Multiple sequence alignment - TraesCS7A01G447800

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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 TraesCS7A01G447800 chr7A 100.000 4445 0 0 1 4445 642328431 642323987 0.000000e+00 8209
1 TraesCS7A01G447800 chr7A 82.307 2436 368 35 1057 3455 625603888 625601479 0.000000e+00 2052
2 TraesCS7A01G447800 chr7A 81.957 2422 390 30 997 3390 625535241 625532839 0.000000e+00 2008
3 TraesCS7A01G447800 chr7A 97.719 789 16 2 3506 4294 632189967 632189181 0.000000e+00 1356
4 TraesCS7A01G447800 chr7A 83.461 1439 221 13 994 2425 735764814 735763386 0.000000e+00 1323
5 TraesCS7A01G447800 chr7A 96.831 789 22 3 3507 4295 573610016 573609231 0.000000e+00 1315
6 TraesCS7A01G447800 chr7A 95.094 795 26 7 3503 4295 543441757 543440974 0.000000e+00 1240
7 TraesCS7A01G447800 chr7A 95.652 207 7 2 4091 4296 632189763 632189968 9.220000e-87 331
8 TraesCS7A01G447800 chr7A 86.096 187 25 1 92 278 642325179 642324994 2.710000e-47 200
9 TraesCS7A01G447800 chr7A 92.500 80 6 0 281 360 624820959 624820880 1.010000e-21 115
10 TraesCS7A01G447800 chr7D 96.053 3243 98 14 280 3498 556720334 556717098 0.000000e+00 5252
11 TraesCS7A01G447800 chr7D 87.144 2878 317 35 639 3505 541967218 541964383 0.000000e+00 3216
12 TraesCS7A01G447800 chr7D 85.234 2350 314 19 1174 3505 542099621 542097287 0.000000e+00 2386
13 TraesCS7A01G447800 chr7D 90.876 274 24 1 2 275 556720760 556720488 2.530000e-97 366
14 TraesCS7A01G447800 chr7D 85.561 187 26 1 92 278 556717341 556717156 1.260000e-45 195
15 TraesCS7A01G447800 chr7D 85.484 186 26 1 92 277 541964632 541964448 4.540000e-45 193
16 TraesCS7A01G447800 chr7D 89.535 86 8 1 281 365 541964270 541964185 1.690000e-19 108
17 TraesCS7A01G447800 chr7B 94.481 2881 122 19 639 3498 604101175 604098311 0.000000e+00 4405
18 TraesCS7A01G447800 chr7B 84.813 1982 260 29 639 2612 585515491 585513543 0.000000e+00 1954
19 TraesCS7A01G447800 chr7B 91.204 955 82 2 2551 3504 585579369 585578416 0.000000e+00 1297
20 TraesCS7A01G447800 chr7B 81.421 366 29 23 281 638 604101549 604101215 3.410000e-66 263
21 TraesCS7A01G447800 chr7B 85.484 186 26 1 92 277 604098554 604098370 4.540000e-45 193
22 TraesCS7A01G447800 chr7B 85.207 169 24 1 92 260 585511163 585510996 5.910000e-39 172
23 TraesCS7A01G447800 chrUn 86.125 2400 323 7 994 3388 88864142 88866536 0.000000e+00 2579
24 TraesCS7A01G447800 chrUn 85.948 2021 273 8 994 3008 88843071 88845086 0.000000e+00 2148
25 TraesCS7A01G447800 chrUn 86.454 1757 208 21 1761 3505 365696699 365694961 0.000000e+00 1899
26 TraesCS7A01G447800 chr3A 97.604 793 15 4 3503 4295 311448302 311449090 0.000000e+00 1356
27 TraesCS7A01G447800 chr3A 95.346 795 28 8 3503 4295 131574730 131575517 0.000000e+00 1254
28 TraesCS7A01G447800 chr2A 96.977 794 20 4 3506 4298 636058787 636057997 0.000000e+00 1330
29 TraesCS7A01G447800 chr6A 96.863 797 13 3 3499 4295 453910160 453909376 0.000000e+00 1323
30 TraesCS7A01G447800 chr6A 95.844 818 28 5 3498 4313 401211073 401210260 0.000000e+00 1317
31 TraesCS7A01G447800 chr1A 96.101 795 23 6 3506 4298 316715937 316715149 0.000000e+00 1290


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 TraesCS7A01G447800 chr7A 642323987 642328431 4444 True 4204.500000 8209 93.048000 1 4445 2 chr7A.!!$R8 4444
1 TraesCS7A01G447800 chr7A 625601479 625603888 2409 True 2052.000000 2052 82.307000 1057 3455 1 chr7A.!!$R5 2398
2 TraesCS7A01G447800 chr7A 625532839 625535241 2402 True 2008.000000 2008 81.957000 997 3390 1 chr7A.!!$R4 2393
3 TraesCS7A01G447800 chr7A 632189181 632189967 786 True 1356.000000 1356 97.719000 3506 4294 1 chr7A.!!$R6 788
4 TraesCS7A01G447800 chr7A 735763386 735764814 1428 True 1323.000000 1323 83.461000 994 2425 1 chr7A.!!$R7 1431
5 TraesCS7A01G447800 chr7A 573609231 573610016 785 True 1315.000000 1315 96.831000 3507 4295 1 chr7A.!!$R2 788
6 TraesCS7A01G447800 chr7A 543440974 543441757 783 True 1240.000000 1240 95.094000 3503 4295 1 chr7A.!!$R1 792
7 TraesCS7A01G447800 chr7D 542097287 542099621 2334 True 2386.000000 2386 85.234000 1174 3505 1 chr7D.!!$R1 2331
8 TraesCS7A01G447800 chr7D 556717098 556720760 3662 True 1937.666667 5252 90.830000 2 3498 3 chr7D.!!$R3 3496
9 TraesCS7A01G447800 chr7D 541964185 541967218 3033 True 1172.333333 3216 87.387667 92 3505 3 chr7D.!!$R2 3413
10 TraesCS7A01G447800 chr7B 604098311 604101549 3238 True 1620.333333 4405 87.128667 92 3498 3 chr7B.!!$R3 3406
11 TraesCS7A01G447800 chr7B 585578416 585579369 953 True 1297.000000 1297 91.204000 2551 3504 1 chr7B.!!$R1 953
12 TraesCS7A01G447800 chr7B 585510996 585515491 4495 True 1063.000000 1954 85.010000 92 2612 2 chr7B.!!$R2 2520
13 TraesCS7A01G447800 chrUn 88864142 88866536 2394 False 2579.000000 2579 86.125000 994 3388 1 chrUn.!!$F2 2394
14 TraesCS7A01G447800 chrUn 88843071 88845086 2015 False 2148.000000 2148 85.948000 994 3008 1 chrUn.!!$F1 2014
15 TraesCS7A01G447800 chrUn 365694961 365696699 1738 True 1899.000000 1899 86.454000 1761 3505 1 chrUn.!!$R1 1744
16 TraesCS7A01G447800 chr3A 311448302 311449090 788 False 1356.000000 1356 97.604000 3503 4295 1 chr3A.!!$F2 792
17 TraesCS7A01G447800 chr3A 131574730 131575517 787 False 1254.000000 1254 95.346000 3503 4295 1 chr3A.!!$F1 792
18 TraesCS7A01G447800 chr2A 636057997 636058787 790 True 1330.000000 1330 96.977000 3506 4298 1 chr2A.!!$R1 792
19 TraesCS7A01G447800 chr6A 453909376 453910160 784 True 1323.000000 1323 96.863000 3499 4295 1 chr6A.!!$R2 796
20 TraesCS7A01G447800 chr6A 401210260 401211073 813 True 1317.000000 1317 95.844000 3498 4313 1 chr6A.!!$R1 815
21 TraesCS7A01G447800 chr1A 316715149 316715937 788 True 1290.000000 1290 96.101000 3506 4298 1 chr1A.!!$R1 792

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
216 217 0.036010 GCCAAGACTGCTCCAAGCTA 60.036 55.0 0.11 0.00 42.97 3.32 F
243 244 0.039256 AAGCGCGCATTCAACATGTT 60.039 45.0 35.10 11.75 0.00 2.71 F
1581 1861 0.178903 AGCAGTTAGACCCCAGTGGA 60.179 55.0 11.95 0.00 38.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 2420 0.457035 AGGCAAACTTGTGCACACTG 59.543 50.000 21.56 17.65 46.81 3.66 R
2234 2517 1.962807 TGCCACTGCATTTTAGTGCTT 59.037 42.857 0.00 0.00 44.23 3.91 R
3524 5557 1.930914 ACTAGGGCTAGAGTTGAGGGA 59.069 52.381 0.00 0.00 36.97 4.20 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
33 34 8.558700 ACCAATTCATAATTTTGTTGTTGAAGC 58.441 29.630 9.95 0.00 0.00 3.86
46 47 6.872920 TGTTGTTGAAGCTAGGTTTCAAATT 58.127 32.000 8.87 0.00 42.43 1.82
54 55 3.996363 GCTAGGTTTCAAATTTTGCTGGG 59.004 43.478 4.19 0.00 0.00 4.45
56 57 4.071961 AGGTTTCAAATTTTGCTGGGTC 57.928 40.909 4.19 0.00 0.00 4.46
60 61 5.356751 GGTTTCAAATTTTGCTGGGTCTTTT 59.643 36.000 4.19 0.00 0.00 2.27
66 67 8.156165 TCAAATTTTGCTGGGTCTTTTTGATAT 58.844 29.630 4.19 0.00 29.62 1.63
99 100 2.228822 CTGTCCATGGTTACAAGGTTGC 59.771 50.000 12.58 0.00 36.82 4.17
100 101 2.235016 GTCCATGGTTACAAGGTTGCA 58.765 47.619 12.58 0.00 36.82 4.08
130 131 4.811024 TGCATCGAAGATGATAAGGTTGAC 59.189 41.667 13.56 0.00 45.12 3.18
144 145 1.071642 TTGACCGGCCAACAATCGA 59.928 52.632 0.00 0.00 0.00 3.59
152 153 1.086696 GCCAACAATCGAGCAGCTAA 58.913 50.000 0.00 0.00 0.00 3.09
167 168 4.574013 AGCAGCTAATTCGGATTCTTGAAG 59.426 41.667 0.00 0.00 0.00 3.02
187 188 4.851639 AGGGCTAGTTGAGATCACAATT 57.148 40.909 8.86 7.43 32.36 2.32
188 189 5.184892 AGGGCTAGTTGAGATCACAATTT 57.815 39.130 8.86 3.93 32.36 1.82
192 193 4.336713 GCTAGTTGAGATCACAATTTCCCC 59.663 45.833 8.86 0.00 32.36 4.81
193 194 3.701664 AGTTGAGATCACAATTTCCCCC 58.298 45.455 8.86 0.00 32.36 5.40
195 196 3.824001 TGAGATCACAATTTCCCCCAA 57.176 42.857 0.00 0.00 0.00 4.12
196 197 3.430453 TGAGATCACAATTTCCCCCAAC 58.570 45.455 0.00 0.00 0.00 3.77
197 198 2.423538 GAGATCACAATTTCCCCCAACG 59.576 50.000 0.00 0.00 0.00 4.10
199 200 1.182385 TCACAATTTCCCCCAACGCC 61.182 55.000 0.00 0.00 0.00 5.68
201 202 0.760945 ACAATTTCCCCCAACGCCAA 60.761 50.000 0.00 0.00 0.00 4.52
202 203 0.037419 CAATTTCCCCCAACGCCAAG 60.037 55.000 0.00 0.00 0.00 3.61
203 204 0.178947 AATTTCCCCCAACGCCAAGA 60.179 50.000 0.00 0.00 0.00 3.02
204 205 0.898326 ATTTCCCCCAACGCCAAGAC 60.898 55.000 0.00 0.00 0.00 3.01
205 206 2.002018 TTTCCCCCAACGCCAAGACT 62.002 55.000 0.00 0.00 0.00 3.24
206 207 2.672996 CCCCCAACGCCAAGACTG 60.673 66.667 0.00 0.00 0.00 3.51
207 208 3.365265 CCCCAACGCCAAGACTGC 61.365 66.667 0.00 0.00 0.00 4.40
208 209 2.281761 CCCAACGCCAAGACTGCT 60.282 61.111 0.00 0.00 0.00 4.24
210 211 2.328099 CCAACGCCAAGACTGCTCC 61.328 63.158 0.00 0.00 0.00 4.70
212 213 1.148273 AACGCCAAGACTGCTCCAA 59.852 52.632 0.00 0.00 0.00 3.53
213 214 0.886490 AACGCCAAGACTGCTCCAAG 60.886 55.000 0.00 0.00 0.00 3.61
214 215 2.684843 CGCCAAGACTGCTCCAAGC 61.685 63.158 0.00 0.00 42.82 4.01
215 216 1.303155 GCCAAGACTGCTCCAAGCT 60.303 57.895 0.11 0.00 42.97 3.74
216 217 0.036010 GCCAAGACTGCTCCAAGCTA 60.036 55.000 0.11 0.00 42.97 3.32
217 218 1.407989 GCCAAGACTGCTCCAAGCTAT 60.408 52.381 0.11 0.00 42.97 2.97
237 238 2.869646 CTGGAAGCGCGCATTCAA 59.130 55.556 35.10 23.75 0.00 2.69
238 239 1.512734 CTGGAAGCGCGCATTCAAC 60.513 57.895 35.10 19.54 0.00 3.18
239 240 2.186350 CTGGAAGCGCGCATTCAACA 62.186 55.000 35.10 22.41 0.00 3.33
240 241 1.137404 GGAAGCGCGCATTCAACAT 59.863 52.632 35.10 6.63 0.00 2.71
241 242 1.135699 GGAAGCGCGCATTCAACATG 61.136 55.000 35.10 0.00 0.00 3.21
243 244 0.039256 AAGCGCGCATTCAACATGTT 60.039 45.000 35.10 11.75 0.00 2.71
245 246 1.405469 GCGCGCATTCAACATGTTCC 61.405 55.000 29.10 0.00 0.00 3.62
272 273 3.414549 GTTTCAGGAAAACGAGTTGCA 57.585 42.857 0.00 0.00 38.06 4.08
273 274 3.964909 GTTTCAGGAAAACGAGTTGCAT 58.035 40.909 0.00 0.00 38.06 3.96
274 275 5.103290 GTTTCAGGAAAACGAGTTGCATA 57.897 39.130 0.00 0.00 38.06 3.14
275 276 5.147162 GTTTCAGGAAAACGAGTTGCATAG 58.853 41.667 0.00 0.00 38.06 2.23
276 277 2.742053 TCAGGAAAACGAGTTGCATAGC 59.258 45.455 0.00 0.00 0.00 2.97
277 278 1.732259 AGGAAAACGAGTTGCATAGCG 59.268 47.619 0.00 0.00 0.00 4.26
279 280 0.802494 AAAACGAGTTGCATAGCGGG 59.198 50.000 7.38 0.00 0.00 6.13
280 281 0.321298 AAACGAGTTGCATAGCGGGT 60.321 50.000 7.38 0.00 0.00 5.28
281 282 0.533491 AACGAGTTGCATAGCGGGTA 59.467 50.000 7.38 0.00 0.00 3.69
284 285 2.210116 CGAGTTGCATAGCGGGTATTT 58.790 47.619 0.00 0.00 0.00 1.40
295 444 3.532542 AGCGGGTATTTCAGTTTAGCTC 58.467 45.455 0.00 0.00 0.00 4.09
384 533 9.612066 TTGTTTTGCCTTTTTGAAAGAGATTAT 57.388 25.926 0.00 0.00 0.00 1.28
627 786 5.109903 ACGTCACTCTTATCATTAAGCCAC 58.890 41.667 0.00 0.00 35.72 5.01
643 845 7.837202 TTAAGCCACACATACACATTAGTAC 57.163 36.000 0.00 0.00 0.00 2.73
653 855 6.759827 ACATACACATTAGTACCCAACGAATC 59.240 38.462 0.00 0.00 31.79 2.52
660 862 3.714391 AGTACCCAACGAATCGCTATTC 58.286 45.455 1.15 0.90 38.53 1.75
661 863 2.684001 ACCCAACGAATCGCTATTCA 57.316 45.000 11.13 0.00 41.44 2.57
728 933 2.517450 GCGACGGCCAGATTTCGAG 61.517 63.158 2.24 0.00 33.20 4.04
732 937 0.736325 ACGGCCAGATTTCGAGTTCG 60.736 55.000 2.24 0.00 41.45 3.95
781 988 2.124942 CCCAGCGCTCTTCTTCCC 60.125 66.667 7.13 0.00 0.00 3.97
821 1028 2.126346 GCAAATCCTGCCGTGCAC 60.126 61.111 6.82 6.82 46.13 4.57
897 1144 1.331756 GTTGTGCTTGACTCCACAGTG 59.668 52.381 0.00 0.00 42.29 3.66
898 1145 0.815213 TGTGCTTGACTCCACAGTGC 60.815 55.000 0.00 0.00 37.07 4.40
899 1146 1.227943 TGCTTGACTCCACAGTGCC 60.228 57.895 0.00 0.00 30.63 5.01
900 1147 1.227943 GCTTGACTCCACAGTGCCA 60.228 57.895 0.00 0.00 30.63 4.92
901 1148 0.607489 GCTTGACTCCACAGTGCCAT 60.607 55.000 0.00 0.00 30.63 4.40
902 1149 1.162698 CTTGACTCCACAGTGCCATG 58.837 55.000 0.00 0.00 30.63 3.66
903 1150 0.250858 TTGACTCCACAGTGCCATGG 60.251 55.000 7.63 7.63 37.32 3.66
904 1151 2.034687 ACTCCACAGTGCCATGGC 59.965 61.111 30.54 30.54 42.35 4.40
905 1152 2.753043 CTCCACAGTGCCATGGCC 60.753 66.667 33.44 23.56 41.09 5.36
906 1153 4.720902 TCCACAGTGCCATGGCCG 62.721 66.667 33.44 23.12 41.09 6.13
911 1158 4.790962 AGTGCCATGGCCGCTCAG 62.791 66.667 33.44 0.00 41.09 3.35
952 1199 0.592247 GCCTCTGCACAACAACAACG 60.592 55.000 0.00 0.00 37.47 4.10
1196 1461 1.942657 CCTCGGCATATGGTTCAACAG 59.057 52.381 4.56 0.00 0.00 3.16
1282 1554 0.908198 AGAGCTCACAATCTCCCACC 59.092 55.000 17.77 0.00 0.00 4.61
1302 1575 1.197721 CACGGCAACCTTGTCATCTTC 59.802 52.381 0.00 0.00 31.86 2.87
1414 1690 3.753294 TCCTGACAGACTCTTCAAACC 57.247 47.619 3.32 0.00 0.00 3.27
1581 1861 0.178903 AGCAGTTAGACCCCAGTGGA 60.179 55.000 11.95 0.00 38.00 4.02
1904 2187 3.509575 GTCCATGCAATTTGTGGTCCTTA 59.490 43.478 3.30 0.00 34.61 2.69
2034 2317 7.282450 TCGAGAAATACTCAGTTAGACTGCATA 59.718 37.037 3.26 0.00 45.54 3.14
2216 2499 5.163488 ACAATGGATGTTTCATGTGGCATAG 60.163 40.000 0.00 0.00 40.06 2.23
2234 2517 6.152492 TGGCATAGTGAATTGCTCAACATAAA 59.848 34.615 0.00 0.00 38.88 1.40
2612 4636 1.701847 AGTGAAGAGGCTTGATGGTGT 59.298 47.619 0.00 0.00 0.00 4.16
2890 4917 5.988287 TCATACACTGTGATATCAAGCCAA 58.012 37.500 15.86 0.00 0.00 4.52
3349 5376 3.521126 AGGGCTAGTTGAGATCACAATGT 59.479 43.478 8.86 2.92 32.36 2.71
3456 5487 7.201644 GCATTGCGCACCTAGACATTATAATAT 60.202 37.037 11.12 0.00 41.79 1.28
3457 5488 9.313118 CATTGCGCACCTAGACATTATAATATA 57.687 33.333 11.12 0.00 0.00 0.86
3458 5489 8.697846 TTGCGCACCTAGACATTATAATATAC 57.302 34.615 11.12 0.00 0.00 1.47
3846 5882 0.389391 CCCTCAGTCACTGTTCACGT 59.611 55.000 4.28 0.00 32.61 4.49
4258 6300 6.464039 GGAGTTGGGGGTTGTATATTAGACTC 60.464 46.154 0.00 0.00 0.00 3.36
4295 6337 4.051922 GGGTGTAATATGCACTTCTCTCG 58.948 47.826 9.60 0.00 37.07 4.04
4301 6343 7.010552 GTGTAATATGCACTTCTCTCGATTTGT 59.989 37.037 0.00 0.00 34.30 2.83
4306 6348 4.093408 TGCACTTCTCTCGATTTGTAATGC 59.907 41.667 0.00 0.00 0.00 3.56
4309 6351 6.036083 GCACTTCTCTCGATTTGTAATGCTTA 59.964 38.462 0.00 0.00 0.00 3.09
4310 6352 7.254590 GCACTTCTCTCGATTTGTAATGCTTAT 60.255 37.037 0.00 0.00 0.00 1.73
4313 6355 7.700322 TCTCTCGATTTGTAATGCTTATGAC 57.300 36.000 0.00 0.00 0.00 3.06
4318 6360 8.437360 TCGATTTGTAATGCTTATGACTGAAT 57.563 30.769 0.00 0.00 0.00 2.57
4329 6371 8.840833 TGCTTATGACTGAATAAACAACTGTA 57.159 30.769 0.00 0.00 0.00 2.74
4372 6414 8.777578 ACTGTATATCTTAATGTACCCTCACA 57.222 34.615 0.00 0.00 30.61 3.58
4374 6416 8.777578 TGTATATCTTAATGTACCCTCACAGT 57.222 34.615 0.00 0.00 30.61 3.55
4375 6417 8.857098 TGTATATCTTAATGTACCCTCACAGTC 58.143 37.037 0.00 0.00 30.61 3.51
4376 6418 7.914427 ATATCTTAATGTACCCTCACAGTCA 57.086 36.000 0.00 0.00 0.00 3.41
4377 6419 5.401531 TCTTAATGTACCCTCACAGTCAC 57.598 43.478 0.00 0.00 0.00 3.67
4378 6420 4.836175 TCTTAATGTACCCTCACAGTCACA 59.164 41.667 0.00 0.00 0.00 3.58
4379 6421 3.685139 AATGTACCCTCACAGTCACAG 57.315 47.619 0.00 0.00 0.00 3.66
4380 6422 0.679505 TGTACCCTCACAGTCACAGC 59.320 55.000 0.00 0.00 0.00 4.40
4381 6423 0.679505 GTACCCTCACAGTCACAGCA 59.320 55.000 0.00 0.00 0.00 4.41
4382 6424 1.276421 GTACCCTCACAGTCACAGCAT 59.724 52.381 0.00 0.00 0.00 3.79
4397 6439 6.644181 AGTCACAGCATCATCGTTATAATCTG 59.356 38.462 0.00 0.00 0.00 2.90
4400 6442 6.592994 CACAGCATCATCGTTATAATCTGGAT 59.407 38.462 0.00 0.00 0.00 3.41
4402 6444 7.040494 CAGCATCATCGTTATAATCTGGATCT 58.960 38.462 0.00 0.00 0.00 2.75
4403 6445 7.010275 CAGCATCATCGTTATAATCTGGATCTG 59.990 40.741 0.00 0.00 0.00 2.90
4404 6446 6.257411 GCATCATCGTTATAATCTGGATCTGG 59.743 42.308 0.00 0.00 0.00 3.86
4406 6448 7.163001 TCATCGTTATAATCTGGATCTGGAG 57.837 40.000 0.00 0.00 0.00 3.86
4407 6449 5.392767 TCGTTATAATCTGGATCTGGAGC 57.607 43.478 0.00 0.00 0.00 4.70
4408 6450 4.220821 TCGTTATAATCTGGATCTGGAGCC 59.779 45.833 0.00 0.00 37.40 4.70
4409 6451 4.021104 CGTTATAATCTGGATCTGGAGCCA 60.021 45.833 7.38 7.38 45.85 4.75
4410 6452 5.337894 CGTTATAATCTGGATCTGGAGCCAT 60.338 44.000 8.06 0.00 46.90 4.40
4411 6453 6.127338 CGTTATAATCTGGATCTGGAGCCATA 60.127 42.308 8.06 1.80 46.90 2.74
4412 6454 7.418368 CGTTATAATCTGGATCTGGAGCCATAT 60.418 40.741 8.06 4.16 46.90 1.78
4413 6455 6.905067 ATAATCTGGATCTGGAGCCATATT 57.095 37.500 17.85 17.85 46.90 1.28
4414 6456 4.840716 ATCTGGATCTGGAGCCATATTC 57.159 45.455 8.06 0.00 46.90 1.75
4440 6482 7.755373 CGAAATAGGCGTCATAGATATTTCAGA 59.245 37.037 14.98 0.00 40.44 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.558700 GCTTCAACAACAAAATTATGAATTGGT 58.441 29.630 0.00 0.00 0.00 3.67
17 18 7.327214 TGAAACCTAGCTTCAACAACAAAATT 58.673 30.769 0.00 0.00 29.93 1.82
33 34 5.011023 AGACCCAGCAAAATTTGAAACCTAG 59.989 40.000 10.26 0.00 0.00 3.02
46 47 6.211184 ACATGATATCAAAAAGACCCAGCAAA 59.789 34.615 9.99 0.00 0.00 3.68
60 61 9.444600 CATGGACAGATGAATACATGATATCAA 57.555 33.333 9.99 0.00 38.29 2.57
66 67 5.635278 ACCATGGACAGATGAATACATGA 57.365 39.130 21.47 0.00 38.29 3.07
85 86 1.402259 CAACGTGCAACCTTGTAACCA 59.598 47.619 0.00 0.00 29.85 3.67
99 100 1.078709 ATCTTCGATGCACCAACGTG 58.921 50.000 0.00 0.00 43.35 4.49
100 101 1.078709 CATCTTCGATGCACCAACGT 58.921 50.000 0.00 0.00 31.79 3.99
115 116 1.141053 GGCCGGTCAACCTTATCATCT 59.859 52.381 0.00 0.00 0.00 2.90
130 131 2.745884 TGCTCGATTGTTGGCCGG 60.746 61.111 0.00 0.00 0.00 6.13
144 145 4.142609 TCAAGAATCCGAATTAGCTGCT 57.857 40.909 7.57 7.57 0.00 4.24
152 153 3.456277 ACTAGCCCTTCAAGAATCCGAAT 59.544 43.478 0.00 0.00 0.00 3.34
167 168 4.336713 GGAAATTGTGATCTCAACTAGCCC 59.663 45.833 12.15 6.47 0.00 5.19
187 188 2.114411 GTCTTGGCGTTGGGGGAA 59.886 61.111 0.00 0.00 0.00 3.97
188 189 2.852075 AGTCTTGGCGTTGGGGGA 60.852 61.111 0.00 0.00 0.00 4.81
192 193 2.328099 GGAGCAGTCTTGGCGTTGG 61.328 63.158 0.00 0.00 36.08 3.77
193 194 1.165907 TTGGAGCAGTCTTGGCGTTG 61.166 55.000 0.00 0.00 36.08 4.10
195 196 1.302033 CTTGGAGCAGTCTTGGCGT 60.302 57.895 0.00 0.00 36.08 5.68
196 197 2.684843 GCTTGGAGCAGTCTTGGCG 61.685 63.158 0.00 0.00 41.89 5.69
197 198 0.036010 TAGCTTGGAGCAGTCTTGGC 60.036 55.000 0.00 0.00 45.56 4.52
213 214 3.643978 CGCGCTTCCAGCCATAGC 61.644 66.667 5.56 0.00 38.18 2.97
214 215 3.643978 GCGCGCTTCCAGCCATAG 61.644 66.667 26.67 0.00 38.18 2.23
215 216 3.755526 ATGCGCGCTTCCAGCCATA 62.756 57.895 33.29 7.91 38.18 2.74
219 220 3.326889 TTGAATGCGCGCTTCCAGC 62.327 57.895 33.29 15.80 38.02 4.85
221 222 1.585267 ATGTTGAATGCGCGCTTCCA 61.585 50.000 33.29 18.46 0.00 3.53
223 224 0.454957 ACATGTTGAATGCGCGCTTC 60.455 50.000 33.29 28.87 0.00 3.86
225 226 0.454957 GAACATGTTGAATGCGCGCT 60.455 50.000 33.29 13.70 0.00 5.92
226 227 1.405469 GGAACATGTTGAATGCGCGC 61.405 55.000 27.26 27.26 0.00 6.86
227 228 0.168788 AGGAACATGTTGAATGCGCG 59.831 50.000 17.58 0.00 0.00 6.86
228 229 2.352503 AAGGAACATGTTGAATGCGC 57.647 45.000 17.58 0.00 0.00 6.09
251 252 2.750166 TGCAACTCGTTTTCCTGAAACA 59.250 40.909 3.00 0.00 46.39 2.83
252 253 3.414549 TGCAACTCGTTTTCCTGAAAC 57.585 42.857 0.00 0.00 43.36 2.78
255 256 2.742053 GCTATGCAACTCGTTTTCCTGA 59.258 45.455 0.00 0.00 0.00 3.86
256 257 2.474526 CGCTATGCAACTCGTTTTCCTG 60.475 50.000 0.00 0.00 0.00 3.86
257 258 1.732259 CGCTATGCAACTCGTTTTCCT 59.268 47.619 0.00 0.00 0.00 3.36
258 259 1.202031 CCGCTATGCAACTCGTTTTCC 60.202 52.381 0.00 0.00 0.00 3.13
259 260 1.202031 CCCGCTATGCAACTCGTTTTC 60.202 52.381 0.00 0.00 0.00 2.29
263 264 0.750850 ATACCCGCTATGCAACTCGT 59.249 50.000 0.00 0.00 0.00 4.18
264 265 1.865865 AATACCCGCTATGCAACTCG 58.134 50.000 0.00 0.00 0.00 4.18
265 266 3.202906 TGAAATACCCGCTATGCAACTC 58.797 45.455 0.00 0.00 0.00 3.01
266 267 3.206150 CTGAAATACCCGCTATGCAACT 58.794 45.455 0.00 0.00 0.00 3.16
267 268 2.943033 ACTGAAATACCCGCTATGCAAC 59.057 45.455 0.00 0.00 0.00 4.17
269 270 3.275617 AACTGAAATACCCGCTATGCA 57.724 42.857 0.00 0.00 0.00 3.96
270 271 4.319549 GCTAAACTGAAATACCCGCTATGC 60.320 45.833 0.00 0.00 0.00 3.14
271 272 5.057149 AGCTAAACTGAAATACCCGCTATG 58.943 41.667 0.00 0.00 0.00 2.23
272 273 5.070580 AGAGCTAAACTGAAATACCCGCTAT 59.929 40.000 0.00 0.00 0.00 2.97
273 274 4.404715 AGAGCTAAACTGAAATACCCGCTA 59.595 41.667 0.00 0.00 0.00 4.26
274 275 3.197983 AGAGCTAAACTGAAATACCCGCT 59.802 43.478 0.00 0.00 0.00 5.52
275 276 3.532542 AGAGCTAAACTGAAATACCCGC 58.467 45.455 0.00 0.00 0.00 6.13
276 277 5.903810 AGTAGAGCTAAACTGAAATACCCG 58.096 41.667 0.00 0.00 0.00 5.28
277 278 9.096160 GTTAAGTAGAGCTAAACTGAAATACCC 57.904 37.037 1.38 0.00 0.00 3.69
281 282 9.944376 TCATGTTAAGTAGAGCTAAACTGAAAT 57.056 29.630 1.38 0.00 0.00 2.17
284 285 9.944376 ATTTCATGTTAAGTAGAGCTAAACTGA 57.056 29.630 1.38 0.00 0.00 3.41
384 533 3.557054 CCTGCTAGCTGTTGTAACAAGGA 60.557 47.826 17.23 0.00 38.66 3.36
508 657 2.447887 CGCTGTCTTGGCAGTAGCG 61.448 63.158 17.48 17.48 43.22 4.26
515 664 1.023513 AAGATGAGCGCTGTCTTGGC 61.024 55.000 25.55 8.22 31.41 4.52
519 668 4.802424 CGAAGATGAGCGCTGTCT 57.198 55.556 18.48 15.87 0.00 3.41
576 731 7.209471 TCCTTTTGTTTGGTGTACATGTATC 57.791 36.000 9.18 5.73 0.00 2.24
627 786 5.412640 TCGTTGGGTACTAATGTGTATGTG 58.587 41.667 0.00 0.00 37.12 3.21
643 845 2.276201 TGTGAATAGCGATTCGTTGGG 58.724 47.619 13.86 0.00 43.92 4.12
653 855 2.076100 TCTTTGCACCTGTGAATAGCG 58.924 47.619 0.51 0.00 0.00 4.26
728 933 0.320160 AGTTGGCTTACCGGTCGAAC 60.320 55.000 12.40 11.13 39.70 3.95
732 937 2.038837 GGCAGTTGGCTTACCGGTC 61.039 63.158 12.40 0.00 44.01 4.79
771 978 1.076438 AAAGGGTGGGGGAAGAAGAG 58.924 55.000 0.00 0.00 0.00 2.85
781 988 1.623311 GGTGGAAATGAAAAGGGTGGG 59.377 52.381 0.00 0.00 0.00 4.61
903 1150 2.593468 TAGATTGGGTGCTGAGCGGC 62.593 60.000 0.00 0.00 0.00 6.53
904 1151 0.107456 ATAGATTGGGTGCTGAGCGG 59.893 55.000 0.00 0.00 0.00 5.52
905 1152 2.224042 TGTATAGATTGGGTGCTGAGCG 60.224 50.000 0.00 0.00 0.00 5.03
906 1153 3.475566 TGTATAGATTGGGTGCTGAGC 57.524 47.619 0.00 0.00 0.00 4.26
907 1154 5.471456 GGAAATGTATAGATTGGGTGCTGAG 59.529 44.000 0.00 0.00 0.00 3.35
908 1155 5.104151 TGGAAATGTATAGATTGGGTGCTGA 60.104 40.000 0.00 0.00 0.00 4.26
909 1156 5.132502 TGGAAATGTATAGATTGGGTGCTG 58.867 41.667 0.00 0.00 0.00 4.41
910 1157 5.380043 CTGGAAATGTATAGATTGGGTGCT 58.620 41.667 0.00 0.00 0.00 4.40
911 1158 4.022849 GCTGGAAATGTATAGATTGGGTGC 60.023 45.833 0.00 0.00 0.00 5.01
912 1159 4.520492 GGCTGGAAATGTATAGATTGGGTG 59.480 45.833 0.00 0.00 0.00 4.61
913 1160 4.416848 AGGCTGGAAATGTATAGATTGGGT 59.583 41.667 0.00 0.00 0.00 4.51
914 1161 4.990526 AGGCTGGAAATGTATAGATTGGG 58.009 43.478 0.00 0.00 0.00 4.12
915 1162 5.704515 CAGAGGCTGGAAATGTATAGATTGG 59.295 44.000 0.00 0.00 0.00 3.16
916 1163 5.180868 GCAGAGGCTGGAAATGTATAGATTG 59.819 44.000 0.00 0.00 36.96 2.67
917 1164 5.163163 TGCAGAGGCTGGAAATGTATAGATT 60.163 40.000 0.00 0.00 41.91 2.40
918 1165 4.349048 TGCAGAGGCTGGAAATGTATAGAT 59.651 41.667 0.00 0.00 41.91 1.98
919 1166 3.711190 TGCAGAGGCTGGAAATGTATAGA 59.289 43.478 0.00 0.00 41.91 1.98
1196 1461 2.489722 GCTGAAGTGAATTTGGGGACTC 59.510 50.000 0.00 0.00 0.00 3.36
1245 1517 2.894126 CTCTAGTGAGGTGGTGTTCTGT 59.106 50.000 0.00 0.00 36.70 3.41
1246 1518 2.353208 GCTCTAGTGAGGTGGTGTTCTG 60.353 54.545 0.00 0.00 40.53 3.02
1282 1554 1.197721 GAAGATGACAAGGTTGCCGTG 59.802 52.381 0.00 0.00 38.88 4.94
1302 1575 1.883021 GGATTTGGCAGACCGGTTG 59.117 57.895 9.42 10.53 39.70 3.77
1581 1861 8.823220 ATGCTACAAGAAATACCTGGTTAATT 57.177 30.769 3.84 0.00 0.00 1.40
1904 2187 6.864685 CACTTCATTATCAGTGCAAATTGTGT 59.135 34.615 0.00 0.00 34.33 3.72
1990 2273 3.061848 GCACCCACCCAACCGATG 61.062 66.667 0.00 0.00 0.00 3.84
2034 2317 2.736192 GTGTGTTGTGCTTTTGTTGCTT 59.264 40.909 0.00 0.00 0.00 3.91
2137 2420 0.457035 AGGCAAACTTGTGCACACTG 59.543 50.000 21.56 17.65 46.81 3.66
2216 2499 5.922544 AGTGCTTTTATGTTGAGCAATTCAC 59.077 36.000 0.00 0.00 46.77 3.18
2234 2517 1.962807 TGCCACTGCATTTTAGTGCTT 59.037 42.857 0.00 0.00 44.23 3.91
2612 4636 7.397221 TCTGAATTGCTTCTCTCCTTGATAAA 58.603 34.615 0.00 0.00 32.29 1.40
2890 4917 9.415544 GAGTGAAGCATCAAGAAATATGTTTTT 57.584 29.630 0.00 0.00 37.30 1.94
2899 4926 4.074970 GGAAGGAGTGAAGCATCAAGAAA 58.925 43.478 0.00 0.00 37.30 2.52
3113 5140 5.457633 GGGTTGCCACCACTAGGATATAAAT 60.458 44.000 9.52 0.00 46.43 1.40
3349 5376 2.025155 GAGCAGTCTTGGTATCGGAGA 58.975 52.381 0.00 0.00 36.39 3.71
3489 5522 8.012241 GCACTTTTCTCTTACAAATCTGTAGTG 58.988 37.037 0.00 0.00 39.21 2.74
3509 5542 6.426587 AGTTGAGGGATGTAATATGCACTTT 58.573 36.000 0.00 0.00 0.00 2.66
3524 5557 1.930914 ACTAGGGCTAGAGTTGAGGGA 59.069 52.381 0.00 0.00 36.97 4.20
4258 6300 1.686110 ACCCCTCAACTCTAGCCCG 60.686 63.158 0.00 0.00 0.00 6.13
4309 6351 9.507329 ACAGAATACAGTTGTTTATTCAGTCAT 57.493 29.630 9.31 0.00 32.88 3.06
4310 6352 8.902540 ACAGAATACAGTTGTTTATTCAGTCA 57.097 30.769 9.31 0.00 32.88 3.41
4350 6392 8.857098 TGACTGTGAGGGTACATTAAGATATAC 58.143 37.037 0.00 0.00 0.00 1.47
4359 6401 2.289694 GCTGTGACTGTGAGGGTACATT 60.290 50.000 0.00 0.00 0.00 2.71
4372 6414 6.644181 CAGATTATAACGATGATGCTGTGACT 59.356 38.462 0.00 0.00 0.00 3.41
4374 6416 5.928264 CCAGATTATAACGATGATGCTGTGA 59.072 40.000 0.00 0.00 0.00 3.58
4375 6417 5.928264 TCCAGATTATAACGATGATGCTGTG 59.072 40.000 0.00 0.00 0.00 3.66
4376 6418 6.101650 TCCAGATTATAACGATGATGCTGT 57.898 37.500 0.00 0.00 0.00 4.40
4377 6419 7.010275 CAGATCCAGATTATAACGATGATGCTG 59.990 40.741 0.00 0.00 0.00 4.41
4378 6420 7.040494 CAGATCCAGATTATAACGATGATGCT 58.960 38.462 0.00 0.00 0.00 3.79
4379 6421 6.257411 CCAGATCCAGATTATAACGATGATGC 59.743 42.308 0.00 0.00 0.00 3.91
4380 6422 7.550712 TCCAGATCCAGATTATAACGATGATG 58.449 38.462 0.00 0.00 0.00 3.07
4381 6423 7.632462 GCTCCAGATCCAGATTATAACGATGAT 60.632 40.741 0.00 0.00 0.00 2.45
4382 6424 6.350528 GCTCCAGATCCAGATTATAACGATGA 60.351 42.308 0.00 0.00 0.00 2.92
4397 6439 3.685139 TTCGAATATGGCTCCAGATCC 57.315 47.619 0.00 0.00 0.00 3.36
4400 6442 4.563580 GCCTATTTCGAATATGGCTCCAGA 60.564 45.833 21.05 0.00 37.58 3.86
4402 6444 3.674997 GCCTATTTCGAATATGGCTCCA 58.325 45.455 21.05 0.00 37.58 3.86
4403 6445 2.673368 CGCCTATTTCGAATATGGCTCC 59.327 50.000 23.65 5.91 38.33 4.70
4404 6446 3.326747 ACGCCTATTTCGAATATGGCTC 58.673 45.455 23.65 6.41 38.33 4.70
4406 6448 3.064207 TGACGCCTATTTCGAATATGGC 58.936 45.455 19.41 19.41 37.24 4.40
4407 6449 6.330278 TCTATGACGCCTATTTCGAATATGG 58.670 40.000 0.00 2.53 0.00 2.74
4408 6450 7.993821 ATCTATGACGCCTATTTCGAATATG 57.006 36.000 0.00 0.00 0.00 1.78
4411 6453 9.088512 GAAATATCTATGACGCCTATTTCGAAT 57.911 33.333 0.00 0.00 32.36 3.34
4412 6454 8.085909 TGAAATATCTATGACGCCTATTTCGAA 58.914 33.333 0.00 0.00 39.75 3.71
4413 6455 7.599171 TGAAATATCTATGACGCCTATTTCGA 58.401 34.615 0.00 0.00 39.75 3.71
4414 6456 7.755373 TCTGAAATATCTATGACGCCTATTTCG 59.245 37.037 0.00 0.00 39.75 3.46


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

AutoCloner maintained by Alex Coulton.