.947 342 47 16 2051 2373 8577257 8576922 2.530000e-50 209.0
22 TraesCS6B01G395400 chr6D 77.315 216 43 5 1977 2191 7904276 7904486 3.390000e-24 122.0
23 TraesCS6B01G395400 chr6A 82.960 1338 194 21 352 1679 9364602 9365915 0.000000e+00 1177.0
24 TraesCS6B01G395400 chr6A 77.018 1214 228 45 331 1511 15873219 15872024 0.000000e+00 649.0
25 TraesCS6B01G395400 chr6A 91.375 371 28 4 1669 2036 9366103 9366472 2.880000e-139 505.0
26 TraesCS6B01G395400 chr6A 85.194 439 52 10 1946 2373 35567493 35567057 2.960000e-119 438.0
27 TraesCS6B01G395400 chr6A 94.444 36 2 0 2311 2346 28429068 28429103 3.480000e-04 56.5
28 TraesCS6B01G395400 chr5D 80.532 1428 231 19 621 2036 42073869 42075261 0.000000e+00 1053.0
29 TraesCS6B01G395400 chr5D 77.891 1081 213 21 421 1485 27979237 27978167 0.000000e+00 649.0
30 TraesCS6B01G395400 chrUn 80.505 1385 248 19 586 1953 65790534 65789155 0.000000e+00 1042.0
31 TraesCS6B01G395400 chr1A 82.051 1170 188 18 354 1512 589248496 589247338 0.000000e+00 977.0
32 TraesCS6B01G395400 chr7D 80.366 1202 226 6 328 1525 161390626 161391821 0.000000e+00 904.0
33 TraesCS6B01G395400 chr2D 81.529 1099 181 17 425 1512 588162348 588163435 0.000000e+00 885.0
34 TraesCS6B01G395400 chr7B 79.818 1209 230 9 328 1532 123655550 123656748 0.000000e+00 869.0
35 TraesCS6B01G395400 chr5B 81.496 508 62 16 1859 2344 621234280 621233783 3.020000e-104 388.0


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 TraesCS6B01G395400 chr6B 670600031 670602537 2506 True 4630.0 4630 100.0000 1 2507 1 chr6B.!!$R7 2506
1 TraesCS6B01G395400 chr6B 15247482 15249511 2029 True 1760.0 1760 82.6400 343 2373 1 chr6B.!!$R1 2030
2 TraesCS6B01G395400 chr6B 53074604 53077240 2636 True 1033.5 1138 81.8200 249 2373 2 chr6B.!!$R8 2124
3 TraesCS6B01G395400 chr6B 16255614 16256713 1099 False 900.0 900 81.6050 714 1812 1 chr6B.!!$F1 1098
4 TraesCS6B01G395400 chr6B 15742913 15744168 1255 True 782.0 782 78.3020 263 1509 1 chr6B.!!$R2 1246
5 TraesCS6B01G395400 chr6B 670591565 670592778 1213 True 723.0 723 77.6890 249 1485 1 chr6B.!!$R6 1236
6 TraesCS6B01G395400 chr6B 27064833 27065867 1034 True 577.0 577 77.0550 450 1479 1 chr6B.!!$R3 1029
7 TraesCS6B01G395400 chr6B 16338711 16339289 578 False 521.0 521 83.0220 235 819 1 chr6B.!!$F2 584
8 TraesCS6B01G395400 chr2B 89494606 89496650 2044 False 1609.0 1609 81.2710 342 2373 1 chr2B.!!$F1 2031
9 TraesCS6B01G395400 chr2B 709486110 709487505 1395 True 1068.0 1068 80.7200 621 2018 1 chr2B.!!$R2 1397
10 TraesCS6B01G395400 chr6D 8395999 8397165 1166 True 798.0 798 79.0960 342 1508 1 chr6D.!!$R1 1166
11 TraesCS6B01G395400 chr6D 8576922 8578870 1948 True 793.5 1378 80.6285 410 2373 2 chr6D.!!$R3 1963
12 TraesCS6B01G395400 chr6D 16774601 16775767 1166 True 671.0 671 77.3230 334 1489 1 chr6D.!!$R2 1155
13 TraesCS6B01G395400 chr6A 9364602 9366472 1870 False 841.0 1177 87.1675 352 2036 2 chr6A.!!$F2 1684
14 TraesCS6B01G395400 chr6A 15872024 15873219 1195 True 649.0 649 77.0180 331 1511 1 chr6A.!!$R1 1180
15 TraesCS6B01G395400 chr5D 42073869 42075261 1392 False 1053.0 1053 80.5320 621 2036 1 chr5D.!!$F1 1415
16 TraesCS6B01G395400 chr5D 27978167 27979237 1070 True 649.0 649 77.8910 421 1485 1 chr5D.!!$R1 1064
17 TraesCS6B01G395400 chrUn 65789155 65790534 1379 True 1042.0 1042 80.5050 586 1953 1 chrUn.!!$R1 1367
18 TraesCS6B01G395400 chr1A 589247338 589248496 1158 True 977.0 977 82.0510 354 1512 1 chr1A.!!$R1 1158
19 TraesCS6B01G395400 chr7D 161390626 161391821 1195 False 904.0 904 80.3660 328 1525 1 chr7D.!!$F1 1197
20 TraesCS6B01G395400 chr2D 588162348 588163435 1087 False 885.0 885 81.5290 425 1512 1 chr2D.!!$F1 1087
21 TraesCS6B01G395400 chr7B 123655550 123656748 1198 False 869.0 869 79.8180 328 1532 1 chr7B.!!$F1 1204

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
69 70 0.031585 GGTTTTTCCAGTTGGTCCGC 59.968 55.0 0.0 0.0 36.34 5.54 F
76 77 0.108615 CCAGTTGGTCCGCTAGTCTG 60.109 60.0 0.0 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1093 1168 0.610174 TGCTCTAGCTTGGTGGTGAG 59.390 55.000 3.26 0.0 42.66 3.51 R
2048 2870 2.624838 CTCTGTTTTTCAGCACCATGGT 59.375 45.455 13.00 13.0 43.32 3.55 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
25 26 6.912951 ACTAAGAGACTGCTACACCTTAAA 57.087 37.500 0.00 0.00 0.00 1.52
26 27 7.299246 ACTAAGAGACTGCTACACCTTAAAA 57.701 36.000 0.00 0.00 0.00 1.52
27 28 7.732996 ACTAAGAGACTGCTACACCTTAAAAA 58.267 34.615 0.00 0.00 0.00 1.94
41 42 3.836151 AAAAACCGAGCAAGGCGT 58.164 50.000 0.00 0.00 33.69 5.68
42 43 1.652563 AAAAACCGAGCAAGGCGTC 59.347 52.632 0.00 0.00 33.69 5.19
43 44 2.113131 AAAAACCGAGCAAGGCGTCG 62.113 55.000 0.00 0.00 35.91 5.12
47 48 3.479269 CGAGCAAGGCGTCGGTTC 61.479 66.667 0.00 0.00 32.40 3.62
48 49 3.119096 GAGCAAGGCGTCGGTTCC 61.119 66.667 0.00 0.00 0.00 3.62
49 50 3.591254 GAGCAAGGCGTCGGTTCCT 62.591 63.158 0.00 0.00 0.00 3.36
50 51 3.423154 GCAAGGCGTCGGTTCCTG 61.423 66.667 0.00 0.00 32.00 3.86
51 52 2.742372 CAAGGCGTCGGTTCCTGG 60.742 66.667 0.00 0.00 32.00 4.45
52 53 3.239253 AAGGCGTCGGTTCCTGGT 61.239 61.111 0.00 0.00 32.00 4.00
53 54 2.814835 AAGGCGTCGGTTCCTGGTT 61.815 57.895 0.00 0.00 32.00 3.67
54 55 2.281276 GGCGTCGGTTCCTGGTTT 60.281 61.111 0.00 0.00 0.00 3.27
55 56 1.895231 GGCGTCGGTTCCTGGTTTT 60.895 57.895 0.00 0.00 0.00 2.43
56 57 1.449726 GGCGTCGGTTCCTGGTTTTT 61.450 55.000 0.00 0.00 0.00 1.94
57 58 0.040692 GCGTCGGTTCCTGGTTTTTC 60.041 55.000 0.00 0.00 0.00 2.29
58 59 0.589708 CGTCGGTTCCTGGTTTTTCC 59.410 55.000 0.00 0.00 0.00 3.13
59 60 1.682740 GTCGGTTCCTGGTTTTTCCA 58.317 50.000 0.00 0.00 45.01 3.53
68 69 1.394618 TGGTTTTTCCAGTTGGTCCG 58.605 50.000 0.00 0.00 41.93 4.79
69 70 0.031585 GGTTTTTCCAGTTGGTCCGC 59.968 55.000 0.00 0.00 36.34 5.54
70 71 1.029681 GTTTTTCCAGTTGGTCCGCT 58.970 50.000 0.00 0.00 36.34 5.52
71 72 2.223745 GTTTTTCCAGTTGGTCCGCTA 58.776 47.619 0.00 0.00 36.34 4.26
72 73 2.178912 TTTTCCAGTTGGTCCGCTAG 57.821 50.000 0.00 0.00 36.34 3.42
73 74 1.053424 TTTCCAGTTGGTCCGCTAGT 58.947 50.000 0.00 0.00 36.34 2.57
74 75 0.606604 TTCCAGTTGGTCCGCTAGTC 59.393 55.000 0.00 0.00 36.34 2.59
75 76 0.251653 TCCAGTTGGTCCGCTAGTCT 60.252 55.000 0.00 0.00 36.34 3.24
76 77 0.108615 CCAGTTGGTCCGCTAGTCTG 60.109 60.000 0.00 0.00 0.00 3.51
77 78 0.108615 CAGTTGGTCCGCTAGTCTGG 60.109 60.000 0.00 0.00 0.00 3.86
78 79 0.542232 AGTTGGTCCGCTAGTCTGGT 60.542 55.000 0.00 0.00 0.00 4.00
79 80 0.108756 GTTGGTCCGCTAGTCTGGTC 60.109 60.000 0.00 0.00 0.00 4.02
80 81 1.255667 TTGGTCCGCTAGTCTGGTCC 61.256 60.000 6.99 6.99 34.49 4.46
81 82 1.681327 GGTCCGCTAGTCTGGTCCA 60.681 63.158 8.44 0.00 34.13 4.02
82 83 1.255667 GGTCCGCTAGTCTGGTCCAA 61.256 60.000 0.00 0.00 34.13 3.53
83 84 0.606604 GTCCGCTAGTCTGGTCCAAA 59.393 55.000 0.00 0.00 0.00 3.28
84 85 1.207329 GTCCGCTAGTCTGGTCCAAAT 59.793 52.381 0.00 0.00 0.00 2.32
85 86 1.906574 TCCGCTAGTCTGGTCCAAATT 59.093 47.619 0.00 0.00 0.00 1.82
86 87 2.304761 TCCGCTAGTCTGGTCCAAATTT 59.695 45.455 0.00 0.00 0.00 1.82
87 88 3.081804 CCGCTAGTCTGGTCCAAATTTT 58.918 45.455 0.00 0.00 0.00 1.82
88 89 4.020039 TCCGCTAGTCTGGTCCAAATTTTA 60.020 41.667 0.00 0.00 0.00 1.52
89 90 4.698304 CCGCTAGTCTGGTCCAAATTTTAA 59.302 41.667 0.00 0.00 0.00 1.52
90 91 5.391629 CCGCTAGTCTGGTCCAAATTTTAAC 60.392 44.000 0.00 0.00 0.00 2.01
91 92 5.180492 CGCTAGTCTGGTCCAAATTTTAACA 59.820 40.000 0.00 0.00 0.00 2.41
92 93 6.379386 GCTAGTCTGGTCCAAATTTTAACAC 58.621 40.000 0.00 0.00 0.00 3.32
93 94 6.206829 GCTAGTCTGGTCCAAATTTTAACACT 59.793 38.462 0.00 0.00 0.00 3.55
94 95 7.389607 GCTAGTCTGGTCCAAATTTTAACACTA 59.610 37.037 0.00 0.00 0.00 2.74
95 96 9.449719 CTAGTCTGGTCCAAATTTTAACACTAT 57.550 33.333 0.00 0.00 0.00 2.12
96 97 8.110860 AGTCTGGTCCAAATTTTAACACTATG 57.889 34.615 0.00 0.00 0.00 2.23
97 98 7.724061 AGTCTGGTCCAAATTTTAACACTATGT 59.276 33.333 0.00 0.00 0.00 2.29
98 99 8.357402 GTCTGGTCCAAATTTTAACACTATGTT 58.643 33.333 0.00 0.00 43.88 2.71
99 100 8.573035 TCTGGTCCAAATTTTAACACTATGTTC 58.427 33.333 0.00 0.00 40.22 3.18
100 101 8.239038 TGGTCCAAATTTTAACACTATGTTCA 57.761 30.769 0.00 0.00 40.22 3.18
101 102 8.138712 TGGTCCAAATTTTAACACTATGTTCAC 58.861 33.333 0.00 0.00 40.22 3.18
102 103 8.138712 GGTCCAAATTTTAACACTATGTTCACA 58.861 33.333 0.00 0.00 40.22 3.58
103 104 9.522804 GTCCAAATTTTAACACTATGTTCACAA 57.477 29.630 0.00 0.00 40.22 3.33
172 173 7.938140 TTTTGAGGGGTACAAGATCATTTAG 57.062 36.000 0.00 0.00 0.00 1.85
173 174 6.884472 TTGAGGGGTACAAGATCATTTAGA 57.116 37.500 0.00 0.00 0.00 2.10
174 175 7.451731 TTGAGGGGTACAAGATCATTTAGAT 57.548 36.000 0.00 0.00 40.48 1.98
175 176 6.830912 TGAGGGGTACAAGATCATTTAGATG 58.169 40.000 0.00 0.00 37.00 2.90
176 177 6.615316 TGAGGGGTACAAGATCATTTAGATGA 59.385 38.462 0.00 0.00 45.81 2.92
177 178 7.072263 AGGGGTACAAGATCATTTAGATGAG 57.928 40.000 2.10 0.00 45.01 2.90
178 179 6.617371 AGGGGTACAAGATCATTTAGATGAGT 59.383 38.462 2.10 0.00 45.01 3.41
179 180 6.931840 GGGGTACAAGATCATTTAGATGAGTC 59.068 42.308 2.10 1.08 45.01 3.36
180 181 7.419057 GGGGTACAAGATCATTTAGATGAGTCA 60.419 40.741 0.00 0.00 45.01 3.41
181 182 7.439655 GGGTACAAGATCATTTAGATGAGTCAC 59.560 40.741 0.00 0.00 45.01 3.67
182 183 8.200792 GGTACAAGATCATTTAGATGAGTCACT 58.799 37.037 0.00 0.00 45.01 3.41
183 184 9.593134 GTACAAGATCATTTAGATGAGTCACTT 57.407 33.333 0.00 3.06 45.01 3.16
185 186 9.512588 ACAAGATCATTTAGATGAGTCACTTTT 57.487 29.630 0.00 0.00 45.01 2.27
207 208 5.506730 TTTTTCCTTGGGTGGTTCTTTTT 57.493 34.783 0.00 0.00 0.00 1.94
225 226 2.969821 TTTTAGGGCCTTTGAGCTGA 57.030 45.000 13.45 0.00 0.00 4.26
226 227 3.456380 TTTTAGGGCCTTTGAGCTGAT 57.544 42.857 13.45 0.00 0.00 2.90
227 228 2.717639 TTAGGGCCTTTGAGCTGATC 57.282 50.000 13.45 0.00 0.00 2.92
228 229 1.885049 TAGGGCCTTTGAGCTGATCT 58.115 50.000 13.45 0.00 0.00 2.75
229 230 1.885049 AGGGCCTTTGAGCTGATCTA 58.115 50.000 0.00 0.00 0.00 1.98
230 231 2.200081 AGGGCCTTTGAGCTGATCTAA 58.800 47.619 0.00 0.00 0.00 2.10
231 232 2.578021 AGGGCCTTTGAGCTGATCTAAA 59.422 45.455 0.00 0.00 0.00 1.85
232 233 3.203934 AGGGCCTTTGAGCTGATCTAAAT 59.796 43.478 0.00 0.00 0.00 1.40
233 234 3.317430 GGGCCTTTGAGCTGATCTAAATG 59.683 47.826 0.84 0.00 0.00 2.32
245 246 0.548031 TCTAAATGAGCCCAGCCCAG 59.452 55.000 0.00 0.00 0.00 4.45
246 247 1.076777 TAAATGAGCCCAGCCCAGC 60.077 57.895 0.00 0.00 0.00 4.85
247 248 2.572333 TAAATGAGCCCAGCCCAGCC 62.572 60.000 0.00 0.00 0.00 4.85
401 430 1.304952 CCCAGGTCCTCTCGTCTCT 59.695 63.158 0.00 0.00 0.00 3.10
478 528 1.755200 TTCCCCAAACCCTAGCTTCT 58.245 50.000 0.00 0.00 0.00 2.85
480 530 1.203440 TCCCCAAACCCTAGCTTCTCT 60.203 52.381 0.00 0.00 0.00 3.10
492 542 3.290948 AGCTTCTCTGTCGAGGAGTAT 57.709 47.619 13.01 0.00 43.67 2.12
507 557 2.645802 GAGTATCTCGTCTCCACCTGT 58.354 52.381 0.00 0.00 0.00 4.00
522 572 4.954118 TGTGGCCTCACCCGACCT 62.954 66.667 3.32 0.00 42.98 3.85
569 620 2.606519 CCACCTCAAGTCCCCCGA 60.607 66.667 0.00 0.00 0.00 5.14
823 880 3.672295 CTGCACCTCTTCGGCTCCC 62.672 68.421 0.00 0.00 35.61 4.30
874 943 0.408309 TTCCCTTCTCTCCTCCGACA 59.592 55.000 0.00 0.00 0.00 4.35
928 997 2.127869 CAGGAGTGCGGGCTAGCTA 61.128 63.158 15.72 0.00 38.13 3.32
965 1034 2.965831 AGCTTTGTATCTCCTGGCGATA 59.034 45.455 2.29 2.29 0.00 2.92
973 1042 0.246086 CTCCTGGCGATATCTGCTCC 59.754 60.000 15.69 6.43 0.00 4.70
975 1044 0.394192 CCTGGCGATATCTGCTCCAA 59.606 55.000 15.69 3.59 0.00 3.53
987 1056 1.304134 GCTCCAAACCAACCCGGAT 60.304 57.895 0.73 0.00 38.63 4.18
993 1062 1.555477 AAACCAACCCGGATCGCCTA 61.555 55.000 0.73 0.00 38.63 3.93
1105 1180 1.202818 AGGAGAAACTCACCACCAAGC 60.203 52.381 0.00 0.00 31.08 4.01
1133 1208 5.127682 AGCACTTGAAGAAAATGTTCAGGTT 59.872 36.000 0.00 0.00 40.28 3.50
1227 1302 0.460987 GCAGGTCCGAGTTCCTCATG 60.461 60.000 0.00 0.00 30.91 3.07
1503 2089 3.334691 TCCTGCCAGATTCAGTTTTACG 58.665 45.455 0.00 0.00 0.00 3.18
1536 2122 6.990349 AGACCGGTATGAAAATTGGTATGTAG 59.010 38.462 7.34 0.00 0.00 2.74
1578 2164 2.423538 AGGAAAAATCGCACTGGTATGC 59.576 45.455 0.00 0.00 42.48 3.14
1589 2175 3.751175 GCACTGGTATGCACTTGTTCTTA 59.249 43.478 0.00 0.00 45.39 2.10
1590 2176 4.396166 GCACTGGTATGCACTTGTTCTTAT 59.604 41.667 0.00 0.00 45.39 1.73
1604 2192 8.443160 CACTTGTTCTTATTCGTGTCATATTGT 58.557 33.333 0.00 0.00 0.00 2.71
1696 2512 5.073311 TGAGTAGTATTTCTGCACACTCC 57.927 43.478 0.00 0.00 31.96 3.85
1707 2523 0.582005 GCACACTCCGTGTCTTTGTC 59.418 55.000 0.00 0.00 43.92 3.18
1753 2572 2.549754 CAATGCAATCGTCCATCTACCC 59.450 50.000 0.00 0.00 0.00 3.69
1771 2590 6.180472 TCTACCCTTCATGAAAGAATGTTCC 58.820 40.000 9.88 0.00 37.12 3.62
1777 2596 6.592607 CCTTCATGAAAGAATGTTCCCATTTG 59.407 38.462 9.88 0.00 41.37 2.32
1783 2603 2.767960 AGAATGTTCCCATTTGGCCATC 59.232 45.455 6.09 0.00 41.37 3.51
1889 2710 3.686016 TCTTGTAGTTTTGGATGGCCTC 58.314 45.455 3.32 0.00 34.31 4.70
1900 2721 1.366319 GATGGCCTCCTGGGTGATAT 58.634 55.000 3.32 0.00 37.43 1.63
1915 2737 6.372931 TGGGTGATATTTTTCTAGGGGAATG 58.627 40.000 0.00 0.00 33.53 2.67
1959 2781 7.778853 AGTTGAGTAGTAGGCTAGTAGCATTTA 59.221 37.037 23.24 9.98 44.75 1.40
2271 3120 6.515272 TGCAAATTTCTATCTGGAAAGTCC 57.485 37.500 0.00 0.00 38.38 3.85
2272 3121 6.248433 TGCAAATTTCTATCTGGAAAGTCCT 58.752 36.000 0.00 0.00 38.38 3.85
2275 3124 8.184848 GCAAATTTCTATCTGGAAAGTCCTAAC 58.815 37.037 0.00 0.00 38.38 2.34
2278 3127 7.792364 TTTCTATCTGGAAAGTCCTAACAGA 57.208 36.000 0.00 0.00 41.79 3.41
2282 3131 8.826765 TCTATCTGGAAAGTCCTAACAGAAAAT 58.173 33.333 0.00 0.00 41.03 1.82
2285 3134 8.202461 TCTGGAAAGTCCTAACAGAAAATAGA 57.798 34.615 0.00 0.00 37.46 1.98
2286 3135 8.656806 TCTGGAAAGTCCTAACAGAAAATAGAA 58.343 33.333 0.00 0.00 37.46 2.10
2344 3196 9.241919 TCTTGCAGAATTTCAAACATAGGAATA 57.758 29.630 0.00 0.00 0.00 1.75
2345 3197 9.512435 CTTGCAGAATTTCAAACATAGGAATAG 57.488 33.333 0.00 0.00 0.00 1.73
2382 3235 8.757164 GTTTATGAACCAACCTAAGGAAATTG 57.243 34.615 0.00 0.00 0.00 2.32
2383 3236 8.364894 GTTTATGAACCAACCTAAGGAAATTGT 58.635 33.333 0.00 0.00 0.00 2.71
2384 3237 6.994421 ATGAACCAACCTAAGGAAATTGTT 57.006 33.333 0.00 0.00 0.00 2.83
2385 3238 6.155475 TGAACCAACCTAAGGAAATTGTTG 57.845 37.500 0.00 0.00 36.83 3.33
2386 3239 4.600692 ACCAACCTAAGGAAATTGTTGC 57.399 40.909 0.00 0.00 36.00 4.17
2387 3240 3.323691 ACCAACCTAAGGAAATTGTTGCC 59.676 43.478 0.00 0.00 36.00 4.52
2388 3241 3.578282 CCAACCTAAGGAAATTGTTGCCT 59.422 43.478 0.00 0.00 36.00 4.75
2389 3242 4.559153 CAACCTAAGGAAATTGTTGCCTG 58.441 43.478 0.00 0.00 31.10 4.85
2390 3243 2.562738 ACCTAAGGAAATTGTTGCCTGC 59.437 45.455 0.00 0.00 31.06 4.85
2391 3244 2.562298 CCTAAGGAAATTGTTGCCTGCA 59.438 45.455 0.00 0.00 31.06 4.41
2392 3245 2.531522 AAGGAAATTGTTGCCTGCAC 57.468 45.000 0.00 0.00 31.06 4.57
2393 3246 1.708341 AGGAAATTGTTGCCTGCACT 58.292 45.000 0.00 0.00 0.00 4.40
2394 3247 2.875296 AGGAAATTGTTGCCTGCACTA 58.125 42.857 0.00 0.00 0.00 2.74
2395 3248 3.230134 AGGAAATTGTTGCCTGCACTAA 58.770 40.909 0.00 0.00 0.00 2.24
2396 3249 3.256631 AGGAAATTGTTGCCTGCACTAAG 59.743 43.478 0.00 0.00 0.00 2.18
2397 3250 3.255642 GGAAATTGTTGCCTGCACTAAGA 59.744 43.478 0.00 0.00 0.00 2.10
2398 3251 4.261994 GGAAATTGTTGCCTGCACTAAGAA 60.262 41.667 0.00 0.00 0.00 2.52
2399 3252 5.473039 GAAATTGTTGCCTGCACTAAGAAT 58.527 37.500 0.00 0.00 0.00 2.40
2400 3253 6.350110 GGAAATTGTTGCCTGCACTAAGAATA 60.350 38.462 0.00 0.00 0.00 1.75
2401 3254 5.567138 ATTGTTGCCTGCACTAAGAATAC 57.433 39.130 0.00 0.00 0.00 1.89
2402 3255 4.286297 TGTTGCCTGCACTAAGAATACT 57.714 40.909 0.00 0.00 0.00 2.12
2403 3256 4.253685 TGTTGCCTGCACTAAGAATACTC 58.746 43.478 0.00 0.00 0.00 2.59
2404 3257 4.253685 GTTGCCTGCACTAAGAATACTCA 58.746 43.478 0.00 0.00 0.00 3.41
2405 3258 4.760530 TGCCTGCACTAAGAATACTCAT 57.239 40.909 0.00 0.00 0.00 2.90
2406 3259 5.869649 TGCCTGCACTAAGAATACTCATA 57.130 39.130 0.00 0.00 0.00 2.15
2407 3260 6.425210 TGCCTGCACTAAGAATACTCATAT 57.575 37.500 0.00 0.00 0.00 1.78
2408 3261 6.459066 TGCCTGCACTAAGAATACTCATATC 58.541 40.000 0.00 0.00 0.00 1.63
2409 3262 6.268617 TGCCTGCACTAAGAATACTCATATCT 59.731 38.462 0.00 0.00 0.00 1.98
2410 3263 7.451566 TGCCTGCACTAAGAATACTCATATCTA 59.548 37.037 0.00 0.00 0.00 1.98
2411 3264 8.307483 GCCTGCACTAAGAATACTCATATCTAA 58.693 37.037 0.00 0.00 0.00 2.10
2412 3265 9.632807 CCTGCACTAAGAATACTCATATCTAAC 57.367 37.037 0.00 0.00 0.00 2.34
2413 3266 9.632807 CTGCACTAAGAATACTCATATCTAACC 57.367 37.037 0.00 0.00 0.00 2.85
2414 3267 8.585881 TGCACTAAGAATACTCATATCTAACCC 58.414 37.037 0.00 0.00 0.00 4.11
2415 3268 8.808092 GCACTAAGAATACTCATATCTAACCCT 58.192 37.037 0.00 0.00 0.00 4.34
2425 3278 8.511604 ACTCATATCTAACCCTTTTTCACATG 57.488 34.615 0.00 0.00 0.00 3.21
2426 3279 7.067494 ACTCATATCTAACCCTTTTTCACATGC 59.933 37.037 0.00 0.00 0.00 4.06
2427 3280 6.889177 TCATATCTAACCCTTTTTCACATGCA 59.111 34.615 0.00 0.00 0.00 3.96
2428 3281 7.560991 TCATATCTAACCCTTTTTCACATGCAT 59.439 33.333 0.00 0.00 0.00 3.96
2429 3282 6.610075 ATCTAACCCTTTTTCACATGCATT 57.390 33.333 0.00 0.00 0.00 3.56
2430 3283 6.418057 TCTAACCCTTTTTCACATGCATTT 57.582 33.333 0.00 0.00 0.00 2.32
2431 3284 6.222389 TCTAACCCTTTTTCACATGCATTTG 58.778 36.000 6.50 6.50 0.00 2.32
2432 3285 4.420522 ACCCTTTTTCACATGCATTTGT 57.579 36.364 12.39 0.00 0.00 2.83
2433 3286 4.128643 ACCCTTTTTCACATGCATTTGTG 58.871 39.130 13.22 13.22 46.70 3.33
2434 3287 4.128643 CCCTTTTTCACATGCATTTGTGT 58.871 39.130 17.64 2.66 45.73 3.72
2435 3288 5.163364 ACCCTTTTTCACATGCATTTGTGTA 60.163 36.000 17.64 7.81 45.73 2.90
2436 3289 5.177327 CCCTTTTTCACATGCATTTGTGTAC 59.823 40.000 17.64 0.00 45.73 2.90
2437 3290 5.984926 CCTTTTTCACATGCATTTGTGTACT 59.015 36.000 17.64 0.00 45.73 2.73
2438 3291 6.074195 CCTTTTTCACATGCATTTGTGTACTG 60.074 38.462 17.64 7.78 45.73 2.74
2439 3292 5.512753 TTTCACATGCATTTGTGTACTGT 57.487 34.783 17.64 0.00 45.73 3.55
2440 3293 4.747540 TCACATGCATTTGTGTACTGTC 57.252 40.909 17.64 0.00 45.73 3.51
2441 3294 4.388485 TCACATGCATTTGTGTACTGTCT 58.612 39.130 17.64 0.00 45.73 3.41
2442 3295 4.213906 TCACATGCATTTGTGTACTGTCTG 59.786 41.667 17.64 0.00 45.73 3.51
2443 3296 4.023792 CACATGCATTTGTGTACTGTCTGT 60.024 41.667 11.53 0.00 41.65 3.41
2444 3297 5.179182 CACATGCATTTGTGTACTGTCTGTA 59.821 40.000 11.53 0.00 41.65 2.74
2457 3310 5.000012 ACTGTCTGTACTATGCAACTAGC 58.000 43.478 0.00 0.00 45.96 3.42
2458 3311 4.707448 ACTGTCTGTACTATGCAACTAGCT 59.293 41.667 0.00 0.00 45.94 3.32
2459 3312 5.186021 ACTGTCTGTACTATGCAACTAGCTT 59.814 40.000 0.00 0.00 45.94 3.74
2460 3313 6.377429 ACTGTCTGTACTATGCAACTAGCTTA 59.623 38.462 0.00 0.00 45.94 3.09
2461 3314 6.561614 TGTCTGTACTATGCAACTAGCTTAC 58.438 40.000 0.00 0.00 45.94 2.34
2462 3315 6.152154 TGTCTGTACTATGCAACTAGCTTACA 59.848 38.462 0.00 0.00 45.94 2.41
2463 3316 6.693545 GTCTGTACTATGCAACTAGCTTACAG 59.306 42.308 13.77 13.77 45.94 2.74
2464 3317 5.902681 TGTACTATGCAACTAGCTTACAGG 58.097 41.667 0.00 0.00 45.94 4.00
2465 3318 5.421056 TGTACTATGCAACTAGCTTACAGGT 59.579 40.000 0.00 0.00 45.94 4.00
2466 3319 6.604396 TGTACTATGCAACTAGCTTACAGGTA 59.396 38.462 0.00 0.00 45.94 3.08
2467 3320 5.903810 ACTATGCAACTAGCTTACAGGTAC 58.096 41.667 0.00 0.00 45.94 3.34
2468 3321 5.657302 ACTATGCAACTAGCTTACAGGTACT 59.343 40.000 0.00 0.00 45.94 2.73
2469 3322 6.832384 ACTATGCAACTAGCTTACAGGTACTA 59.168 38.462 0.00 0.00 45.94 1.82
2470 3323 5.988310 TGCAACTAGCTTACAGGTACTAA 57.012 39.130 0.00 0.00 45.94 2.24
2471 3324 5.717119 TGCAACTAGCTTACAGGTACTAAC 58.283 41.667 0.00 0.00 45.94 2.34
2472 3325 5.244402 TGCAACTAGCTTACAGGTACTAACA 59.756 40.000 0.00 0.00 45.94 2.41
2473 3326 6.070995 TGCAACTAGCTTACAGGTACTAACAT 60.071 38.462 0.00 0.00 45.94 2.71
2474 3327 6.255887 GCAACTAGCTTACAGGTACTAACATG 59.744 42.308 0.00 0.00 40.82 3.21
2475 3328 5.903810 ACTAGCTTACAGGTACTAACATGC 58.096 41.667 0.00 0.00 41.08 4.06
2476 3329 3.782046 AGCTTACAGGTACTAACATGCG 58.218 45.455 0.00 0.00 41.08 4.73
2477 3330 3.194968 AGCTTACAGGTACTAACATGCGT 59.805 43.478 0.00 0.00 41.08 5.24
2478 3331 3.930848 GCTTACAGGTACTAACATGCGTT 59.069 43.478 0.00 0.00 41.08 4.84
2479 3332 4.390909 GCTTACAGGTACTAACATGCGTTT 59.609 41.667 0.00 0.00 41.08 3.60
2480 3333 5.577945 GCTTACAGGTACTAACATGCGTTTA 59.422 40.000 0.00 0.00 41.08 2.01
2481 3334 6.257193 GCTTACAGGTACTAACATGCGTTTAT 59.743 38.462 0.00 0.00 41.08 1.40
2482 3335 7.516312 GCTTACAGGTACTAACATGCGTTTATC 60.516 40.741 0.00 0.00 41.08 1.75
2483 3336 5.726397 ACAGGTACTAACATGCGTTTATCA 58.274 37.500 0.00 0.00 41.08 2.15
2484 3337 6.167685 ACAGGTACTAACATGCGTTTATCAA 58.832 36.000 0.00 0.00 41.08 2.57
2485 3338 6.651643 ACAGGTACTAACATGCGTTTATCAAA 59.348 34.615 0.00 0.00 41.08 2.69
2486 3339 7.335924 ACAGGTACTAACATGCGTTTATCAAAT 59.664 33.333 0.00 0.00 41.08 2.32
2487 3340 7.639850 CAGGTACTAACATGCGTTTATCAAATG 59.360 37.037 0.00 0.00 36.02 2.32
2488 3341 7.551262 AGGTACTAACATGCGTTTATCAAATGA 59.449 33.333 0.00 0.00 36.02 2.57
2489 3342 8.342634 GGTACTAACATGCGTTTATCAAATGAT 58.657 33.333 1.01 1.01 36.52 2.45
2490 3343 9.716507 GTACTAACATGCGTTTATCAAATGATT 57.283 29.630 0.55 0.00 36.52 2.57
2494 3347 7.684062 ACATGCGTTTATCAAATGATTTAGC 57.316 32.000 0.55 4.09 36.05 3.09
2495 3348 7.483307 ACATGCGTTTATCAAATGATTTAGCT 58.517 30.769 0.55 0.00 36.05 3.32
2496 3349 7.975616 ACATGCGTTTATCAAATGATTTAGCTT 59.024 29.630 0.55 0.00 36.05 3.74
2497 3350 7.739022 TGCGTTTATCAAATGATTTAGCTTG 57.261 32.000 0.55 0.00 36.05 4.01
2498 3351 6.253298 TGCGTTTATCAAATGATTTAGCTTGC 59.747 34.615 0.55 0.00 36.05 4.01
2499 3352 6.473455 GCGTTTATCAAATGATTTAGCTTGCT 59.527 34.615 0.55 0.00 36.05 3.91
2500 3353 7.514125 GCGTTTATCAAATGATTTAGCTTGCTG 60.514 37.037 5.26 0.00 36.05 4.41
2501 3354 7.485913 CGTTTATCAAATGATTTAGCTTGCTGT 59.514 33.333 5.26 0.00 36.05 4.40
2502 3355 8.801913 GTTTATCAAATGATTTAGCTTGCTGTC 58.198 33.333 5.26 2.09 36.05 3.51
2503 3356 6.770746 ATCAAATGATTTAGCTTGCTGTCT 57.229 33.333 5.26 0.00 0.00 3.41
2504 3357 6.579666 TCAAATGATTTAGCTTGCTGTCTT 57.420 33.333 5.26 0.00 0.00 3.01
2505 3358 6.985117 TCAAATGATTTAGCTTGCTGTCTTT 58.015 32.000 5.26 3.43 0.00 2.52
2506 3359 7.436118 TCAAATGATTTAGCTTGCTGTCTTTT 58.564 30.769 5.26 8.34 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.912951 TTTAAGGTGTAGCAGTCTCTTAGT 57.087 37.500 0.00 0.00 0.00 2.24
24 25 1.652563 GACGCCTTGCTCGGTTTTT 59.347 52.632 0.00 0.00 0.00 1.94
25 26 2.604174 CGACGCCTTGCTCGGTTTT 61.604 57.895 0.00 0.00 0.00 2.43
26 27 3.041940 CGACGCCTTGCTCGGTTT 61.042 61.111 0.00 0.00 0.00 3.27
30 31 3.479269 GAACCGACGCCTTGCTCG 61.479 66.667 0.00 0.00 0.00 5.03
31 32 3.119096 GGAACCGACGCCTTGCTC 61.119 66.667 0.00 0.00 0.00 4.26
32 33 3.626924 AGGAACCGACGCCTTGCT 61.627 61.111 0.00 0.00 0.00 3.91
33 34 3.423154 CAGGAACCGACGCCTTGC 61.423 66.667 0.00 0.00 30.41 4.01
34 35 2.742372 CCAGGAACCGACGCCTTG 60.742 66.667 0.00 0.00 30.41 3.61
35 36 2.333701 AAACCAGGAACCGACGCCTT 62.334 55.000 0.00 0.00 30.41 4.35
36 37 2.333701 AAAACCAGGAACCGACGCCT 62.334 55.000 0.00 0.00 33.99 5.52
37 38 1.449726 AAAAACCAGGAACCGACGCC 61.450 55.000 0.00 0.00 0.00 5.68
38 39 0.040692 GAAAAACCAGGAACCGACGC 60.041 55.000 0.00 0.00 0.00 5.19
39 40 0.589708 GGAAAAACCAGGAACCGACG 59.410 55.000 0.00 0.00 38.79 5.12
40 41 1.682740 TGGAAAAACCAGGAACCGAC 58.317 50.000 0.00 0.00 44.64 4.79
50 51 0.031585 GCGGACCAACTGGAAAAACC 59.968 55.000 1.86 0.00 38.94 3.27
51 52 1.029681 AGCGGACCAACTGGAAAAAC 58.970 50.000 1.86 0.00 38.94 2.43
52 53 2.158726 ACTAGCGGACCAACTGGAAAAA 60.159 45.455 1.86 0.00 38.94 1.94
53 54 1.418637 ACTAGCGGACCAACTGGAAAA 59.581 47.619 1.86 0.00 38.94 2.29
54 55 1.001633 GACTAGCGGACCAACTGGAAA 59.998 52.381 1.86 0.00 38.94 3.13
55 56 0.606604 GACTAGCGGACCAACTGGAA 59.393 55.000 1.86 0.00 38.94 3.53
56 57 0.251653 AGACTAGCGGACCAACTGGA 60.252 55.000 1.86 0.00 38.94 3.86
57 58 0.108615 CAGACTAGCGGACCAACTGG 60.109 60.000 0.00 0.00 42.17 4.00
58 59 0.108615 CCAGACTAGCGGACCAACTG 60.109 60.000 0.00 0.00 0.00 3.16
59 60 0.542232 ACCAGACTAGCGGACCAACT 60.542 55.000 0.66 0.00 0.00 3.16
60 61 0.108756 GACCAGACTAGCGGACCAAC 60.109 60.000 0.66 0.00 0.00 3.77
61 62 1.255667 GGACCAGACTAGCGGACCAA 61.256 60.000 9.19 0.00 37.12 3.67
62 63 1.681327 GGACCAGACTAGCGGACCA 60.681 63.158 9.19 0.00 37.12 4.02
63 64 1.255667 TTGGACCAGACTAGCGGACC 61.256 60.000 0.00 7.66 37.59 4.46
64 65 0.606604 TTTGGACCAGACTAGCGGAC 59.393 55.000 0.00 0.00 0.00 4.79
65 66 1.568504 ATTTGGACCAGACTAGCGGA 58.431 50.000 0.00 0.00 0.00 5.54
66 67 2.403252 AATTTGGACCAGACTAGCGG 57.597 50.000 0.00 0.00 0.00 5.52
67 68 5.180492 TGTTAAAATTTGGACCAGACTAGCG 59.820 40.000 0.00 0.00 0.00 4.26
68 69 6.206829 AGTGTTAAAATTTGGACCAGACTAGC 59.793 38.462 0.00 0.00 0.00 3.42
69 70 7.745620 AGTGTTAAAATTTGGACCAGACTAG 57.254 36.000 0.00 0.00 0.00 2.57
70 71 9.226606 CATAGTGTTAAAATTTGGACCAGACTA 57.773 33.333 0.00 0.00 0.00 2.59
71 72 7.724061 ACATAGTGTTAAAATTTGGACCAGACT 59.276 33.333 0.00 0.00 0.00 3.24
72 73 7.882179 ACATAGTGTTAAAATTTGGACCAGAC 58.118 34.615 0.00 0.00 0.00 3.51
73 74 8.472007 AACATAGTGTTAAAATTTGGACCAGA 57.528 30.769 0.00 0.00 39.09 3.86
74 75 8.356657 TGAACATAGTGTTAAAATTTGGACCAG 58.643 33.333 0.00 0.00 41.28 4.00
75 76 8.138712 GTGAACATAGTGTTAAAATTTGGACCA 58.861 33.333 0.00 0.00 41.28 4.02
76 77 8.138712 TGTGAACATAGTGTTAAAATTTGGACC 58.861 33.333 0.00 0.00 41.28 4.46
77 78 9.522804 TTGTGAACATAGTGTTAAAATTTGGAC 57.477 29.630 0.00 0.00 41.28 4.02
147 148 8.167392 TCTAAATGATCTTGTACCCCTCAAAAA 58.833 33.333 0.00 0.00 0.00 1.94
148 149 7.695055 TCTAAATGATCTTGTACCCCTCAAAA 58.305 34.615 0.00 0.00 0.00 2.44
149 150 7.265599 TCTAAATGATCTTGTACCCCTCAAA 57.734 36.000 0.00 0.00 0.00 2.69
150 151 6.884472 TCTAAATGATCTTGTACCCCTCAA 57.116 37.500 0.00 0.00 0.00 3.02
151 152 6.615316 TCATCTAAATGATCTTGTACCCCTCA 59.385 38.462 0.00 0.00 36.98 3.86
152 153 7.067496 TCATCTAAATGATCTTGTACCCCTC 57.933 40.000 0.00 0.00 36.98 4.30
153 154 6.617371 ACTCATCTAAATGATCTTGTACCCCT 59.383 38.462 0.00 0.00 41.05 4.79
154 155 6.831976 ACTCATCTAAATGATCTTGTACCCC 58.168 40.000 0.00 0.00 41.05 4.95
155 156 7.439655 GTGACTCATCTAAATGATCTTGTACCC 59.560 40.741 0.00 0.00 41.05 3.69
156 157 8.200792 AGTGACTCATCTAAATGATCTTGTACC 58.799 37.037 0.00 0.00 41.05 3.34
157 158 9.593134 AAGTGACTCATCTAAATGATCTTGTAC 57.407 33.333 0.00 0.00 41.05 2.90
159 160 9.512588 AAAAGTGACTCATCTAAATGATCTTGT 57.487 29.630 0.00 0.00 41.05 3.16
185 186 5.506730 AAAAAGAACCACCCAAGGAAAAA 57.493 34.783 0.00 0.00 0.00 1.94
205 206 3.237268 TCAGCTCAAAGGCCCTAAAAA 57.763 42.857 0.00 0.00 0.00 1.94
206 207 2.969821 TCAGCTCAAAGGCCCTAAAA 57.030 45.000 0.00 0.00 0.00 1.52
207 208 2.578021 AGATCAGCTCAAAGGCCCTAAA 59.422 45.455 0.00 0.00 0.00 1.85
208 209 2.200081 AGATCAGCTCAAAGGCCCTAA 58.800 47.619 0.00 0.00 0.00 2.69
209 210 1.885049 AGATCAGCTCAAAGGCCCTA 58.115 50.000 0.00 0.00 0.00 3.53
210 211 1.885049 TAGATCAGCTCAAAGGCCCT 58.115 50.000 0.00 0.00 0.00 5.19
211 212 2.717639 TTAGATCAGCTCAAAGGCCC 57.282 50.000 0.00 0.00 0.00 5.80
212 213 4.202441 TCATTTAGATCAGCTCAAAGGCC 58.798 43.478 0.00 0.00 0.00 5.19
213 214 4.261114 GCTCATTTAGATCAGCTCAAAGGC 60.261 45.833 0.00 0.00 0.00 4.35
214 215 4.275443 GGCTCATTTAGATCAGCTCAAAGG 59.725 45.833 0.00 0.00 32.14 3.11
215 216 4.275443 GGGCTCATTTAGATCAGCTCAAAG 59.725 45.833 0.00 0.00 32.16 2.77
216 217 4.202441 GGGCTCATTTAGATCAGCTCAAA 58.798 43.478 0.00 0.00 32.16 2.69
217 218 3.200605 TGGGCTCATTTAGATCAGCTCAA 59.799 43.478 0.76 0.00 39.46 3.02
218 219 2.773661 TGGGCTCATTTAGATCAGCTCA 59.226 45.455 0.00 0.00 40.13 4.26
219 220 3.401182 CTGGGCTCATTTAGATCAGCTC 58.599 50.000 0.00 0.00 32.53 4.09
220 221 2.486907 GCTGGGCTCATTTAGATCAGCT 60.487 50.000 0.00 0.00 43.48 4.24
221 222 1.878734 GCTGGGCTCATTTAGATCAGC 59.121 52.381 0.00 0.00 41.85 4.26
222 223 2.502295 GGCTGGGCTCATTTAGATCAG 58.498 52.381 0.00 0.00 32.93 2.90
223 224 1.143684 GGGCTGGGCTCATTTAGATCA 59.856 52.381 0.00 0.00 0.00 2.92
224 225 1.143684 TGGGCTGGGCTCATTTAGATC 59.856 52.381 0.00 0.00 32.27 2.75
225 226 1.144503 CTGGGCTGGGCTCATTTAGAT 59.855 52.381 0.00 0.00 38.82 1.98
226 227 0.548031 CTGGGCTGGGCTCATTTAGA 59.452 55.000 0.00 0.00 38.82 2.10
227 228 1.105759 GCTGGGCTGGGCTCATTTAG 61.106 60.000 0.00 0.00 38.82 1.85
228 229 1.076777 GCTGGGCTGGGCTCATTTA 60.077 57.895 0.00 0.00 38.82 1.40
229 230 2.363406 GCTGGGCTGGGCTCATTT 60.363 61.111 0.00 0.00 38.82 2.32
230 231 4.453892 GGCTGGGCTGGGCTCATT 62.454 66.667 0.00 0.00 38.82 2.57
245 246 0.038166 TTGAGGATGACCAACTGGGC 59.962 55.000 0.00 0.00 45.93 5.36
246 247 1.340405 CCTTGAGGATGACCAACTGGG 60.340 57.143 0.00 0.00 39.37 4.45
247 248 1.352352 ACCTTGAGGATGACCAACTGG 59.648 52.381 3.59 0.00 38.94 4.00
378 404 2.043852 GAGAGGACCTGGGCGAGA 60.044 66.667 0.00 0.00 0.00 4.04
388 414 1.433837 GCGGAGAGAGACGAGAGGAC 61.434 65.000 0.00 0.00 0.00 3.85
401 430 1.228184 GATACGGGAGAGGCGGAGA 60.228 63.158 0.00 0.00 0.00 3.71
507 557 4.631740 TGAGGTCGGGTGAGGCCA 62.632 66.667 5.01 0.00 38.64 5.36
678 729 3.995506 GACGTTGGGGGCCAGGATG 62.996 68.421 4.39 0.00 33.81 3.51
874 943 1.296715 GCTTGACCACACCCTCGAT 59.703 57.895 0.00 0.00 0.00 3.59
928 997 4.281688 ACAAAGCTTGGCAATATCACAAGT 59.718 37.500 0.00 0.00 42.60 3.16
965 1034 0.609131 CGGGTTGGTTTGGAGCAGAT 60.609 55.000 0.00 0.00 34.28 2.90
973 1042 2.696759 GGCGATCCGGGTTGGTTTG 61.697 63.158 3.54 0.00 39.52 2.93
975 1044 1.991167 TAGGCGATCCGGGTTGGTT 60.991 57.895 3.54 0.00 39.52 3.67
993 1062 2.350458 GCATGCCACCATTTCCCGT 61.350 57.895 6.36 0.00 0.00 5.28
1093 1168 0.610174 TGCTCTAGCTTGGTGGTGAG 59.390 55.000 3.26 0.00 42.66 3.51
1105 1180 7.194607 TGAACATTTTCTTCAAGTGCTCTAG 57.805 36.000 0.00 0.00 32.36 2.43
1133 1208 2.659063 CCCACCTCGGCATCTGACA 61.659 63.158 0.00 0.00 0.00 3.58
1227 1302 2.890766 TTCCAAGCCCACCTCGGAC 61.891 63.158 0.00 0.00 36.56 4.79
1503 2089 2.754946 TCATACCGGTCTTGGTTCAC 57.245 50.000 12.40 0.00 43.56 3.18
1553 2139 3.716601 ACCAGTGCGATTTTTCCTTTTG 58.283 40.909 0.00 0.00 0.00 2.44
1555 2141 4.618227 GCATACCAGTGCGATTTTTCCTTT 60.618 41.667 0.00 0.00 35.10 3.11
1578 2164 8.443160 ACAATATGACACGAATAAGAACAAGTG 58.557 33.333 0.00 0.00 35.89 3.16
1589 2175 6.831769 GTCAAACTGACAATATGACACGAAT 58.168 36.000 1.92 0.00 46.22 3.34
1590 2176 6.223138 GTCAAACTGACAATATGACACGAA 57.777 37.500 1.92 0.00 46.22 3.85
1604 2192 6.061441 AGTTCCAATATGTGTGTCAAACTGA 58.939 36.000 0.00 0.00 0.00 3.41
1696 2512 4.776743 CCATTTCAGAAGACAAAGACACG 58.223 43.478 0.00 0.00 0.00 4.49
1699 2515 6.749923 ATAGCCATTTCAGAAGACAAAGAC 57.250 37.500 0.00 0.00 0.00 3.01
1707 2523 4.978083 ACTGCAATAGCCATTTCAGAAG 57.022 40.909 11.02 0.00 37.53 2.85
1771 2590 6.526526 TCATATCATTTTGATGGCCAAATGG 58.473 36.000 22.03 10.33 43.59 3.16
1777 2596 6.263842 TGAGACTTCATATCATTTTGATGGCC 59.736 38.462 0.00 0.00 37.70 5.36
1889 2710 4.415512 TCCCCTAGAAAAATATCACCCAGG 59.584 45.833 0.00 0.00 0.00 4.45
1900 2721 5.188948 TCGAGATCACATTCCCCTAGAAAAA 59.811 40.000 0.00 0.00 38.21 1.94
1915 2737 6.809196 ACTCAACTATTCAGTTTCGAGATCAC 59.191 38.462 10.24 0.00 42.51 3.06
1984 2806 9.516314 GGGCATTAGAAATTTCTGTTTACATAC 57.484 33.333 27.37 10.43 38.19 2.39
2042 2864 5.048364 TGTTTTTCAGCACCATGGTATACAC 60.048 40.000 19.28 7.11 0.00 2.90
2048 2870 2.624838 CTCTGTTTTTCAGCACCATGGT 59.375 45.455 13.00 13.00 43.32 3.55
2049 2871 2.886523 TCTCTGTTTTTCAGCACCATGG 59.113 45.455 11.19 11.19 43.32 3.66
2081 2903 9.398538 GTTACCATAACATAAGTTCCCATGTTA 57.601 33.333 10.62 10.62 46.25 2.41
2084 2906 7.060421 AGGTTACCATAACATAAGTTCCCATG 58.940 38.462 3.51 0.00 39.15 3.66
2086 2908 6.645884 AGGTTACCATAACATAAGTTCCCA 57.354 37.500 3.51 0.00 39.15 4.37
2213 3039 5.659971 ACATAAGACCCACTTTACGGATAGT 59.340 40.000 0.00 0.00 39.72 2.12
2214 3040 6.158023 ACATAAGACCCACTTTACGGATAG 57.842 41.667 0.00 0.00 39.72 2.08
2215 3041 6.040842 GGTACATAAGACCCACTTTACGGATA 59.959 42.308 0.00 0.00 39.72 2.59
2216 3042 5.163374 GGTACATAAGACCCACTTTACGGAT 60.163 44.000 0.00 0.00 39.72 4.18
2217 3043 4.160252 GGTACATAAGACCCACTTTACGGA 59.840 45.833 0.00 0.00 39.72 4.69
2218 3044 4.081531 TGGTACATAAGACCCACTTTACGG 60.082 45.833 0.00 0.00 39.72 4.02
2219 3045 5.075858 TGGTACATAAGACCCACTTTACG 57.924 43.478 0.00 0.00 39.72 3.18
2345 3197 3.002348 GGTTCATAAACCGAGCTACATGC 59.998 47.826 0.00 0.00 45.33 4.06
2359 3212 8.364142 CAACAATTTCCTTAGGTTGGTTCATAA 58.636 33.333 0.00 0.00 36.19 1.90
2373 3226 2.041701 AGTGCAGGCAACAATTTCCTT 58.958 42.857 0.00 0.00 41.41 3.36
2374 3227 1.708341 AGTGCAGGCAACAATTTCCT 58.292 45.000 0.00 0.00 41.41 3.36
2375 3228 3.255642 TCTTAGTGCAGGCAACAATTTCC 59.744 43.478 0.00 0.00 41.41 3.13
2376 3229 4.503741 TCTTAGTGCAGGCAACAATTTC 57.496 40.909 0.00 0.00 41.41 2.17
2377 3230 4.935352 TTCTTAGTGCAGGCAACAATTT 57.065 36.364 0.00 0.00 41.41 1.82
2378 3231 5.711976 AGTATTCTTAGTGCAGGCAACAATT 59.288 36.000 0.00 0.00 41.41 2.32
2379 3232 5.256474 AGTATTCTTAGTGCAGGCAACAAT 58.744 37.500 0.00 0.00 41.41 2.71
2380 3233 4.651778 AGTATTCTTAGTGCAGGCAACAA 58.348 39.130 0.00 0.00 41.41 2.83
2381 3234 4.253685 GAGTATTCTTAGTGCAGGCAACA 58.746 43.478 0.00 0.00 41.41 3.33
2382 3235 4.253685 TGAGTATTCTTAGTGCAGGCAAC 58.746 43.478 0.00 0.00 0.00 4.17
2383 3236 4.551702 TGAGTATTCTTAGTGCAGGCAA 57.448 40.909 0.00 0.00 0.00 4.52
2384 3237 4.760530 ATGAGTATTCTTAGTGCAGGCA 57.239 40.909 0.00 0.00 0.00 4.75
2385 3238 6.696411 AGATATGAGTATTCTTAGTGCAGGC 58.304 40.000 0.00 0.00 0.00 4.85
2386 3239 9.632807 GTTAGATATGAGTATTCTTAGTGCAGG 57.367 37.037 0.00 0.00 0.00 4.85
2387 3240 9.632807 GGTTAGATATGAGTATTCTTAGTGCAG 57.367 37.037 0.00 0.00 0.00 4.41
2388 3241 8.585881 GGGTTAGATATGAGTATTCTTAGTGCA 58.414 37.037 0.00 0.00 0.00 4.57
2389 3242 8.808092 AGGGTTAGATATGAGTATTCTTAGTGC 58.192 37.037 0.00 0.00 0.00 4.40
2399 3252 9.613428 CATGTGAAAAAGGGTTAGATATGAGTA 57.387 33.333 0.00 0.00 0.00 2.59
2400 3253 7.067494 GCATGTGAAAAAGGGTTAGATATGAGT 59.933 37.037 0.00 0.00 0.00 3.41
2401 3254 7.067372 TGCATGTGAAAAAGGGTTAGATATGAG 59.933 37.037 0.00 0.00 0.00 2.90
2402 3255 6.889177 TGCATGTGAAAAAGGGTTAGATATGA 59.111 34.615 0.00 0.00 0.00 2.15
2403 3256 7.099266 TGCATGTGAAAAAGGGTTAGATATG 57.901 36.000 0.00 0.00 0.00 1.78
2404 3257 7.902920 ATGCATGTGAAAAAGGGTTAGATAT 57.097 32.000 0.00 0.00 0.00 1.63
2405 3258 7.716799 AATGCATGTGAAAAAGGGTTAGATA 57.283 32.000 0.00 0.00 0.00 1.98
2406 3259 6.610075 AATGCATGTGAAAAAGGGTTAGAT 57.390 33.333 0.00 0.00 0.00 1.98
2407 3260 6.183360 ACAAATGCATGTGAAAAAGGGTTAGA 60.183 34.615 23.90 0.00 30.82 2.10
2408 3261 5.990996 ACAAATGCATGTGAAAAAGGGTTAG 59.009 36.000 23.90 0.00 30.82 2.34
2409 3262 5.923204 ACAAATGCATGTGAAAAAGGGTTA 58.077 33.333 23.90 0.00 30.82 2.85
2410 3263 4.779696 ACAAATGCATGTGAAAAAGGGTT 58.220 34.783 23.90 0.00 30.82 4.11
2411 3264 4.420522 ACAAATGCATGTGAAAAAGGGT 57.579 36.364 23.90 0.00 30.82 4.34
2421 3274 4.136796 ACAGACAGTACACAAATGCATGT 58.863 39.130 0.00 0.00 0.00 3.21
2422 3275 4.754372 ACAGACAGTACACAAATGCATG 57.246 40.909 0.00 0.00 0.00 4.06
2433 3286 5.972382 GCTAGTTGCATAGTACAGACAGTAC 59.028 44.000 0.05 0.05 46.06 2.73
2434 3287 5.886474 AGCTAGTTGCATAGTACAGACAGTA 59.114 40.000 0.00 0.00 45.94 2.74
2435 3288 4.707448 AGCTAGTTGCATAGTACAGACAGT 59.293 41.667 0.00 0.00 45.94 3.55
2436 3289 5.255710 AGCTAGTTGCATAGTACAGACAG 57.744 43.478 0.00 0.00 45.94 3.51
2437 3290 5.661056 AAGCTAGTTGCATAGTACAGACA 57.339 39.130 0.00 0.00 45.94 3.41
2438 3291 6.561614 TGTAAGCTAGTTGCATAGTACAGAC 58.438 40.000 0.00 0.00 45.94 3.51
2439 3292 6.183360 CCTGTAAGCTAGTTGCATAGTACAGA 60.183 42.308 18.10 0.00 45.94 3.41
2440 3293 5.980116 CCTGTAAGCTAGTTGCATAGTACAG 59.020 44.000 13.33 13.33 45.94 2.74
2441 3294 5.421056 ACCTGTAAGCTAGTTGCATAGTACA 59.579 40.000 0.00 1.71 45.94 2.90
2442 3295 5.903810 ACCTGTAAGCTAGTTGCATAGTAC 58.096 41.667 0.00 0.00 45.94 2.73
2443 3296 6.832384 AGTACCTGTAAGCTAGTTGCATAGTA 59.168 38.462 0.00 0.00 45.94 1.82
2444 3297 5.657302 AGTACCTGTAAGCTAGTTGCATAGT 59.343 40.000 0.00 0.00 45.94 2.12
2445 3298 6.150396 AGTACCTGTAAGCTAGTTGCATAG 57.850 41.667 0.00 0.00 45.94 2.23
2446 3299 7.123098 TGTTAGTACCTGTAAGCTAGTTGCATA 59.877 37.037 0.00 0.00 45.94 3.14
2447 3300 6.070995 TGTTAGTACCTGTAAGCTAGTTGCAT 60.071 38.462 0.00 0.00 45.94 3.96
2448 3301 5.244402 TGTTAGTACCTGTAAGCTAGTTGCA 59.756 40.000 0.00 0.00 45.94 4.08
2449 3302 5.717119 TGTTAGTACCTGTAAGCTAGTTGC 58.283 41.667 0.00 0.00 43.29 4.17
2450 3303 6.255887 GCATGTTAGTACCTGTAAGCTAGTTG 59.744 42.308 0.00 0.00 0.00 3.16
2451 3304 6.338937 GCATGTTAGTACCTGTAAGCTAGTT 58.661 40.000 0.00 0.00 0.00 2.24
2452 3305 5.450137 CGCATGTTAGTACCTGTAAGCTAGT 60.450 44.000 0.00 0.00 0.00 2.57
2453 3306 4.976731 CGCATGTTAGTACCTGTAAGCTAG 59.023 45.833 0.00 0.00 0.00 3.42
2454 3307 4.400251 ACGCATGTTAGTACCTGTAAGCTA 59.600 41.667 0.00 0.00 0.00 3.32
2455 3308 3.194968 ACGCATGTTAGTACCTGTAAGCT 59.805 43.478 0.00 0.00 0.00 3.74
2456 3309 3.518590 ACGCATGTTAGTACCTGTAAGC 58.481 45.455 0.00 0.00 0.00 3.09
2457 3310 7.490079 TGATAAACGCATGTTAGTACCTGTAAG 59.510 37.037 0.00 0.00 37.31 2.34
2458 3311 7.321908 TGATAAACGCATGTTAGTACCTGTAA 58.678 34.615 0.00 0.00 37.31 2.41
2459 3312 6.865411 TGATAAACGCATGTTAGTACCTGTA 58.135 36.000 0.00 0.00 37.31 2.74
2460 3313 5.726397 TGATAAACGCATGTTAGTACCTGT 58.274 37.500 0.00 0.00 37.31 4.00
2461 3314 6.656314 TTGATAAACGCATGTTAGTACCTG 57.344 37.500 0.00 0.00 37.31 4.00
2462 3315 7.551262 TCATTTGATAAACGCATGTTAGTACCT 59.449 33.333 0.00 0.00 37.31 3.08
2463 3316 7.690228 TCATTTGATAAACGCATGTTAGTACC 58.310 34.615 0.00 0.00 37.31 3.34
2464 3317 9.716507 AATCATTTGATAAACGCATGTTAGTAC 57.283 29.630 0.00 0.00 33.22 2.73
2468 3321 9.232082 GCTAAATCATTTGATAAACGCATGTTA 57.768 29.630 0.00 0.00 33.22 2.41
2469 3322 7.975616 AGCTAAATCATTTGATAAACGCATGTT 59.024 29.630 0.00 0.00 34.94 2.71
2470 3323 7.483307 AGCTAAATCATTTGATAAACGCATGT 58.517 30.769 0.00 0.00 33.73 3.21
2471 3324 7.919313 AGCTAAATCATTTGATAAACGCATG 57.081 32.000 0.00 0.00 33.73 4.06
2472 3325 7.043192 GCAAGCTAAATCATTTGATAAACGCAT 60.043 33.333 0.00 0.00 33.73 4.73
2473 3326 6.253298 GCAAGCTAAATCATTTGATAAACGCA 59.747 34.615 0.00 0.00 33.73 5.24
2474 3327 6.473455 AGCAAGCTAAATCATTTGATAAACGC 59.527 34.615 0.00 0.00 33.73 4.84
2475 3328 7.485913 ACAGCAAGCTAAATCATTTGATAAACG 59.514 33.333 0.00 0.00 33.73 3.60
2476 3329 8.693542 ACAGCAAGCTAAATCATTTGATAAAC 57.306 30.769 0.00 0.00 33.73 2.01
2477 3330 8.742777 AGACAGCAAGCTAAATCATTTGATAAA 58.257 29.630 0.00 0.00 33.73 1.40
2478 3331 8.284945 AGACAGCAAGCTAAATCATTTGATAA 57.715 30.769 0.00 0.00 33.73 1.75
2479 3332 7.870509 AGACAGCAAGCTAAATCATTTGATA 57.129 32.000 0.00 0.00 33.73 2.15
2480 3333 6.770746 AGACAGCAAGCTAAATCATTTGAT 57.229 33.333 0.00 0.00 36.07 2.57
2481 3334 6.579666 AAGACAGCAAGCTAAATCATTTGA 57.420 33.333 0.00 0.00 0.00 2.69
2482 3335 7.647907 AAAAGACAGCAAGCTAAATCATTTG 57.352 32.000 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.