Multiple sequence alignment - TraesCS5B01G506300

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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 TraesCS5B01G506300 chr5B 100.000 5928 0 0 1 5928 671715327 671709400 0.000000e+00 10948.0
1 TraesCS5B01G506300 chr5B 84.823 1891 177 52 3282 5145 671494367 671496174 0.000000e+00 1801.0
2 TraesCS5B01G506300 chr5B 77.993 1654 235 61 1433 3031 671503150 671504729 0.000000e+00 918.0
3 TraesCS5B01G506300 chr5B 87.484 791 62 13 1634 2390 671487669 671488456 0.000000e+00 878.0
4 TraesCS5B01G506300 chr5B 90.712 646 45 5 957 1587 671487020 671487665 0.000000e+00 846.0
5 TraesCS5B01G506300 chr5B 81.908 912 137 17 4149 5039 671506663 671507567 0.000000e+00 745.0
6 TraesCS5B01G506300 chr5B 87.662 616 53 17 2444 3054 671493732 671494329 0.000000e+00 695.0
7 TraesCS5B01G506300 chr5B 83.401 494 68 5 3504 3990 671505956 671506442 4.210000e-121 446.0
8 TraesCS5B01G506300 chr5B 78.571 714 122 25 1004 1701 671706458 671707156 5.450000e-120 442.0
9 TraesCS5B01G506300 chr5B 90.991 111 8 2 5690 5798 671496637 671496747 1.330000e-31 148.0
10 TraesCS5B01G506300 chr5B 82.877 146 25 0 1934 2079 671356182 671356037 1.340000e-26 132.0
11 TraesCS5B01G506300 chr5D 94.734 4975 169 41 506 5432 532279439 532274510 0.000000e+00 7649.0
12 TraesCS5B01G506300 chr5D 80.280 715 110 21 1011 1707 534605586 534606287 1.470000e-140 510.0
13 TraesCS5B01G506300 chr5D 77.024 914 162 35 1019 1905 532248792 532247900 1.160000e-131 481.0
14 TraesCS5B01G506300 chr5D 93.189 323 14 1 5614 5928 532274325 532274003 9.000000e-128 468.0
15 TraesCS5B01G506300 chr5D 78.732 710 120 24 1004 1701 532271366 532272056 4.210000e-121 446.0
16 TraesCS5B01G506300 chr5D 74.882 211 51 1 1930 2138 532272327 532272537 1.760000e-15 95.3
17 TraesCS5B01G506300 chr5D 96.364 55 2 0 5469 5523 532274509 532274455 2.280000e-14 91.6
18 TraesCS5B01G506300 chr4A 93.335 4966 226 45 355 5260 639992848 639997768 0.000000e+00 7239.0
19 TraesCS5B01G506300 chr4A 80.553 1049 142 38 3489 4496 637194890 637193863 0.000000e+00 750.0
20 TraesCS5B01G506300 chr4A 90.149 538 30 11 871 1391 639961919 639962450 0.000000e+00 678.0
21 TraesCS5B01G506300 chr4A 81.286 871 130 17 4191 5045 637229067 637228214 0.000000e+00 675.0
22 TraesCS5B01G506300 chr4A 81.319 728 96 16 4099 4812 637204503 637203802 6.710000e-154 555.0
23 TraesCS5B01G506300 chr4A 75.379 1121 202 52 1007 2079 640002539 640003633 1.930000e-129 473.0
24 TraesCS5B01G506300 chr4A 93.168 322 15 1 5614 5928 639997975 639998296 3.240000e-127 466.0
25 TraesCS5B01G506300 chr4A 78.631 716 122 24 1004 1707 640001127 640000431 4.210000e-121 446.0
26 TraesCS5B01G506300 chr4A 93.496 123 7 1 5501 5623 639997794 639997915 1.310000e-41 182.0
27 TraesCS5B01G506300 chr4A 83.505 194 24 5 4862 5048 637203791 637203599 2.200000e-39 174.0
28 TraesCS5B01G506300 chr4A 80.000 210 41 1 1930 2138 640000166 639999957 2.860000e-33 154.0
29 TraesCS5B01G506300 chr4B 89.546 2114 149 23 946 3024 15421299 15419223 0.000000e+00 2614.0
30 TraesCS5B01G506300 chr4B 89.541 2113 150 22 946 3024 14533798 14531723 0.000000e+00 2612.0
31 TraesCS5B01G506300 chr4B 95.824 1317 40 7 3057 4373 14531729 14530428 0.000000e+00 2113.0
32 TraesCS5B01G506300 chr4B 95.537 1098 34 7 3276 4373 15418895 15417813 0.000000e+00 1742.0
33 TraesCS5B01G506300 chr4B 96.283 565 21 0 4330 4894 15417772 15417208 0.000000e+00 928.0
34 TraesCS5B01G506300 chr4B 96.106 565 22 0 4330 4894 14530387 14529823 0.000000e+00 922.0
35 TraesCS5B01G506300 chr4B 92.308 325 15 2 5614 5928 14529450 14529126 2.520000e-123 453.0
36 TraesCS5B01G506300 chr4B 98.190 221 4 0 3057 3277 15419229 15419009 2.590000e-103 387.0
37 TraesCS5B01G506300 chr4B 93.960 149 9 0 5620 5768 15416815 15416667 5.980000e-55 226.0
38 TraesCS5B01G506300 chr4B 89.286 140 5 2 5799 5928 15416672 15416533 3.670000e-37 167.0
39 TraesCS5B01G506300 chr4B 87.500 144 13 4 5480 5623 14529648 14529510 1.710000e-35 161.0
40 TraesCS5B01G506300 chr2D 90.390 333 20 2 2202 2522 605563107 605562775 1.530000e-115 427.0
41 TraesCS5B01G506300 chrUn 98.190 221 4 0 3057 3277 479679219 479678999 2.590000e-103 387.0
42 TraesCS5B01G506300 chrUn 97.191 178 5 0 2847 3024 479679390 479679213 9.650000e-78 302.0
43 TraesCS5B01G506300 chr7D 92.683 164 10 2 5144 5306 397554913 397555075 9.930000e-58 235.0
44 TraesCS5B01G506300 chr4D 91.765 170 12 2 5141 5309 64390638 64390470 9.930000e-58 235.0
45 TraesCS5B01G506300 chr7A 92.547 161 10 2 5147 5306 451519972 451519813 4.620000e-56 230.0
46 TraesCS5B01G506300 chr7A 92.073 164 11 2 5147 5309 494786990 494786828 4.620000e-56 230.0
47 TraesCS5B01G506300 chr6D 92.073 164 11 2 5144 5306 48458137 48457975 4.620000e-56 230.0
48 TraesCS5B01G506300 chr1A 91.617 167 13 1 5144 5309 39439002 39438836 4.620000e-56 230.0
49 TraesCS5B01G506300 chr1D 90.286 175 15 2 5133 5306 225704960 225704787 1.660000e-55 228.0


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 TraesCS5B01G506300 chr5B 671709400 671715327 5927 True 10948.000000 10948 100.000000 1 5928 1 chr5B.!!$R2 5927
1 TraesCS5B01G506300 chr5B 671493732 671496747 3015 False 881.333333 1801 87.825333 2444 5798 3 chr5B.!!$F3 3354
2 TraesCS5B01G506300 chr5B 671487020 671488456 1436 False 862.000000 878 89.098000 957 2390 2 chr5B.!!$F2 1433
3 TraesCS5B01G506300 chr5B 671503150 671507567 4417 False 703.000000 918 81.100667 1433 5039 3 chr5B.!!$F4 3606
4 TraesCS5B01G506300 chr5B 671706458 671707156 698 False 442.000000 442 78.571000 1004 1701 1 chr5B.!!$F1 697
5 TraesCS5B01G506300 chr5D 532274003 532279439 5436 True 2736.200000 7649 94.762333 506 5928 3 chr5D.!!$R2 5422
6 TraesCS5B01G506300 chr5D 534605586 534606287 701 False 510.000000 510 80.280000 1011 1707 1 chr5D.!!$F1 696
7 TraesCS5B01G506300 chr5D 532247900 532248792 892 True 481.000000 481 77.024000 1019 1905 1 chr5D.!!$R1 886
8 TraesCS5B01G506300 chr5D 532271366 532272537 1171 False 270.650000 446 76.807000 1004 2138 2 chr5D.!!$F2 1134
9 TraesCS5B01G506300 chr4A 639992848 639998296 5448 False 2629.000000 7239 93.333000 355 5928 3 chr4A.!!$F3 5573
10 TraesCS5B01G506300 chr4A 637193863 637194890 1027 True 750.000000 750 80.553000 3489 4496 1 chr4A.!!$R1 1007
11 TraesCS5B01G506300 chr4A 639961919 639962450 531 False 678.000000 678 90.149000 871 1391 1 chr4A.!!$F1 520
12 TraesCS5B01G506300 chr4A 637228214 637229067 853 True 675.000000 675 81.286000 4191 5045 1 chr4A.!!$R2 854
13 TraesCS5B01G506300 chr4A 640002539 640003633 1094 False 473.000000 473 75.379000 1007 2079 1 chr4A.!!$F2 1072
14 TraesCS5B01G506300 chr4A 637203599 637204503 904 True 364.500000 555 82.412000 4099 5048 2 chr4A.!!$R3 949
15 TraesCS5B01G506300 chr4A 639999957 640001127 1170 True 300.000000 446 79.315500 1004 2138 2 chr4A.!!$R4 1134
16 TraesCS5B01G506300 chr4B 14529126 14533798 4672 True 1252.200000 2612 92.255800 946 5928 5 chr4B.!!$R1 4982
17 TraesCS5B01G506300 chr4B 15416533 15421299 4766 True 1010.666667 2614 93.800333 946 5928 6 chr4B.!!$R2 4982

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
484 485 0.031449 TCGCTGACACGAACATGACA 59.969 50.000 0.00 0.0 39.54 3.58 F
967 1006 0.250081 GATCCGATCTGGTTGAGCCC 60.250 60.000 0.75 0.0 39.52 5.19 F
2173 2336 0.044092 TCAGCAAGGGGTATGGGAGA 59.956 55.000 0.00 0.0 0.00 3.71 F
2274 2437 2.038164 TGACTGCTTCAGACATGCTCTT 59.962 45.455 0.29 0.0 32.09 2.85 F
3481 4438 3.581755 GCATTTGTGTGCATCTCATTGT 58.418 40.909 0.00 0.0 44.43 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2129 2291 0.457851 CCTCCTCAGTAGGTTCAGCG 59.542 60.000 0.00 0.0 44.09 5.18 R
2700 2897 2.672098 TCTGAGGAAGAGGAGCCATAC 58.328 52.381 0.00 0.0 0.00 2.39 R
3626 4790 0.400213 ATCCGTCTGACCTTTGCCAA 59.600 50.000 1.55 0.0 0.00 4.52 R
3717 4881 3.196469 TCTCTGGACTCTTGGCAACTATG 59.804 47.826 0.00 0.0 37.61 2.23 R
4957 6364 1.003118 GGGCGTCCCATGCATATCTTA 59.997 52.381 0.00 0.0 44.65 2.10 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
17 18 4.838152 CTGGGACCCGCGATGGTG 62.838 72.222 11.99 0.00 39.24 4.17
26 27 4.504596 GCGATGGTGGGGCATGGA 62.505 66.667 0.00 0.00 0.00 3.41
27 28 2.516930 CGATGGTGGGGCATGGAC 60.517 66.667 0.00 0.00 0.00 4.02
28 29 2.516930 GATGGTGGGGCATGGACG 60.517 66.667 0.00 0.00 0.00 4.79
29 30 3.338250 ATGGTGGGGCATGGACGT 61.338 61.111 0.00 0.00 0.00 4.34
30 31 3.643595 ATGGTGGGGCATGGACGTG 62.644 63.158 0.00 0.00 0.00 4.49
32 33 4.028490 GTGGGGCATGGACGTGGA 62.028 66.667 0.00 0.00 0.00 4.02
33 34 4.028490 TGGGGCATGGACGTGGAC 62.028 66.667 0.00 0.00 0.00 4.02
48 49 4.465512 GACGTTGCCGCTGCCATG 62.466 66.667 0.00 0.00 37.70 3.66
61 62 3.499737 CCATGCACGCCGGAGTTC 61.500 66.667 8.62 4.06 0.00 3.01
62 63 3.853330 CATGCACGCCGGAGTTCG 61.853 66.667 8.62 2.18 38.88 3.95
63 64 4.373116 ATGCACGCCGGAGTTCGT 62.373 61.111 8.62 1.47 39.79 3.85
161 162 4.329545 TGGCAGCCACCTCCGTTC 62.330 66.667 11.22 0.00 0.00 3.95
163 164 4.681978 GCAGCCACCTCCGTTCGT 62.682 66.667 0.00 0.00 0.00 3.85
164 165 2.432628 CAGCCACCTCCGTTCGTC 60.433 66.667 0.00 0.00 0.00 4.20
165 166 4.052229 AGCCACCTCCGTTCGTCG 62.052 66.667 0.00 0.00 39.52 5.12
166 167 4.047059 GCCACCTCCGTTCGTCGA 62.047 66.667 0.00 0.00 42.86 4.20
167 168 2.126580 CCACCTCCGTTCGTCGAC 60.127 66.667 5.18 5.18 42.86 4.20
168 169 2.126580 CACCTCCGTTCGTCGACC 60.127 66.667 10.58 0.00 42.86 4.79
169 170 2.282040 ACCTCCGTTCGTCGACCT 60.282 61.111 10.58 0.00 42.86 3.85
170 171 2.331132 ACCTCCGTTCGTCGACCTC 61.331 63.158 10.58 0.00 42.86 3.85
171 172 2.330372 CCTCCGTTCGTCGACCTCA 61.330 63.158 10.58 0.00 42.86 3.86
172 173 1.154263 CTCCGTTCGTCGACCTCAC 60.154 63.158 10.58 3.17 42.86 3.51
173 174 2.126580 CCGTTCGTCGACCTCACC 60.127 66.667 10.58 0.00 42.86 4.02
174 175 2.640989 CGTTCGTCGACCTCACCA 59.359 61.111 10.58 0.00 42.86 4.17
175 176 1.728426 CGTTCGTCGACCTCACCAC 60.728 63.158 10.58 0.00 42.86 4.16
176 177 1.728426 GTTCGTCGACCTCACCACG 60.728 63.158 10.58 0.00 0.00 4.94
177 178 2.911484 TTCGTCGACCTCACCACGG 61.911 63.158 10.58 0.00 33.02 4.94
178 179 3.359523 CGTCGACCTCACCACGGA 61.360 66.667 10.58 0.00 0.00 4.69
179 180 2.697761 CGTCGACCTCACCACGGAT 61.698 63.158 10.58 0.00 0.00 4.18
180 181 1.153823 GTCGACCTCACCACGGATG 60.154 63.158 3.51 0.00 0.00 3.51
190 191 4.794439 CACGGATGGCAGCGACGA 62.794 66.667 8.33 0.00 0.00 4.20
191 192 3.838271 ACGGATGGCAGCGACGAT 61.838 61.111 8.33 0.00 0.00 3.73
192 193 3.333189 CGGATGGCAGCGACGATG 61.333 66.667 9.11 9.11 0.00 3.84
193 194 2.202932 GGATGGCAGCGACGATGT 60.203 61.111 15.31 0.00 0.00 3.06
194 195 2.240500 GGATGGCAGCGACGATGTC 61.241 63.158 11.38 11.38 0.00 3.06
209 210 6.380111 GACGATGTCGACTAGTACTAGATC 57.620 45.833 31.93 22.07 43.02 2.75
210 211 6.088016 ACGATGTCGACTAGTACTAGATCT 57.912 41.667 31.93 13.38 43.02 2.75
211 212 7.213216 ACGATGTCGACTAGTACTAGATCTA 57.787 40.000 31.93 16.33 43.02 1.98
212 213 7.307694 ACGATGTCGACTAGTACTAGATCTAG 58.692 42.308 31.93 25.26 43.02 2.43
213 214 6.748658 CGATGTCGACTAGTACTAGATCTAGG 59.251 46.154 31.93 15.74 43.02 3.02
214 215 6.975196 TGTCGACTAGTACTAGATCTAGGT 57.025 41.667 31.93 18.46 38.24 3.08
215 216 7.358770 TGTCGACTAGTACTAGATCTAGGTT 57.641 40.000 31.93 17.71 38.24 3.50
216 217 7.790027 TGTCGACTAGTACTAGATCTAGGTTT 58.210 38.462 31.93 17.41 38.24 3.27
217 218 8.263640 TGTCGACTAGTACTAGATCTAGGTTTT 58.736 37.037 31.93 13.79 38.24 2.43
218 219 9.757227 GTCGACTAGTACTAGATCTAGGTTTTA 57.243 37.037 31.93 12.87 38.24 1.52
219 220 9.979578 TCGACTAGTACTAGATCTAGGTTTTAG 57.020 37.037 31.93 23.69 38.24 1.85
220 221 9.762933 CGACTAGTACTAGATCTAGGTTTTAGT 57.237 37.037 31.93 25.88 38.24 2.24
279 280 8.420374 AAGTTTAATGTATGATAGTGGACGTG 57.580 34.615 0.00 0.00 0.00 4.49
280 281 7.778083 AGTTTAATGTATGATAGTGGACGTGA 58.222 34.615 0.00 0.00 0.00 4.35
281 282 8.255206 AGTTTAATGTATGATAGTGGACGTGAA 58.745 33.333 0.00 0.00 0.00 3.18
282 283 7.997107 TTAATGTATGATAGTGGACGTGAAC 57.003 36.000 0.00 0.00 0.00 3.18
283 284 5.854010 ATGTATGATAGTGGACGTGAACT 57.146 39.130 0.00 0.00 0.00 3.01
284 285 5.654603 TGTATGATAGTGGACGTGAACTT 57.345 39.130 0.00 0.00 0.00 2.66
285 286 6.032956 TGTATGATAGTGGACGTGAACTTT 57.967 37.500 0.00 0.00 0.00 2.66
286 287 6.460781 TGTATGATAGTGGACGTGAACTTTT 58.539 36.000 0.00 0.00 0.00 2.27
287 288 5.862924 ATGATAGTGGACGTGAACTTTTG 57.137 39.130 0.00 0.00 0.00 2.44
288 289 4.062293 TGATAGTGGACGTGAACTTTTGG 58.938 43.478 0.00 0.00 0.00 3.28
289 290 2.413310 AGTGGACGTGAACTTTTGGT 57.587 45.000 0.00 0.00 0.00 3.67
290 291 3.547054 AGTGGACGTGAACTTTTGGTA 57.453 42.857 0.00 0.00 0.00 3.25
291 292 4.081322 AGTGGACGTGAACTTTTGGTAT 57.919 40.909 0.00 0.00 0.00 2.73
292 293 3.813166 AGTGGACGTGAACTTTTGGTATG 59.187 43.478 0.00 0.00 0.00 2.39
293 294 2.550606 TGGACGTGAACTTTTGGTATGC 59.449 45.455 0.00 0.00 0.00 3.14
294 295 2.550606 GGACGTGAACTTTTGGTATGCA 59.449 45.455 0.00 0.00 0.00 3.96
295 296 3.190535 GGACGTGAACTTTTGGTATGCAT 59.809 43.478 3.79 3.79 0.00 3.96
296 297 4.158384 GACGTGAACTTTTGGTATGCATG 58.842 43.478 10.16 0.00 0.00 4.06
297 298 3.057596 ACGTGAACTTTTGGTATGCATGG 60.058 43.478 10.16 0.00 0.00 3.66
298 299 3.057596 CGTGAACTTTTGGTATGCATGGT 60.058 43.478 10.16 0.00 0.00 3.55
299 300 4.558496 CGTGAACTTTTGGTATGCATGGTT 60.558 41.667 10.16 3.09 0.00 3.67
300 301 5.296748 GTGAACTTTTGGTATGCATGGTTT 58.703 37.500 10.16 0.00 0.00 3.27
301 302 6.451393 GTGAACTTTTGGTATGCATGGTTTA 58.549 36.000 10.16 0.00 0.00 2.01
302 303 6.926272 GTGAACTTTTGGTATGCATGGTTTAA 59.074 34.615 10.16 0.00 0.00 1.52
303 304 7.602265 GTGAACTTTTGGTATGCATGGTTTAAT 59.398 33.333 10.16 0.00 0.00 1.40
304 305 8.153550 TGAACTTTTGGTATGCATGGTTTAATT 58.846 29.630 10.16 0.00 0.00 1.40
305 306 8.916628 AACTTTTGGTATGCATGGTTTAATTT 57.083 26.923 10.16 0.00 0.00 1.82
306 307 8.321650 ACTTTTGGTATGCATGGTTTAATTTG 57.678 30.769 10.16 0.00 0.00 2.32
307 308 8.153550 ACTTTTGGTATGCATGGTTTAATTTGA 58.846 29.630 10.16 0.00 0.00 2.69
308 309 9.165035 CTTTTGGTATGCATGGTTTAATTTGAT 57.835 29.630 10.16 0.00 0.00 2.57
309 310 9.512588 TTTTGGTATGCATGGTTTAATTTGATT 57.487 25.926 10.16 0.00 0.00 2.57
310 311 9.512588 TTTGGTATGCATGGTTTAATTTGATTT 57.487 25.926 10.16 0.00 0.00 2.17
311 312 9.512588 TTGGTATGCATGGTTTAATTTGATTTT 57.487 25.926 10.16 0.00 0.00 1.82
312 313 8.944029 TGGTATGCATGGTTTAATTTGATTTTG 58.056 29.630 10.16 0.00 0.00 2.44
313 314 7.909641 GGTATGCATGGTTTAATTTGATTTTGC 59.090 33.333 10.16 0.00 0.00 3.68
314 315 6.872628 TGCATGGTTTAATTTGATTTTGCA 57.127 29.167 0.00 0.00 34.33 4.08
315 316 7.268199 TGCATGGTTTAATTTGATTTTGCAA 57.732 28.000 0.00 0.00 33.85 4.08
316 317 7.709947 TGCATGGTTTAATTTGATTTTGCAAA 58.290 26.923 8.05 8.05 41.49 3.68
317 318 8.192774 TGCATGGTTTAATTTGATTTTGCAAAA 58.807 25.926 25.76 25.76 40.72 2.44
318 319 9.194271 GCATGGTTTAATTTGATTTTGCAAAAT 57.806 25.926 32.11 32.11 40.72 1.82
320 321 9.694137 ATGGTTTAATTTGATTTTGCAAAATGG 57.306 25.926 35.57 0.00 40.72 3.16
321 322 8.139989 TGGTTTAATTTGATTTTGCAAAATGGG 58.860 29.630 35.57 0.00 40.72 4.00
322 323 8.355913 GGTTTAATTTGATTTTGCAAAATGGGA 58.644 29.630 35.57 22.16 40.72 4.37
323 324 9.911138 GTTTAATTTGATTTTGCAAAATGGGAT 57.089 25.926 35.57 23.13 40.72 3.85
325 326 5.859521 TTTGATTTTGCAAAATGGGATCG 57.140 34.783 35.57 0.00 38.64 3.69
326 327 4.533919 TGATTTTGCAAAATGGGATCGT 57.466 36.364 35.57 15.10 38.64 3.73
327 328 4.493547 TGATTTTGCAAAATGGGATCGTC 58.506 39.130 35.57 21.97 38.64 4.20
328 329 3.311486 TTTTGCAAAATGGGATCGTCC 57.689 42.857 20.46 0.00 35.23 4.79
329 330 0.808125 TTGCAAAATGGGATCGTCCG 59.192 50.000 0.00 0.00 37.43 4.79
330 331 0.322098 TGCAAAATGGGATCGTCCGT 60.322 50.000 0.00 0.00 37.43 4.69
331 332 0.098728 GCAAAATGGGATCGTCCGTG 59.901 55.000 0.00 0.00 37.43 4.94
332 333 1.448985 CAAAATGGGATCGTCCGTGT 58.551 50.000 0.00 0.00 37.43 4.49
333 334 1.810151 CAAAATGGGATCGTCCGTGTT 59.190 47.619 0.00 0.00 37.43 3.32
334 335 1.448985 AAATGGGATCGTCCGTGTTG 58.551 50.000 0.00 0.00 37.43 3.33
335 336 0.392461 AATGGGATCGTCCGTGTTGG 60.392 55.000 0.00 0.00 37.43 3.77
336 337 2.125269 GGGATCGTCCGTGTTGGG 60.125 66.667 0.00 0.00 37.43 4.12
337 338 2.818274 GGATCGTCCGTGTTGGGC 60.818 66.667 0.00 0.00 39.78 5.36
338 339 2.264794 GATCGTCCGTGTTGGGCT 59.735 61.111 0.00 0.00 41.63 5.19
339 340 1.810030 GATCGTCCGTGTTGGGCTC 60.810 63.158 0.00 0.00 41.63 4.70
340 341 2.501223 GATCGTCCGTGTTGGGCTCA 62.501 60.000 0.00 0.00 41.63 4.26
341 342 2.507110 ATCGTCCGTGTTGGGCTCAG 62.507 60.000 0.00 0.00 41.63 3.35
342 343 3.050275 GTCCGTGTTGGGCTCAGC 61.050 66.667 0.00 0.00 40.15 4.26
343 344 3.241530 TCCGTGTTGGGCTCAGCT 61.242 61.111 0.92 0.00 38.76 4.24
344 345 1.911269 TCCGTGTTGGGCTCAGCTA 60.911 57.895 0.92 0.00 38.76 3.32
345 346 1.741770 CCGTGTTGGGCTCAGCTAC 60.742 63.158 0.92 0.00 0.00 3.58
346 347 2.094659 CGTGTTGGGCTCAGCTACG 61.095 63.158 0.92 6.50 0.00 3.51
347 348 1.741770 GTGTTGGGCTCAGCTACGG 60.742 63.158 0.92 0.00 0.00 4.02
348 349 2.125106 GTTGGGCTCAGCTACGGG 60.125 66.667 0.00 0.00 0.00 5.28
349 350 4.096003 TTGGGCTCAGCTACGGGC 62.096 66.667 0.00 0.00 42.19 6.13
353 354 4.874977 GCTCAGCTACGGGCCGAC 62.875 72.222 35.78 21.00 43.05 4.79
363 364 2.746277 GGGCCGACTGACGCAAAT 60.746 61.111 0.00 0.00 41.07 2.32
365 366 2.032634 GGCCGACTGACGCAAATGA 61.033 57.895 0.00 0.00 41.07 2.57
367 368 0.452784 GCCGACTGACGCAAATGAAC 60.453 55.000 0.00 0.00 41.07 3.18
368 369 1.148310 CCGACTGACGCAAATGAACT 58.852 50.000 0.00 0.00 41.07 3.01
374 375 3.242518 CTGACGCAAATGAACTCTCGTA 58.757 45.455 0.00 0.00 0.00 3.43
376 377 3.857665 TGACGCAAATGAACTCTCGTATC 59.142 43.478 0.00 0.00 0.00 2.24
379 380 2.033662 GCAAATGAACTCTCGTATCCGC 60.034 50.000 0.00 0.00 0.00 5.54
385 386 0.393944 ACTCTCGTATCCGCCTGACA 60.394 55.000 0.00 0.00 0.00 3.58
395 396 0.321564 CCGCCTGACAGATCCAAACA 60.322 55.000 3.32 0.00 0.00 2.83
396 397 1.522668 CGCCTGACAGATCCAAACAA 58.477 50.000 3.32 0.00 0.00 2.83
398 399 2.489329 CGCCTGACAGATCCAAACAAAT 59.511 45.455 3.32 0.00 0.00 2.32
403 404 6.928492 GCCTGACAGATCCAAACAAATAAAAA 59.072 34.615 3.32 0.00 0.00 1.94
417 418 7.722795 ACAAATAAAAATCGGACAAAAAGGG 57.277 32.000 0.00 0.00 0.00 3.95
418 419 7.276658 ACAAATAAAAATCGGACAAAAAGGGT 58.723 30.769 0.00 0.00 0.00 4.34
420 421 8.616942 CAAATAAAAATCGGACAAAAAGGGTTT 58.383 29.630 0.00 0.00 0.00 3.27
421 422 7.956420 ATAAAAATCGGACAAAAAGGGTTTC 57.044 32.000 0.00 0.00 0.00 2.78
422 423 4.330944 AAATCGGACAAAAAGGGTTTCC 57.669 40.909 0.00 0.00 0.00 3.13
434 435 0.389817 GGGTTTCCTTTTGCATCGGC 60.390 55.000 0.00 0.00 41.68 5.54
446 447 2.046314 ATCGGCCGGTTGGAGTTG 60.046 61.111 27.83 0.00 37.49 3.16
456 457 1.408822 GGTTGGAGTTGGCCATAGAGG 60.409 57.143 6.09 0.00 37.86 3.69
467 468 2.160822 CCATAGAGGCATGGTCTTCG 57.839 55.000 0.00 0.00 40.62 3.79
470 471 0.461548 TAGAGGCATGGTCTTCGCTG 59.538 55.000 0.00 0.00 0.00 5.18
482 483 1.000717 TCTTCGCTGACACGAACATGA 60.001 47.619 0.00 3.86 46.39 3.07
483 484 1.125021 CTTCGCTGACACGAACATGAC 59.875 52.381 0.00 0.00 46.39 3.06
484 485 0.031449 TCGCTGACACGAACATGACA 59.969 50.000 0.00 0.00 39.54 3.58
485 486 0.858583 CGCTGACACGAACATGACAA 59.141 50.000 0.00 0.00 34.06 3.18
487 488 2.722706 CGCTGACACGAACATGACAATG 60.723 50.000 0.00 0.00 35.98 2.82
488 489 2.413239 GCTGACACGAACATGACAATGG 60.413 50.000 0.00 0.00 38.19 3.16
493 494 1.812571 ACGAACATGACAATGGAAGGC 59.187 47.619 0.00 0.00 38.19 4.35
498 499 2.435938 GACAATGGAAGGCGGCGA 60.436 61.111 12.98 0.00 0.00 5.54
499 500 2.033448 ACAATGGAAGGCGGCGAA 59.967 55.556 12.98 0.00 0.00 4.70
503 504 0.893727 AATGGAAGGCGGCGAAAAGT 60.894 50.000 12.98 0.00 0.00 2.66
511 512 1.599797 CGGCGAAAAGTGGGGAAGT 60.600 57.895 0.00 0.00 0.00 3.01
518 519 0.779997 AAAGTGGGGAAGTGGCAGAT 59.220 50.000 0.00 0.00 0.00 2.90
567 571 5.888105 ACTTGCAATCTATTCATCAACTGC 58.112 37.500 0.00 0.00 0.00 4.40
570 574 4.096833 TGCAATCTATTCATCAACTGCCAC 59.903 41.667 0.00 0.00 0.00 5.01
669 676 0.947244 GATCATGGTCGTTGGATGGC 59.053 55.000 0.00 0.00 0.00 4.40
674 681 2.237751 GGTCGTTGGATGGCGATCG 61.238 63.158 11.69 11.69 39.38 3.69
678 685 1.081556 CGTTGGATGGCGATCGAACA 61.082 55.000 27.21 17.13 43.78 3.18
732 742 3.165498 GCCCGATAAATAGGCGCG 58.835 61.111 0.00 0.00 36.84 6.86
735 745 1.019278 CCCGATAAATAGGCGCGCAT 61.019 55.000 34.42 30.20 0.00 4.73
736 746 0.370273 CCGATAAATAGGCGCGCATC 59.630 55.000 34.42 23.33 0.00 3.91
753 763 5.220873 CGCGCATCATACATATACTACCTCT 60.221 44.000 8.75 0.00 0.00 3.69
820 836 7.739498 TTTTATATTTTGATACGGAGGGAGC 57.261 36.000 0.00 0.00 0.00 4.70
831 847 1.412710 CGGAGGGAGCAGCTATGTTTA 59.587 52.381 0.00 0.00 0.00 2.01
840 857 6.017523 GGGAGCAGCTATGTTTAGAGAATTTC 60.018 42.308 0.00 0.00 0.00 2.17
858 875 0.395586 TCCAAATGGATTCCGCAGGG 60.396 55.000 0.00 0.00 44.68 4.45
885 902 8.830201 ACGAATTTTCAAATGGATTCATCAAA 57.170 26.923 0.00 0.00 32.24 2.69
929 968 2.368655 CCATTAGTGGGCAAAACAGC 57.631 50.000 0.00 0.00 42.11 4.40
967 1006 0.250081 GATCCGATCTGGTTGAGCCC 60.250 60.000 0.75 0.00 39.52 5.19
1331 1414 2.833582 CCGCGCCCTCTTCCTCTA 60.834 66.667 0.00 0.00 0.00 2.43
1344 1430 4.124351 CTCTACGACCGCGGCCAA 62.124 66.667 28.58 7.56 43.17 4.52
2173 2336 0.044092 TCAGCAAGGGGTATGGGAGA 59.956 55.000 0.00 0.00 0.00 3.71
2274 2437 2.038164 TGACTGCTTCAGACATGCTCTT 59.962 45.455 0.29 0.00 32.09 2.85
2345 2519 6.431852 TGCTGTAGCGTAACATATGGATAGTA 59.568 38.462 7.80 0.00 45.83 1.82
2629 2826 8.477709 GTTATGTCTGTAATAGTGTAATGCGAC 58.522 37.037 0.00 0.00 0.00 5.19
2700 2897 4.492791 TGATCACTGTGCAGTTCATTTG 57.507 40.909 2.12 0.00 40.20 2.32
2785 3005 7.291411 AGACAGTCAACAGAACATAGTTACT 57.709 36.000 2.66 0.00 0.00 2.24
3197 3551 4.722361 GTTGACCCCACAACTTTAACAA 57.278 40.909 0.00 0.00 44.34 2.83
3319 3789 7.977789 TGCAATAAGTTCTCATTGTCTGTTA 57.022 32.000 0.00 0.00 35.12 2.41
3481 4438 3.581755 GCATTTGTGTGCATCTCATTGT 58.418 40.909 0.00 0.00 44.43 2.71
3585 4749 6.866010 AAATGTTTTTCTTCCTTCAATGGC 57.134 33.333 0.00 0.00 0.00 4.40
3717 4881 5.391312 AAATGTTGAATACTGCAAGGGTC 57.609 39.130 0.00 0.00 39.30 4.46
3786 4950 4.366586 TGATTGCTCTAGCTGAAATCTCG 58.633 43.478 13.74 0.00 42.66 4.04
4109 5379 3.896888 TCACCTGCTTTTGAATCCACATT 59.103 39.130 0.00 0.00 0.00 2.71
4791 6168 0.898326 TCTACGGCAGCACCAAGAGA 60.898 55.000 0.00 0.00 39.03 3.10
4957 6364 7.495279 CAGCTAGATAGAAATTCTGAAACTGCT 59.505 37.037 5.64 5.73 0.00 4.24
4985 6398 0.748005 CATGGGACGCCCTAACAAGG 60.748 60.000 14.76 0.00 45.70 3.61
5000 6413 2.980548 ACAAGGTGTTACTACTCCCCA 58.019 47.619 0.00 0.00 38.44 4.96
5074 6509 6.620877 ATTTGATCTGGTCACTAGGTGTTA 57.379 37.500 0.00 0.00 36.32 2.41
5082 6517 3.877508 GGTCACTAGGTGTTATTGGCATC 59.122 47.826 0.00 0.00 34.79 3.91
5139 6574 2.766313 GCGGTGCAATACTCATCCATA 58.234 47.619 0.00 0.00 0.00 2.74
5252 6687 9.938670 CTCTAAACTATGTCTATATACATCCGC 57.061 37.037 7.00 0.00 40.52 5.54
5306 6741 9.155785 AGATTTATATTTAGAAACGGAGGGAGA 57.844 33.333 0.00 0.00 0.00 3.71
5437 6879 4.862018 CGTATTTGCGAAACCATTTTGGAT 59.138 37.500 0.00 0.00 40.96 3.41
5440 6882 3.296322 TGCGAAACCATTTTGGATGTC 57.704 42.857 0.00 0.00 40.96 3.06
5443 6885 3.233578 CGAAACCATTTTGGATGTCACG 58.766 45.455 0.00 0.00 40.96 4.35
5444 6886 2.723124 AACCATTTTGGATGTCACGC 57.277 45.000 0.00 0.00 40.96 5.34
5446 6888 0.521291 CCATTTTGGATGTCACGCGT 59.479 50.000 5.58 5.58 40.96 6.01
5447 6889 1.735018 CCATTTTGGATGTCACGCGTA 59.265 47.619 13.44 0.00 40.96 4.42
5448 6890 2.160615 CCATTTTGGATGTCACGCGTAA 59.839 45.455 13.44 0.00 40.96 3.18
5449 6891 3.365465 CCATTTTGGATGTCACGCGTAAA 60.365 43.478 13.44 6.74 40.96 2.01
5450 6892 3.965292 TTTTGGATGTCACGCGTAAAA 57.035 38.095 13.44 10.72 0.00 1.52
5457 6899 4.491924 GGATGTCACGCGTAAAATGTAGTG 60.492 45.833 13.44 0.00 0.00 2.74
5567 7146 6.698766 AGTTTTTGCAAGTCAGTGATCATTTC 59.301 34.615 0.00 0.00 0.00 2.17
5593 7196 8.067784 CAGAAACATTTATTGTCTACGTGTTGT 58.932 33.333 0.00 0.00 37.68 3.32
5649 7323 8.795786 TCTTTCCGAATTGAAGTTAAACAATG 57.204 30.769 0.00 0.00 36.92 2.82
5706 7381 9.874215 CTAGATGCATTTACAGATTACACATTG 57.126 33.333 0.00 0.00 0.00 2.82
5892 7578 0.687354 TGAGAAGTCTGGACAAGGCC 59.313 55.000 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.504596 TCCATGCCCCACCATCGC 62.505 66.667 0.00 0.00 0.00 4.58
12 13 3.338250 ACGTCCATGCCCCACCAT 61.338 61.111 0.00 0.00 0.00 3.55
13 14 4.343323 CACGTCCATGCCCCACCA 62.343 66.667 0.00 0.00 0.00 4.17
15 16 4.028490 TCCACGTCCATGCCCCAC 62.028 66.667 0.00 0.00 0.00 4.61
16 17 4.028490 GTCCACGTCCATGCCCCA 62.028 66.667 0.00 0.00 0.00 4.96
44 45 3.499737 GAACTCCGGCGTGCATGG 61.500 66.667 8.27 0.00 0.00 3.66
45 46 3.853330 CGAACTCCGGCGTGCATG 61.853 66.667 6.01 0.09 33.91 4.06
46 47 4.373116 ACGAACTCCGGCGTGCAT 62.373 61.111 6.01 0.00 43.93 3.96
144 145 4.329545 GAACGGAGGTGGCTGCCA 62.330 66.667 19.30 19.30 0.00 4.92
146 147 4.681978 ACGAACGGAGGTGGCTGC 62.682 66.667 0.00 0.00 0.00 5.25
147 148 2.432628 GACGAACGGAGGTGGCTG 60.433 66.667 0.00 0.00 0.00 4.85
148 149 4.052229 CGACGAACGGAGGTGGCT 62.052 66.667 0.00 0.00 38.46 4.75
149 150 4.047059 TCGACGAACGGAGGTGGC 62.047 66.667 0.00 0.00 42.82 5.01
150 151 2.126580 GTCGACGAACGGAGGTGG 60.127 66.667 0.00 0.00 42.82 4.61
151 152 2.126580 GGTCGACGAACGGAGGTG 60.127 66.667 9.92 0.00 42.82 4.00
152 153 2.282040 AGGTCGACGAACGGAGGT 60.282 61.111 9.92 0.00 42.82 3.85
153 154 2.330372 TGAGGTCGACGAACGGAGG 61.330 63.158 9.92 0.00 42.82 4.30
154 155 1.154263 GTGAGGTCGACGAACGGAG 60.154 63.158 9.92 0.00 42.82 4.63
155 156 2.620112 GGTGAGGTCGACGAACGGA 61.620 63.158 9.92 0.00 42.82 4.69
156 157 2.126580 GGTGAGGTCGACGAACGG 60.127 66.667 9.92 0.00 42.82 4.44
157 158 1.728426 GTGGTGAGGTCGACGAACG 60.728 63.158 9.92 0.00 44.09 3.95
158 159 1.728426 CGTGGTGAGGTCGACGAAC 60.728 63.158 9.92 4.26 40.81 3.95
159 160 2.640989 CGTGGTGAGGTCGACGAA 59.359 61.111 9.92 0.00 40.81 3.85
160 161 3.359523 CCGTGGTGAGGTCGACGA 61.360 66.667 9.92 0.00 40.81 4.20
161 162 2.697761 ATCCGTGGTGAGGTCGACG 61.698 63.158 9.92 0.00 38.77 5.12
162 163 1.153823 CATCCGTGGTGAGGTCGAC 60.154 63.158 7.13 7.13 0.00 4.20
163 164 2.348104 CCATCCGTGGTGAGGTCGA 61.348 63.158 0.00 0.00 40.83 4.20
164 165 2.184322 CCATCCGTGGTGAGGTCG 59.816 66.667 0.00 0.00 40.83 4.79
173 174 4.794439 TCGTCGCTGCCATCCGTG 62.794 66.667 0.00 0.00 0.00 4.94
174 175 3.838271 ATCGTCGCTGCCATCCGT 61.838 61.111 0.00 0.00 0.00 4.69
175 176 3.333189 CATCGTCGCTGCCATCCG 61.333 66.667 0.00 0.00 0.00 4.18
176 177 2.202932 ACATCGTCGCTGCCATCC 60.203 61.111 0.00 0.00 0.00 3.51
177 178 3.313750 GACATCGTCGCTGCCATC 58.686 61.111 0.00 0.00 0.00 3.51
183 184 7.443249 TCTAGTACTAGTCGACATCGTCGCT 62.443 48.000 25.58 13.30 42.05 4.93
184 185 5.312452 TCTAGTACTAGTCGACATCGTCGC 61.312 50.000 25.58 7.15 42.05 5.19
185 186 4.286101 TCTAGTACTAGTCGACATCGTCG 58.714 47.826 25.58 10.16 42.78 5.12
186 187 6.151691 AGATCTAGTACTAGTCGACATCGTC 58.848 44.000 25.58 12.47 34.98 4.20
187 188 6.088016 AGATCTAGTACTAGTCGACATCGT 57.912 41.667 25.58 13.30 34.98 3.73
188 189 6.748658 CCTAGATCTAGTACTAGTCGACATCG 59.251 46.154 25.58 7.75 35.65 3.84
189 190 7.605449 ACCTAGATCTAGTACTAGTCGACATC 58.395 42.308 25.58 20.14 35.65 3.06
190 191 7.543359 ACCTAGATCTAGTACTAGTCGACAT 57.457 40.000 25.58 13.79 35.65 3.06
191 192 6.975196 ACCTAGATCTAGTACTAGTCGACA 57.025 41.667 25.58 9.80 35.65 4.35
192 193 8.661352 AAAACCTAGATCTAGTACTAGTCGAC 57.339 38.462 25.58 7.70 35.65 4.20
193 194 9.979578 CTAAAACCTAGATCTAGTACTAGTCGA 57.020 37.037 25.58 17.53 35.65 4.20
194 195 9.762933 ACTAAAACCTAGATCTAGTACTAGTCG 57.237 37.037 25.58 11.66 35.65 4.18
253 254 9.524106 CACGTCCACTATCATACATTAAACTTA 57.476 33.333 0.00 0.00 0.00 2.24
254 255 8.255206 TCACGTCCACTATCATACATTAAACTT 58.745 33.333 0.00 0.00 0.00 2.66
255 256 7.778083 TCACGTCCACTATCATACATTAAACT 58.222 34.615 0.00 0.00 0.00 2.66
256 257 7.997107 TCACGTCCACTATCATACATTAAAC 57.003 36.000 0.00 0.00 0.00 2.01
257 258 8.255206 AGTTCACGTCCACTATCATACATTAAA 58.745 33.333 0.00 0.00 0.00 1.52
258 259 7.778083 AGTTCACGTCCACTATCATACATTAA 58.222 34.615 0.00 0.00 0.00 1.40
259 260 7.342769 AGTTCACGTCCACTATCATACATTA 57.657 36.000 0.00 0.00 0.00 1.90
260 261 6.222038 AGTTCACGTCCACTATCATACATT 57.778 37.500 0.00 0.00 0.00 2.71
261 262 5.854010 AGTTCACGTCCACTATCATACAT 57.146 39.130 0.00 0.00 0.00 2.29
262 263 5.654603 AAGTTCACGTCCACTATCATACA 57.345 39.130 0.00 0.00 0.00 2.29
263 264 6.183360 CCAAAAGTTCACGTCCACTATCATAC 60.183 42.308 0.00 0.00 0.00 2.39
264 265 5.872617 CCAAAAGTTCACGTCCACTATCATA 59.127 40.000 0.00 0.00 0.00 2.15
265 266 4.695455 CCAAAAGTTCACGTCCACTATCAT 59.305 41.667 0.00 0.00 0.00 2.45
266 267 4.062293 CCAAAAGTTCACGTCCACTATCA 58.938 43.478 0.00 0.00 0.00 2.15
267 268 4.062991 ACCAAAAGTTCACGTCCACTATC 58.937 43.478 0.00 0.00 0.00 2.08
268 269 4.081322 ACCAAAAGTTCACGTCCACTAT 57.919 40.909 0.00 0.00 0.00 2.12
269 270 3.547054 ACCAAAAGTTCACGTCCACTA 57.453 42.857 0.00 0.00 0.00 2.74
270 271 2.413310 ACCAAAAGTTCACGTCCACT 57.587 45.000 0.00 0.00 0.00 4.00
271 272 3.608474 GCATACCAAAAGTTCACGTCCAC 60.608 47.826 0.00 0.00 0.00 4.02
272 273 2.550606 GCATACCAAAAGTTCACGTCCA 59.449 45.455 0.00 0.00 0.00 4.02
273 274 2.550606 TGCATACCAAAAGTTCACGTCC 59.449 45.455 0.00 0.00 0.00 4.79
274 275 3.889196 TGCATACCAAAAGTTCACGTC 57.111 42.857 0.00 0.00 0.00 4.34
275 276 3.057596 CCATGCATACCAAAAGTTCACGT 60.058 43.478 0.00 0.00 0.00 4.49
276 277 3.057596 ACCATGCATACCAAAAGTTCACG 60.058 43.478 0.00 0.00 0.00 4.35
277 278 4.519540 ACCATGCATACCAAAAGTTCAC 57.480 40.909 0.00 0.00 0.00 3.18
278 279 5.543507 AAACCATGCATACCAAAAGTTCA 57.456 34.783 0.00 0.00 0.00 3.18
279 280 8.546597 AATTAAACCATGCATACCAAAAGTTC 57.453 30.769 0.00 0.00 0.00 3.01
280 281 8.782144 CAAATTAAACCATGCATACCAAAAGTT 58.218 29.630 0.00 0.00 0.00 2.66
281 282 8.153550 TCAAATTAAACCATGCATACCAAAAGT 58.846 29.630 0.00 0.00 0.00 2.66
282 283 8.545229 TCAAATTAAACCATGCATACCAAAAG 57.455 30.769 0.00 0.00 0.00 2.27
283 284 9.512588 AATCAAATTAAACCATGCATACCAAAA 57.487 25.926 0.00 0.00 0.00 2.44
284 285 9.512588 AAATCAAATTAAACCATGCATACCAAA 57.487 25.926 0.00 0.00 0.00 3.28
285 286 9.512588 AAAATCAAATTAAACCATGCATACCAA 57.487 25.926 0.00 0.00 0.00 3.67
286 287 8.944029 CAAAATCAAATTAAACCATGCATACCA 58.056 29.630 0.00 0.00 0.00 3.25
287 288 7.909641 GCAAAATCAAATTAAACCATGCATACC 59.090 33.333 0.00 0.00 0.00 2.73
288 289 8.449397 TGCAAAATCAAATTAAACCATGCATAC 58.551 29.630 0.00 0.00 35.39 2.39
289 290 8.557592 TGCAAAATCAAATTAAACCATGCATA 57.442 26.923 0.00 0.00 35.39 3.14
290 291 7.450124 TGCAAAATCAAATTAAACCATGCAT 57.550 28.000 0.00 0.00 35.39 3.96
291 292 6.872628 TGCAAAATCAAATTAAACCATGCA 57.127 29.167 0.00 0.00 37.70 3.96
292 293 8.571461 TTTTGCAAAATCAAATTAAACCATGC 57.429 26.923 20.46 0.00 36.04 4.06
294 295 9.694137 CCATTTTGCAAAATCAAATTAAACCAT 57.306 25.926 29.92 6.74 36.52 3.55
295 296 8.139989 CCCATTTTGCAAAATCAAATTAAACCA 58.860 29.630 29.92 3.78 36.52 3.67
296 297 8.355913 TCCCATTTTGCAAAATCAAATTAAACC 58.644 29.630 29.92 0.00 36.52 3.27
297 298 9.911138 ATCCCATTTTGCAAAATCAAATTAAAC 57.089 25.926 29.92 0.00 36.52 2.01
299 300 8.449397 CGATCCCATTTTGCAAAATCAAATTAA 58.551 29.630 29.92 14.18 36.52 1.40
300 301 7.605691 ACGATCCCATTTTGCAAAATCAAATTA 59.394 29.630 29.92 15.07 36.52 1.40
301 302 6.430616 ACGATCCCATTTTGCAAAATCAAATT 59.569 30.769 29.92 16.14 36.52 1.82
302 303 5.939296 ACGATCCCATTTTGCAAAATCAAAT 59.061 32.000 29.92 22.29 36.52 2.32
303 304 5.303971 ACGATCCCATTTTGCAAAATCAAA 58.696 33.333 29.92 19.24 36.52 2.69
304 305 4.892433 ACGATCCCATTTTGCAAAATCAA 58.108 34.783 29.92 19.54 36.52 2.57
305 306 4.493547 GACGATCCCATTTTGCAAAATCA 58.506 39.130 29.92 18.76 36.52 2.57
306 307 3.865164 GGACGATCCCATTTTGCAAAATC 59.135 43.478 29.92 19.89 36.52 2.17
307 308 3.675775 CGGACGATCCCATTTTGCAAAAT 60.676 43.478 27.73 27.73 39.07 1.82
308 309 2.352225 CGGACGATCCCATTTTGCAAAA 60.352 45.455 25.76 25.76 31.13 2.44
309 310 1.201181 CGGACGATCCCATTTTGCAAA 59.799 47.619 8.05 8.05 31.13 3.68
310 311 0.808125 CGGACGATCCCATTTTGCAA 59.192 50.000 0.00 0.00 31.13 4.08
311 312 0.322098 ACGGACGATCCCATTTTGCA 60.322 50.000 0.00 0.00 31.13 4.08
312 313 0.098728 CACGGACGATCCCATTTTGC 59.901 55.000 0.00 0.00 31.13 3.68
313 314 1.448985 ACACGGACGATCCCATTTTG 58.551 50.000 0.00 0.00 31.13 2.44
314 315 1.810151 CAACACGGACGATCCCATTTT 59.190 47.619 0.00 0.00 31.13 1.82
315 316 1.448985 CAACACGGACGATCCCATTT 58.551 50.000 0.00 0.00 31.13 2.32
316 317 0.392461 CCAACACGGACGATCCCATT 60.392 55.000 0.00 0.00 36.56 3.16
317 318 1.220749 CCAACACGGACGATCCCAT 59.779 57.895 0.00 0.00 36.56 4.00
318 319 2.660206 CCAACACGGACGATCCCA 59.340 61.111 0.00 0.00 36.56 4.37
319 320 2.125269 CCCAACACGGACGATCCC 60.125 66.667 0.00 0.00 36.56 3.85
320 321 2.818274 GCCCAACACGGACGATCC 60.818 66.667 0.00 0.00 36.56 3.36
321 322 1.810030 GAGCCCAACACGGACGATC 60.810 63.158 0.00 0.00 36.56 3.69
322 323 2.264794 GAGCCCAACACGGACGAT 59.735 61.111 0.00 0.00 36.56 3.73
323 324 3.220999 CTGAGCCCAACACGGACGA 62.221 63.158 0.00 0.00 36.56 4.20
324 325 2.738521 CTGAGCCCAACACGGACG 60.739 66.667 0.00 0.00 36.56 4.79
325 326 2.167398 TAGCTGAGCCCAACACGGAC 62.167 60.000 0.00 0.00 36.56 4.79
326 327 1.911269 TAGCTGAGCCCAACACGGA 60.911 57.895 0.00 0.00 36.56 4.69
327 328 1.741770 GTAGCTGAGCCCAACACGG 60.742 63.158 0.00 0.00 0.00 4.94
328 329 2.094659 CGTAGCTGAGCCCAACACG 61.095 63.158 0.00 0.00 0.00 4.49
329 330 1.741770 CCGTAGCTGAGCCCAACAC 60.742 63.158 0.00 0.00 0.00 3.32
330 331 2.662596 CCGTAGCTGAGCCCAACA 59.337 61.111 0.00 0.00 0.00 3.33
331 332 2.125106 CCCGTAGCTGAGCCCAAC 60.125 66.667 0.00 0.00 0.00 3.77
332 333 4.096003 GCCCGTAGCTGAGCCCAA 62.096 66.667 0.00 0.00 38.99 4.12
340 341 3.450115 GTCAGTCGGCCCGTAGCT 61.450 66.667 1.63 0.00 43.05 3.32
341 342 4.849329 CGTCAGTCGGCCCGTAGC 62.849 72.222 1.63 0.00 42.60 3.58
342 343 4.849329 GCGTCAGTCGGCCCGTAG 62.849 72.222 1.63 0.00 40.26 3.51
346 347 2.746277 ATTTGCGTCAGTCGGCCC 60.746 61.111 0.00 0.00 40.26 5.80
347 348 1.573829 TTCATTTGCGTCAGTCGGCC 61.574 55.000 0.00 0.00 40.26 6.13
348 349 0.452784 GTTCATTTGCGTCAGTCGGC 60.453 55.000 0.00 0.00 40.26 5.54
349 350 1.126846 GAGTTCATTTGCGTCAGTCGG 59.873 52.381 0.00 0.00 40.26 4.79
350 351 2.061773 AGAGTTCATTTGCGTCAGTCG 58.938 47.619 0.00 0.00 43.12 4.18
351 352 2.091277 CGAGAGTTCATTTGCGTCAGTC 59.909 50.000 0.00 0.00 0.00 3.51
352 353 2.061773 CGAGAGTTCATTTGCGTCAGT 58.938 47.619 0.00 0.00 0.00 3.41
353 354 2.061773 ACGAGAGTTCATTTGCGTCAG 58.938 47.619 0.00 0.00 46.40 3.51
374 375 0.911769 TTTGGATCTGTCAGGCGGAT 59.088 50.000 0.00 0.00 45.41 4.18
376 377 0.321564 TGTTTGGATCTGTCAGGCGG 60.322 55.000 0.00 0.00 0.00 6.13
379 380 9.143631 GATTTTTATTTGTTTGGATCTGTCAGG 57.856 33.333 0.00 0.00 0.00 3.86
385 386 7.891561 TGTCCGATTTTTATTTGTTTGGATCT 58.108 30.769 0.00 0.00 0.00 2.75
395 396 8.740123 AAACCCTTTTTGTCCGATTTTTATTT 57.260 26.923 0.00 0.00 0.00 1.40
396 397 7.442969 GGAAACCCTTTTTGTCCGATTTTTATT 59.557 33.333 0.00 0.00 0.00 1.40
398 399 6.098552 AGGAAACCCTTTTTGTCCGATTTTTA 59.901 34.615 0.00 0.00 33.38 1.52
403 404 3.238788 AGGAAACCCTTTTTGTCCGAT 57.761 42.857 0.00 0.00 33.38 4.18
417 418 0.732538 CGGCCGATGCAAAAGGAAAC 60.733 55.000 24.07 0.00 40.13 2.78
418 419 1.583986 CGGCCGATGCAAAAGGAAA 59.416 52.632 24.07 0.00 40.13 3.13
420 421 2.749839 CCGGCCGATGCAAAAGGA 60.750 61.111 30.73 0.00 40.13 3.36
421 422 2.635443 AACCGGCCGATGCAAAAGG 61.635 57.895 30.73 8.96 40.13 3.11
422 423 1.444212 CAACCGGCCGATGCAAAAG 60.444 57.895 30.73 9.82 40.13 2.27
429 430 2.046314 CAACTCCAACCGGCCGAT 60.046 61.111 30.73 6.36 0.00 4.18
434 435 0.748005 CTATGGCCAACTCCAACCGG 60.748 60.000 10.96 0.00 39.96 5.28
456 457 1.790387 GTGTCAGCGAAGACCATGC 59.210 57.895 5.40 0.00 37.73 4.06
466 467 0.858583 TTGTCATGTTCGTGTCAGCG 59.141 50.000 0.00 0.00 0.00 5.18
467 468 2.413239 CCATTGTCATGTTCGTGTCAGC 60.413 50.000 0.00 0.00 0.00 4.26
470 471 3.120199 CCTTCCATTGTCATGTTCGTGTC 60.120 47.826 0.00 0.00 0.00 3.67
482 483 1.175983 TTTTCGCCGCCTTCCATTGT 61.176 50.000 0.00 0.00 0.00 2.71
483 484 0.456653 CTTTTCGCCGCCTTCCATTG 60.457 55.000 0.00 0.00 0.00 2.82
484 485 0.893727 ACTTTTCGCCGCCTTCCATT 60.894 50.000 0.00 0.00 0.00 3.16
485 486 1.303317 ACTTTTCGCCGCCTTCCAT 60.303 52.632 0.00 0.00 0.00 3.41
487 488 2.561373 CACTTTTCGCCGCCTTCC 59.439 61.111 0.00 0.00 0.00 3.46
488 489 2.561373 CCACTTTTCGCCGCCTTC 59.439 61.111 0.00 0.00 0.00 3.46
493 494 1.599797 ACTTCCCCACTTTTCGCCG 60.600 57.895 0.00 0.00 0.00 6.46
498 499 0.555769 TCTGCCACTTCCCCACTTTT 59.444 50.000 0.00 0.00 0.00 2.27
499 500 0.779997 ATCTGCCACTTCCCCACTTT 59.220 50.000 0.00 0.00 0.00 2.66
503 504 1.852157 ACCATCTGCCACTTCCCCA 60.852 57.895 0.00 0.00 0.00 4.96
511 512 4.478531 TGGCTAGACCATCTGCCA 57.521 55.556 14.22 14.22 46.36 4.92
548 552 4.604976 GTGGCAGTTGATGAATAGATTGC 58.395 43.478 0.00 0.00 0.00 3.56
567 571 4.152402 CCTCTGTTCTTTGTACAATCGTGG 59.848 45.833 9.56 1.09 0.00 4.94
570 574 4.627467 CCTCCTCTGTTCTTTGTACAATCG 59.373 45.833 9.56 4.16 0.00 3.34
629 636 4.732784 TCACACAGCAACTGTTTCTTTTC 58.267 39.130 0.00 0.00 42.59 2.29
633 640 3.544684 TGATCACACAGCAACTGTTTCT 58.455 40.909 0.00 0.00 42.59 2.52
634 641 3.969117 TGATCACACAGCAACTGTTTC 57.031 42.857 0.00 0.00 42.59 2.78
635 642 3.005050 CCATGATCACACAGCAACTGTTT 59.995 43.478 0.00 0.00 42.59 2.83
636 643 2.555325 CCATGATCACACAGCAACTGTT 59.445 45.455 0.00 0.00 42.59 3.16
637 644 2.156917 CCATGATCACACAGCAACTGT 58.843 47.619 0.00 0.00 46.51 3.55
641 648 1.270785 ACGACCATGATCACACAGCAA 60.271 47.619 0.00 0.00 0.00 3.91
642 649 0.321346 ACGACCATGATCACACAGCA 59.679 50.000 0.00 0.00 0.00 4.41
709 719 2.230508 CGCCTATTTATCGGGCACTAGA 59.769 50.000 0.00 0.00 45.50 2.43
718 728 1.067693 TGATGCGCGCCTATTTATCG 58.932 50.000 30.77 0.00 0.00 2.92
731 741 7.089770 ACAGAGGTAGTATATGTATGATGCG 57.910 40.000 0.00 0.00 0.00 4.73
791 801 9.893305 CCCTCCGTATCAAAATATAAAAACATC 57.107 33.333 0.00 0.00 0.00 3.06
792 802 9.635404 TCCCTCCGTATCAAAATATAAAAACAT 57.365 29.630 0.00 0.00 0.00 2.71
793 803 9.116067 CTCCCTCCGTATCAAAATATAAAAACA 57.884 33.333 0.00 0.00 0.00 2.83
794 804 8.074370 GCTCCCTCCGTATCAAAATATAAAAAC 58.926 37.037 0.00 0.00 0.00 2.43
795 805 7.776030 TGCTCCCTCCGTATCAAAATATAAAAA 59.224 33.333 0.00 0.00 0.00 1.94
796 806 7.284074 TGCTCCCTCCGTATCAAAATATAAAA 58.716 34.615 0.00 0.00 0.00 1.52
797 807 6.833041 TGCTCCCTCCGTATCAAAATATAAA 58.167 36.000 0.00 0.00 0.00 1.40
809 825 0.106167 ACATAGCTGCTCCCTCCGTA 60.106 55.000 4.91 0.00 0.00 4.02
815 831 4.408182 TTCTCTAAACATAGCTGCTCCC 57.592 45.455 4.91 0.00 0.00 4.30
820 836 9.512435 CATTTGGAAATTCTCTAAACATAGCTG 57.488 33.333 0.00 0.00 37.34 4.24
840 857 0.395586 TCCCTGCGGAATCCATTTGG 60.396 55.000 0.00 0.00 34.19 3.28
849 866 1.538075 GAAAATTCGTTCCCTGCGGAA 59.462 47.619 0.00 0.00 46.38 4.30
858 875 8.464770 TGATGAATCCATTTGAAAATTCGTTC 57.535 30.769 0.00 0.00 32.09 3.95
910 949 1.066929 GGCTGTTTTGCCCACTAATGG 60.067 52.381 0.00 0.00 46.82 3.16
911 950 2.368655 GGCTGTTTTGCCCACTAATG 57.631 50.000 0.00 0.00 46.82 1.90
929 968 1.024579 CGGAACTGGGAATGGTTCGG 61.025 60.000 0.00 0.00 41.67 4.30
967 1006 1.976474 CGGGTGGGGAATGTGGTTG 60.976 63.158 0.00 0.00 0.00 3.77
1025 1105 3.822192 CGACATCGTCCGGGAGCA 61.822 66.667 0.00 0.00 34.11 4.26
1038 1118 1.065345 AGGAGGATCTCTTCGACGACA 60.065 52.381 0.00 0.00 33.73 4.35
1331 1414 4.612412 TTTCTTGGCCGCGGTCGT 62.612 61.111 26.87 0.00 0.00 4.34
1694 1805 1.468520 CACTGCCCAAATTGTACTCCG 59.531 52.381 0.00 0.00 0.00 4.63
2013 2172 2.194597 TGGCACACCCTTTTCGCT 59.805 55.556 0.00 0.00 33.59 4.93
2129 2291 0.457851 CCTCCTCAGTAGGTTCAGCG 59.542 60.000 0.00 0.00 44.09 5.18
2173 2336 4.009675 TGCGCCAATTCTAGTGATTTCTT 58.990 39.130 4.18 0.00 0.00 2.52
2274 2437 6.071984 GGAGTAGAATCCTAACCTGATCTCA 58.928 44.000 0.00 0.00 36.35 3.27
2605 2802 6.854381 CGTCGCATTACACTATTACAGACATA 59.146 38.462 0.00 0.00 0.00 2.29
2611 2808 5.488645 TCTCGTCGCATTACACTATTACA 57.511 39.130 0.00 0.00 0.00 2.41
2612 2809 6.988109 ATTCTCGTCGCATTACACTATTAC 57.012 37.500 0.00 0.00 0.00 1.89
2613 2810 9.518906 TTTAATTCTCGTCGCATTACACTATTA 57.481 29.630 0.00 0.00 0.00 0.98
2614 2811 7.997107 TTAATTCTCGTCGCATTACACTATT 57.003 32.000 0.00 0.00 0.00 1.73
2615 2812 7.997107 TTTAATTCTCGTCGCATTACACTAT 57.003 32.000 0.00 0.00 0.00 2.12
2616 2813 7.703197 TGATTTAATTCTCGTCGCATTACACTA 59.297 33.333 0.00 0.00 0.00 2.74
2617 2814 6.533723 TGATTTAATTCTCGTCGCATTACACT 59.466 34.615 0.00 0.00 0.00 3.55
2618 2815 6.701937 TGATTTAATTCTCGTCGCATTACAC 58.298 36.000 0.00 0.00 0.00 2.90
2629 2826 6.524586 GCACTTGGACTTTGATTTAATTCTCG 59.475 38.462 0.00 0.00 0.00 4.04
2700 2897 2.672098 TCTGAGGAAGAGGAGCCATAC 58.328 52.381 0.00 0.00 0.00 2.39
2785 3005 7.118496 ACAAAACCATTTTATGACACAAGGA 57.882 32.000 0.00 0.00 0.00 3.36
3273 3627 5.581085 GCAACCAGTAGTGTTATCAACTAGG 59.419 44.000 0.00 0.00 0.00 3.02
3481 4438 2.430332 CAGCCCAAGAGGAAACAAACAA 59.570 45.455 0.00 0.00 38.24 2.83
3576 4740 0.806868 ATCAGCACGTGCCATTGAAG 59.193 50.000 35.51 16.84 43.38 3.02
3585 4749 3.618594 AGCAACAACTATATCAGCACGTG 59.381 43.478 12.28 12.28 0.00 4.49
3626 4790 0.400213 ATCCGTCTGACCTTTGCCAA 59.600 50.000 1.55 0.00 0.00 4.52
3717 4881 3.196469 TCTCTGGACTCTTGGCAACTATG 59.804 47.826 0.00 0.00 37.61 2.23
3786 4950 5.275067 AGCTGAGATTACCTCTTGTCATC 57.725 43.478 0.00 0.00 42.44 2.92
3925 5090 3.515104 CAGGCCTAACCAAATGTTCCAAT 59.485 43.478 3.98 0.00 43.14 3.16
4109 5379 7.453752 ACAGTCCTACTCCAAATCTACACTAAA 59.546 37.037 0.00 0.00 0.00 1.85
4791 6168 3.439129 GGTTACGCTACTTCCAATGCTTT 59.561 43.478 0.00 0.00 0.00 3.51
4957 6364 1.003118 GGGCGTCCCATGCATATCTTA 59.997 52.381 0.00 0.00 44.65 2.10
4985 6398 5.099042 ACATGAATGGGGAGTAGTAACAC 57.901 43.478 0.00 0.00 0.00 3.32
5000 6413 3.346315 TCACCATTGAGCGAACATGAAT 58.654 40.909 0.00 0.00 0.00 2.57
5074 6509 5.829391 TCAGTTATTATGTGCTGATGCCAAT 59.171 36.000 0.00 0.00 38.71 3.16
5082 6517 7.389607 TGATGATCCATCAGTTATTATGTGCTG 59.610 37.037 5.61 0.00 44.60 4.41
5121 6556 6.543831 AGAAAACTATGGATGAGTATTGCACC 59.456 38.462 0.00 0.00 0.00 5.01
5126 6561 8.652290 GGGAGTAGAAAACTATGGATGAGTATT 58.348 37.037 0.00 0.00 39.07 1.89
5139 6574 2.566279 GGAACGGAGGGAGTAGAAAACT 59.434 50.000 0.00 0.00 42.80 2.66
5252 6687 9.645059 TTTAGAGATTTCAACTGAGACTACATG 57.355 33.333 0.00 0.00 0.00 3.21
5437 6879 2.732500 CCACTACATTTTACGCGTGACA 59.267 45.455 24.59 7.29 0.00 3.58
5440 6882 3.922240 AGTACCACTACATTTTACGCGTG 59.078 43.478 24.59 7.13 0.00 5.34
5443 6885 6.716898 AAGAAGTACCACTACATTTTACGC 57.283 37.500 0.00 0.00 0.00 4.42
5444 6886 8.378421 GCTTAAGAAGTACCACTACATTTTACG 58.622 37.037 6.67 0.00 0.00 3.18
5446 6888 9.781633 TTGCTTAAGAAGTACCACTACATTTTA 57.218 29.630 6.67 0.00 0.00 1.52
5447 6889 8.685838 TTGCTTAAGAAGTACCACTACATTTT 57.314 30.769 6.67 0.00 0.00 1.82
5448 6890 8.685838 TTTGCTTAAGAAGTACCACTACATTT 57.314 30.769 6.67 0.00 0.00 2.32
5449 6891 8.565416 GTTTTGCTTAAGAAGTACCACTACATT 58.435 33.333 6.67 0.00 0.00 2.71
5450 6892 7.937394 AGTTTTGCTTAAGAAGTACCACTACAT 59.063 33.333 6.67 0.00 0.00 2.29
5530 7098 7.931407 TGACTTGCAAAAACTACATCTAAGAGA 59.069 33.333 0.00 0.00 0.00 3.10
5567 7146 8.067784 ACAACACGTAGACAATAAATGTTTCTG 58.932 33.333 0.00 0.00 44.12 3.02
5649 7323 7.065085 TGCAACATTCTAGCTTTCTGATAACTC 59.935 37.037 0.00 0.00 0.00 3.01
5662 7336 7.074502 GCATCTAGTATTTGCAACATTCTAGC 58.925 38.462 19.04 11.75 36.40 3.42
5719 7394 7.930325 CCAATTAATGTTAGAGATCTGAGCTCA 59.070 37.037 23.31 17.19 34.85 4.26


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

AutoCloner maintained by Alex Coulton.