Multiple sequence alignment - TraesCS7D01G376500

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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 TraesCS7D01G376500 chr7D 100.000 5289 0 0 1 5289 486732118 486726830 0.000000e+00 9768.0
1 TraesCS7D01G376500 chr7D 87.014 2364 267 23 204 2547 486306198 486308541 0.000000e+00 2628.0
2 TraesCS7D01G376500 chr7D 87.410 1390 157 10 3218 4593 486308911 486310296 0.000000e+00 1581.0
3 TraesCS7D01G376500 chr7D 98.179 604 10 1 4686 5289 486720102 486719500 0.000000e+00 1053.0
4 TraesCS7D01G376500 chr7D 98.176 603 11 0 4687 5289 488143743 488144345 0.000000e+00 1053.0
5 TraesCS7D01G376500 chr7D 95.380 606 24 4 4686 5289 184307001 184306398 0.000000e+00 961.0
6 TraesCS7D01G376500 chr7D 87.822 427 43 2 3218 3635 119753476 119753902 4.760000e-135 492.0
7 TraesCS7D01G376500 chr7D 87.871 404 40 2 3218 3612 110449428 110449025 2.880000e-127 466.0
8 TraesCS7D01G376500 chr7D 87.755 392 39 2 3218 3600 549105195 549105586 2.910000e-122 449.0
9 TraesCS7D01G376500 chr7D 73.764 789 169 23 1095 1872 486242824 486242063 5.220000e-70 276.0
10 TraesCS7D01G376500 chr7D 100.000 90 0 0 4599 4688 486677155 486677066 3.280000e-37 167.0
11 TraesCS7D01G376500 chr7B 92.494 4623 296 30 1 4599 516446665 516442070 0.000000e+00 6567.0
12 TraesCS7D01G376500 chr7B 86.331 1390 171 11 3218 4593 514255146 514256530 0.000000e+00 1496.0
13 TraesCS7D01G376500 chr7B 85.437 1133 137 18 204 1333 514248271 514249378 0.000000e+00 1153.0
14 TraesCS7D01G376500 chr7B 84.459 1036 153 6 1328 2360 514249848 514250878 0.000000e+00 1014.0
15 TraesCS7D01G376500 chr7B 85.784 204 20 5 2356 2552 514253501 514253702 1.930000e-49 207.0
16 TraesCS7D01G376500 chr7B 84.135 208 17 7 1 206 514248034 514248227 2.510000e-43 187.0
17 TraesCS7D01G376500 chr7A 92.836 2331 141 12 2288 4599 555624080 555621757 0.000000e+00 3356.0
18 TraesCS7D01G376500 chr7A 91.464 2015 162 8 211 2224 555626087 555624082 0.000000e+00 2760.0
19 TraesCS7D01G376500 chr7A 86.664 2362 277 17 204 2551 555437098 555439435 0.000000e+00 2582.0
20 TraesCS7D01G376500 chr7A 87.432 1281 143 12 3325 4591 555439929 555441205 0.000000e+00 1458.0
21 TraesCS7D01G376500 chr7A 93.204 206 13 1 1 206 555626338 555626134 8.610000e-78 302.0
22 TraesCS7D01G376500 chr2D 95.537 605 25 2 4686 5289 530398382 530397779 0.000000e+00 966.0
23 TraesCS7D01G376500 chr2D 95.372 605 27 1 4686 5289 280408875 280408271 0.000000e+00 961.0
24 TraesCS7D01G376500 chr2D 88.056 427 41 3 3218 3635 487538200 487537775 1.020000e-136 497.0
25 TraesCS7D01G376500 chr4D 95.530 604 25 2 4687 5289 450545405 450546007 0.000000e+00 965.0
26 TraesCS7D01G376500 chr4D 95.364 604 26 2 4687 5289 100241599 100242201 0.000000e+00 959.0
27 TraesCS7D01G376500 chr4D 87.588 427 44 2 3218 3635 150602362 150602788 2.210000e-133 486.0
28 TraesCS7D01G376500 chr4D 88.119 404 38 3 3218 3612 76206404 76206002 6.200000e-129 472.0
29 TraesCS7D01G376500 chr4D 94.681 94 4 1 4599 4691 311439609 311439702 1.540000e-30 145.0
30 TraesCS7D01G376500 chr4D 93.617 94 6 0 4595 4688 471718913 471718820 1.990000e-29 141.0
31 TraesCS7D01G376500 chr4D 94.444 90 5 0 4599 4688 311472560 311472649 7.140000e-29 139.0
32 TraesCS7D01G376500 chr3D 95.380 606 26 2 4685 5289 372191109 372191713 0.000000e+00 963.0
33 TraesCS7D01G376500 chr3D 95.364 604 26 2 4687 5289 75212719 75213321 0.000000e+00 959.0
34 TraesCS7D01G376500 chr3D 87.822 427 42 3 3218 3635 508570111 508569686 4.760000e-135 492.0
35 TraesCS7D01G376500 chr3D 95.556 90 4 0 4599 4688 332842221 332842310 1.540000e-30 145.0
36 TraesCS7D01G376500 chr3D 95.556 90 4 0 4599 4688 395179461 395179550 1.540000e-30 145.0
37 TraesCS7D01G376500 chr5A 80.220 455 71 9 2104 2552 566147238 566147679 1.840000e-84 324.0
38 TraesCS7D01G376500 chrUn 88.670 203 23 0 3433 3635 395146029 395145827 1.140000e-61 248.0
39 TraesCS7D01G376500 chr6A 71.328 851 186 42 1013 1833 522044504 522045326 3.280000e-37 167.0
40 TraesCS7D01G376500 chr5D 96.667 90 3 0 4599 4688 68944469 68944380 3.300000e-32 150.0
41 TraesCS7D01G376500 chr5D 95.556 90 4 0 4599 4688 109822740 109822651 1.540000e-30 145.0
42 TraesCS7D01G376500 chr5D 94.444 90 5 0 4599 4688 82125337 82125426 7.140000e-29 139.0
43 TraesCS7D01G376500 chr6D 75.287 348 65 12 1013 1357 380565585 380565914 4.270000e-31 147.0
44 TraesCS7D01G376500 chr6D 89.474 57 3 3 1028 1081 349760451 349760507 9.500000e-08 69.4
45 TraesCS7D01G376500 chr6B 74.785 349 63 17 1013 1356 567844228 567844556 3.320000e-27 134.0
46 TraesCS7D01G376500 chr2A 97.826 46 1 0 703 748 570503293 570503248 4.390000e-11 80.5


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 TraesCS7D01G376500 chr7D 486726830 486732118 5288 True 9768.000000 9768 100.000000 1 5289 1 chr7D.!!$R6 5288
1 TraesCS7D01G376500 chr7D 486306198 486310296 4098 False 2104.500000 2628 87.212000 204 4593 2 chr7D.!!$F4 4389
2 TraesCS7D01G376500 chr7D 486719500 486720102 602 True 1053.000000 1053 98.179000 4686 5289 1 chr7D.!!$R5 603
3 TraesCS7D01G376500 chr7D 488143743 488144345 602 False 1053.000000 1053 98.176000 4687 5289 1 chr7D.!!$F2 602
4 TraesCS7D01G376500 chr7D 184306398 184307001 603 True 961.000000 961 95.380000 4686 5289 1 chr7D.!!$R2 603
5 TraesCS7D01G376500 chr7D 486242063 486242824 761 True 276.000000 276 73.764000 1095 1872 1 chr7D.!!$R3 777
6 TraesCS7D01G376500 chr7B 516442070 516446665 4595 True 6567.000000 6567 92.494000 1 4599 1 chr7B.!!$R1 4598
7 TraesCS7D01G376500 chr7B 514248034 514256530 8496 False 811.400000 1496 85.229200 1 4593 5 chr7B.!!$F1 4592
8 TraesCS7D01G376500 chr7A 555621757 555626338 4581 True 2139.333333 3356 92.501333 1 4599 3 chr7A.!!$R1 4598
9 TraesCS7D01G376500 chr7A 555437098 555441205 4107 False 2020.000000 2582 87.048000 204 4591 2 chr7A.!!$F1 4387
10 TraesCS7D01G376500 chr2D 530397779 530398382 603 True 966.000000 966 95.537000 4686 5289 1 chr2D.!!$R3 603
11 TraesCS7D01G376500 chr2D 280408271 280408875 604 True 961.000000 961 95.372000 4686 5289 1 chr2D.!!$R1 603
12 TraesCS7D01G376500 chr4D 450545405 450546007 602 False 965.000000 965 95.530000 4687 5289 1 chr4D.!!$F5 602
13 TraesCS7D01G376500 chr4D 100241599 100242201 602 False 959.000000 959 95.364000 4687 5289 1 chr4D.!!$F1 602
14 TraesCS7D01G376500 chr3D 372191109 372191713 604 False 963.000000 963 95.380000 4685 5289 1 chr3D.!!$F3 604
15 TraesCS7D01G376500 chr3D 75212719 75213321 602 False 959.000000 959 95.364000 4687 5289 1 chr3D.!!$F1 602

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
920 979 0.468226 CTACAAAGCTATCGGGCCCA 59.532 55.000 24.92 9.77 0.0 5.36 F
1665 2203 0.251165 GGTGCTTGTTCCTTGGGCTA 60.251 55.000 0.00 0.00 0.0 3.93 F
2309 2853 0.107017 CCACCGCTTCCTTCCATGAT 60.107 55.000 0.00 0.00 0.0 2.45 F
3292 7902 1.210478 TGCCTCTCCAACCAGCTATTC 59.790 52.381 0.00 0.00 0.0 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2193 2737 0.398318 GTGTTCTCAGGGCTCTGGTT 59.602 55.0 15.13 0.0 41.23 3.67 R
2825 7432 0.537188 ATGTTGGGAGCGGTAGACAG 59.463 55.0 0.00 0.0 0.00 3.51 R
4269 8929 0.534203 TCACCAGCGAAAAGGGTCAC 60.534 55.0 0.00 0.0 31.03 3.67 R
4640 9304 0.253894 AACCACCAGCGGTATAACCC 59.746 55.0 0.00 0.0 38.76 4.11 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
49 50 2.440409 CATGTGGTCTTGGAAGGAAGG 58.560 52.381 0.00 0.00 0.00 3.46
58 59 0.473694 TGGAAGGAAGGAGCTGGTCA 60.474 55.000 9.30 0.00 0.00 4.02
132 133 4.959560 ATGGATTCTCTCTGGATGTCTG 57.040 45.455 0.00 0.00 0.00 3.51
150 151 4.516321 TGTCTGTGGATGATGTTGAAACAG 59.484 41.667 1.94 0.00 43.04 3.16
153 154 5.471116 TCTGTGGATGATGTTGAAACAGAAG 59.529 40.000 1.94 0.00 43.04 2.85
161 162 3.088532 TGTTGAAACAGAAGCACAACCT 58.911 40.909 0.00 0.00 39.66 3.50
238 286 0.667487 ACGAAGATGCACACTGGTCG 60.667 55.000 12.27 12.27 0.00 4.79
377 427 0.692476 TGTGCTGCCAAGTGGATAGT 59.308 50.000 0.18 0.00 37.39 2.12
391 441 1.490490 GGATAGTGTTGCATCCCCAGA 59.510 52.381 0.00 0.00 35.61 3.86
503 553 1.688197 CCTTGTGCAATTTCTGTGGGT 59.312 47.619 0.00 0.00 0.00 4.51
574 624 3.417101 ACAATCATTACCAAGCGACCAA 58.583 40.909 0.00 0.00 0.00 3.67
587 637 2.162208 AGCGACCAATAATGCACAACAG 59.838 45.455 0.00 0.00 0.00 3.16
772 829 9.753674 AATCATTCTGTAAGGGTTTTCTCAATA 57.246 29.630 0.00 0.00 0.00 1.90
861 920 6.600882 TGGTTAGTTAGTTAACTCCAGAGG 57.399 41.667 12.39 0.00 44.77 3.69
920 979 0.468226 CTACAAAGCTATCGGGCCCA 59.532 55.000 24.92 9.77 0.00 5.36
958 1017 1.067060 GTTCTCACACTTGTTTGCCCC 59.933 52.381 0.00 0.00 0.00 5.80
1005 1064 0.911525 CACTCCTCTCCACCATGGGT 60.912 60.000 18.09 0.00 38.32 4.51
1358 1892 0.459237 AAGCGCATCGAGAACCTCTG 60.459 55.000 11.47 0.00 0.00 3.35
1365 1899 1.561643 TCGAGAACCTCTGCTTCCAT 58.438 50.000 0.00 0.00 0.00 3.41
1382 1916 1.895131 CCATAACAAGCAAACCCAGCT 59.105 47.619 0.00 0.00 45.97 4.24
1446 1981 1.379176 CTCGCTCCAGTCCCTCTCA 60.379 63.158 0.00 0.00 0.00 3.27
1467 2002 0.253347 TGGCCTTCTGGAAGATCCCT 60.253 55.000 3.32 0.00 46.36 4.20
1478 2013 0.336737 AAGATCCCTGACGACCTCCT 59.663 55.000 0.00 0.00 0.00 3.69
1479 2014 1.223501 AGATCCCTGACGACCTCCTA 58.776 55.000 0.00 0.00 0.00 2.94
1527 2065 0.458669 GGAAGCTCGGATTGGTACGA 59.541 55.000 0.00 0.00 38.67 3.43
1565 2103 1.884075 TACATCCACCGCTTGCTCGT 61.884 55.000 0.00 0.00 0.00 4.18
1567 2105 1.302511 ATCCACCGCTTGCTCGTTT 60.303 52.632 0.00 0.00 0.00 3.60
1665 2203 0.251165 GGTGCTTGTTCCTTGGGCTA 60.251 55.000 0.00 0.00 0.00 3.93
1719 2257 0.656259 CACTCTTGGAGCGCATCATG 59.344 55.000 11.47 9.72 32.04 3.07
1835 2373 1.376424 ACAAGCTGCAGATCGGTGG 60.376 57.895 20.43 1.85 0.00 4.61
1888 2426 4.072131 TCTCTCCCTTTTTCAATGGAACG 58.928 43.478 0.00 0.00 31.35 3.95
1961 2505 5.502153 AAGAAACGATACAGCTCGAGTAT 57.498 39.130 15.13 4.85 41.12 2.12
2083 2627 5.408880 AAACTAGAACTAGGAGGAAGCAC 57.591 43.478 12.54 0.00 37.49 4.40
2192 2736 1.630369 ACATAGGCCAGTGAAGAAGCA 59.370 47.619 5.01 0.00 0.00 3.91
2193 2737 2.040278 ACATAGGCCAGTGAAGAAGCAA 59.960 45.455 5.01 0.00 0.00 3.91
2195 2739 1.322442 AGGCCAGTGAAGAAGCAAAC 58.678 50.000 5.01 0.00 0.00 2.93
2227 2771 6.065976 TGAGAACACCACATGGATAGAATT 57.934 37.500 4.53 0.00 38.94 2.17
2309 2853 0.107017 CCACCGCTTCCTTCCATGAT 60.107 55.000 0.00 0.00 0.00 2.45
2350 2894 1.544314 GCAAAGTTCCAGTCTGGCTCT 60.544 52.381 14.64 11.32 37.47 4.09
2410 5591 4.953781 TGGAAATCCATTCTCCTCCTTT 57.046 40.909 0.00 0.00 42.01 3.11
2434 5615 2.893489 GCTCCTGAAATGGTTTTGTCCT 59.107 45.455 0.00 0.00 0.00 3.85
2575 7182 9.983024 CTATAGAGGTTTAGAAGAGGATATCCA 57.017 37.037 23.81 0.00 38.89 3.41
2626 7233 5.091261 TCTTCCTCATCTCTAAAAGGTGC 57.909 43.478 0.00 0.00 35.93 5.01
2682 7289 8.579850 TTACACCATTAGCTCATCTGAAAAAT 57.420 30.769 0.00 0.00 0.00 1.82
2834 7441 6.995511 TCCCAAAATTTAATCTGTCTACCG 57.004 37.500 0.00 0.00 0.00 4.02
2889 7496 3.089284 GCCTACAAAGCCCACATAAAGT 58.911 45.455 0.00 0.00 0.00 2.66
2900 7507 5.011023 AGCCCACATAAAGTTTTTCCAGAAG 59.989 40.000 0.00 0.00 0.00 2.85
2938 7545 2.354704 CCTGATAGCAAAGGACGTTGGA 60.355 50.000 0.00 0.00 35.40 3.53
3080 7688 1.729586 TTCCCCATATCCCCTCTTCG 58.270 55.000 0.00 0.00 0.00 3.79
3139 7747 3.658725 AGCCCCTTCACTATCACTACAT 58.341 45.455 0.00 0.00 0.00 2.29
3154 7762 6.925610 TCACTACATAGACAATTTGCCATC 57.074 37.500 0.00 0.00 0.00 3.51
3292 7902 1.210478 TGCCTCTCCAACCAGCTATTC 59.790 52.381 0.00 0.00 0.00 1.75
3295 7905 2.768527 CCTCTCCAACCAGCTATTCTGA 59.231 50.000 0.00 0.00 45.72 3.27
3476 8136 4.805140 TGATAGTTAATTGGCATCCCCA 57.195 40.909 0.00 0.00 43.51 4.96
3527 8187 5.654603 TTTCGGATACAGAGCAACTCTAA 57.345 39.130 0.00 0.00 38.99 2.10
3616 8276 6.620877 TGGAACTGTTCTATGACCAGTTAT 57.379 37.500 19.05 0.00 46.41 1.89
3617 8277 6.406370 TGGAACTGTTCTATGACCAGTTATG 58.594 40.000 19.05 0.00 46.41 1.90
3637 8297 9.632638 AGTTATGGAGTAATATGCATGTTCTTT 57.367 29.630 12.36 0.00 32.95 2.52
3710 8370 2.588034 GCGTCGAGGTATTGGCCC 60.588 66.667 0.00 0.00 0.00 5.80
3733 8393 4.340617 TGAAGGTGAACTTTGGTGTCTTT 58.659 39.130 0.00 0.00 40.21 2.52
3909 8569 2.833794 TGAACTGCAGTCTGTACAACC 58.166 47.619 21.95 2.02 0.00 3.77
3949 8609 1.903877 ATGAACCCACCGGAGAGCAG 61.904 60.000 9.46 0.00 0.00 4.24
4045 8705 7.444792 CACAAATTTCAAGGGGATCAAAATGAA 59.555 33.333 0.00 0.00 0.00 2.57
4048 8708 8.797350 AATTTCAAGGGGATCAAAATGAATTC 57.203 30.769 0.00 0.00 0.00 2.17
4141 8801 1.228644 TGCTTTGGCACTGGCAGAT 60.229 52.632 23.66 2.23 44.28 2.90
4171 8831 4.255833 TGAGATGGCAAACAAATTGGAC 57.744 40.909 0.00 0.00 39.54 4.02
4269 8929 5.422363 AAAGTACCCTTTCTCGGTGTCCG 62.422 52.174 1.45 1.45 41.73 4.79
4296 8956 1.686355 TTTCGCTGGTGAACCAATGT 58.314 45.000 3.33 0.00 46.97 2.71
4298 8958 0.950836 TCGCTGGTGAACCAATGTTG 59.049 50.000 3.33 0.00 46.97 3.33
4523 9186 8.704849 AATTATGACTAGATACTCACAGAGCT 57.295 34.615 0.00 0.00 32.04 4.09
4546 9209 6.536582 GCTAAATGAACTCAATCTCTAGCACA 59.463 38.462 0.00 0.00 0.00 4.57
4593 9257 7.874528 TGTGTAGATCATAAATCACATAGCCAG 59.125 37.037 0.00 0.00 32.19 4.85
4599 9263 9.664332 GATCATAAATCACATAGCCAGACTATT 57.336 33.333 0.00 0.00 39.71 1.73
4600 9264 8.837788 TCATAAATCACATAGCCAGACTATTG 57.162 34.615 0.00 0.00 39.71 1.90
4601 9265 7.879677 TCATAAATCACATAGCCAGACTATTGG 59.120 37.037 0.00 0.00 39.71 3.16
4602 9266 4.630644 ATCACATAGCCAGACTATTGGG 57.369 45.455 0.00 0.00 39.71 4.12
4603 9267 2.705658 TCACATAGCCAGACTATTGGGG 59.294 50.000 0.00 0.00 39.71 4.96
4604 9268 2.705658 CACATAGCCAGACTATTGGGGA 59.294 50.000 0.00 0.00 39.71 4.81
4605 9269 3.328931 CACATAGCCAGACTATTGGGGAT 59.671 47.826 0.00 0.00 39.71 3.85
4606 9270 3.328931 ACATAGCCAGACTATTGGGGATG 59.671 47.826 0.00 0.00 39.71 3.51
4607 9271 1.898863 AGCCAGACTATTGGGGATGT 58.101 50.000 0.00 0.00 38.72 3.06
4608 9272 3.060479 AGCCAGACTATTGGGGATGTA 57.940 47.619 0.00 0.00 38.72 2.29
4609 9273 3.393687 AGCCAGACTATTGGGGATGTAA 58.606 45.455 0.00 0.00 38.72 2.41
4610 9274 3.136626 AGCCAGACTATTGGGGATGTAAC 59.863 47.826 0.00 0.00 38.72 2.50
4611 9275 3.136626 GCCAGACTATTGGGGATGTAACT 59.863 47.826 0.00 0.00 38.72 2.24
4612 9276 4.347000 GCCAGACTATTGGGGATGTAACTA 59.653 45.833 0.00 0.00 38.72 2.24
4613 9277 5.742255 GCCAGACTATTGGGGATGTAACTAC 60.742 48.000 0.00 0.00 38.72 2.73
4614 9278 5.602978 CCAGACTATTGGGGATGTAACTACT 59.397 44.000 0.00 0.00 34.46 2.57
4615 9279 6.463049 CCAGACTATTGGGGATGTAACTACTG 60.463 46.154 0.00 0.00 34.46 2.74
4616 9280 5.602978 AGACTATTGGGGATGTAACTACTGG 59.397 44.000 0.00 0.00 0.00 4.00
4617 9281 4.658901 ACTATTGGGGATGTAACTACTGGG 59.341 45.833 0.00 0.00 0.00 4.45
4618 9282 2.653543 TGGGGATGTAACTACTGGGT 57.346 50.000 0.00 0.00 0.00 4.51
4619 9283 3.780516 TGGGGATGTAACTACTGGGTA 57.219 47.619 0.00 0.00 0.00 3.69
4620 9284 4.289837 TGGGGATGTAACTACTGGGTAT 57.710 45.455 0.00 0.00 0.00 2.73
4621 9285 5.421740 TGGGGATGTAACTACTGGGTATA 57.578 43.478 0.00 0.00 0.00 1.47
4622 9286 5.790642 TGGGGATGTAACTACTGGGTATAA 58.209 41.667 0.00 0.00 0.00 0.98
4623 9287 5.603813 TGGGGATGTAACTACTGGGTATAAC 59.396 44.000 0.00 0.00 0.00 1.89
4624 9288 5.012458 GGGGATGTAACTACTGGGTATAACC 59.988 48.000 0.00 0.00 37.60 2.85
4633 9297 3.975025 GGTATAACCCGCCCAGGA 58.025 61.111 0.00 0.00 45.00 3.86
4634 9298 1.752833 GGTATAACCCGCCCAGGAG 59.247 63.158 0.00 0.00 45.00 3.69
4635 9299 1.752833 GTATAACCCGCCCAGGAGG 59.247 63.158 0.00 0.00 45.00 4.30
4646 9310 2.772622 CAGGAGGGGCCGGGTTAT 60.773 66.667 2.18 0.00 43.43 1.89
4647 9311 1.460689 CAGGAGGGGCCGGGTTATA 60.461 63.158 2.18 0.00 43.43 0.98
4648 9312 1.460882 AGGAGGGGCCGGGTTATAC 60.461 63.158 2.18 0.00 43.43 1.47
4649 9313 2.523285 GGAGGGGCCGGGTTATACC 61.523 68.421 2.18 0.00 37.60 2.73
4657 9321 4.870190 GGGTTATACCGCTGGTGG 57.130 61.111 10.01 0.00 39.83 4.61
4658 9322 1.909975 GGGTTATACCGCTGGTGGT 59.090 57.895 10.74 10.74 46.26 4.16
4659 9323 0.253894 GGGTTATACCGCTGGTGGTT 59.746 55.000 11.19 2.88 43.56 3.67
4660 9324 1.340308 GGGTTATACCGCTGGTGGTTT 60.340 52.381 11.19 6.35 43.56 3.27
4661 9325 1.741145 GGTTATACCGCTGGTGGTTTG 59.259 52.381 11.19 0.00 43.56 2.93
4662 9326 2.429478 GTTATACCGCTGGTGGTTTGT 58.571 47.619 11.19 1.79 43.56 2.83
4663 9327 2.815503 GTTATACCGCTGGTGGTTTGTT 59.184 45.455 11.19 0.00 43.56 2.83
4664 9328 2.863132 ATACCGCTGGTGGTTTGTTA 57.137 45.000 11.19 0.00 43.56 2.41
4665 9329 2.863132 TACCGCTGGTGGTTTGTTAT 57.137 45.000 11.19 0.00 43.56 1.89
4666 9330 1.243902 ACCGCTGGTGGTTTGTTATG 58.756 50.000 0.00 0.00 39.99 1.90
4667 9331 1.202830 ACCGCTGGTGGTTTGTTATGA 60.203 47.619 0.00 0.00 39.99 2.15
4668 9332 1.199097 CCGCTGGTGGTTTGTTATGAC 59.801 52.381 0.00 0.00 0.00 3.06
4669 9333 1.876799 CGCTGGTGGTTTGTTATGACA 59.123 47.619 0.00 0.00 0.00 3.58
4670 9334 2.292016 CGCTGGTGGTTTGTTATGACAA 59.708 45.455 0.00 0.00 43.73 3.18
4683 9347 7.716799 TTGTTATGACAAAGCCCATAAAGAT 57.283 32.000 0.00 0.00 42.54 2.40
4743 9407 1.679153 GTTCTTCCGAGGTTTTTGCCA 59.321 47.619 0.00 0.00 0.00 4.92
4832 9497 1.337118 GGCTTGTCATTCCCAAACCA 58.663 50.000 0.00 0.00 30.19 3.67
5106 9772 1.528161 GCAAATTGTGAAGCAAGTGCC 59.472 47.619 0.00 0.00 41.99 5.01
5167 9833 7.815383 ACACCTTTTCCTATCCATATCATTGA 58.185 34.615 0.00 0.00 0.00 2.57
5209 9875 8.276453 ACCTCAGGTGCCTAGTAATTATTTAT 57.724 34.615 0.00 0.00 32.98 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 3.563390 GCTCCAATAGAAATGACCAGCTC 59.437 47.826 0.00 0.00 0.00 4.09
100 101 5.010112 CAGAGAGAATCCATTTACTAGGCGA 59.990 44.000 0.00 0.00 33.66 5.54
132 133 4.022935 TGCTTCTGTTTCAACATCATCCAC 60.023 41.667 0.00 0.00 38.41 4.02
150 151 3.367395 GCCAAGGATAAAGGTTGTGCTTC 60.367 47.826 0.00 0.00 30.50 3.86
153 154 2.171003 AGCCAAGGATAAAGGTTGTGC 58.829 47.619 0.00 0.00 0.00 4.57
161 162 7.073725 AGGAACTGGATATAAGCCAAGGATAAA 59.926 37.037 0.00 0.00 37.18 1.40
238 286 1.651240 TACCTCTCGGTAGCACACGC 61.651 60.000 0.00 0.00 43.29 5.34
377 427 2.041485 TGATTTCTCTGGGGATGCAACA 59.959 45.455 0.00 0.00 0.00 3.33
391 441 3.376234 CGCCATGTGATGAACTGATTTCT 59.624 43.478 0.00 0.00 34.97 2.52
503 553 3.472652 ACATGCTTTCGTTAGTCCAACA 58.527 40.909 0.00 0.00 36.92 3.33
551 601 4.188462 TGGTCGCTTGGTAATGATTGTAG 58.812 43.478 0.00 0.00 0.00 2.74
560 610 3.127895 GTGCATTATTGGTCGCTTGGTAA 59.872 43.478 0.00 0.00 0.00 2.85
616 666 7.348274 TCATGTTCTCTTTCCATATACCCTTCT 59.652 37.037 0.00 0.00 0.00 2.85
757 814 5.074515 TCCTGGAGTTATTGAGAAAACCCTT 59.925 40.000 0.00 0.00 0.00 3.95
832 889 7.794041 TGGAGTTAACTAACTAACCAAAGTCA 58.206 34.615 8.42 0.00 45.84 3.41
861 920 0.539051 AGCACACTGGCACTATCTCC 59.461 55.000 0.00 0.00 35.83 3.71
891 950 5.067413 CCGATAGCTTTGTAGTCTAGTCCAA 59.933 44.000 0.00 0.00 0.00 3.53
894 953 4.557097 GCCCGATAGCTTTGTAGTCTAGTC 60.557 50.000 0.00 0.00 0.00 2.59
938 997 1.067060 GGGGCAAACAAGTGTGAGAAC 59.933 52.381 0.00 0.00 0.00 3.01
958 1017 0.313672 GGAGAGTGGATCTGCTAGCG 59.686 60.000 10.77 5.22 42.80 4.26
1333 1392 2.434884 CTCGATGCGCTTGGTGGT 60.435 61.111 9.73 0.00 0.00 4.16
1358 1892 2.298729 TGGGTTTGCTTGTTATGGAAGC 59.701 45.455 0.00 0.00 45.12 3.86
1365 1899 1.133637 TGGAGCTGGGTTTGCTTGTTA 60.134 47.619 0.00 0.00 41.30 2.41
1382 1916 2.741092 GCGACAAGGTGGTCTGGA 59.259 61.111 0.00 0.00 35.63 3.86
1446 1981 0.915364 GGATCTTCCAGAAGGCCAGT 59.085 55.000 5.01 0.00 38.88 4.00
1467 2002 1.748122 GGCGAGTAGGAGGTCGTCA 60.748 63.158 0.00 0.00 40.53 4.35
1518 2056 3.309682 CGCTCATGTCATTTCGTACCAAT 59.690 43.478 0.00 0.00 0.00 3.16
1527 2065 2.479566 ACTGGTCGCTCATGTCATTT 57.520 45.000 0.00 0.00 0.00 2.32
1719 2257 1.401905 CCATAAGGCGGCTTGAAGAAC 59.598 52.381 32.24 0.00 0.00 3.01
1835 2373 4.644103 AACCATACTTTGATGATGCTGC 57.356 40.909 0.00 0.00 0.00 5.25
1838 2376 6.699575 AAGGTAACCATACTTTGATGATGC 57.300 37.500 0.00 0.00 30.87 3.91
1918 2458 2.492025 TCTTATGAATGGAGCCAGGGT 58.508 47.619 0.00 0.00 0.00 4.34
1961 2505 9.100554 TGATCTTAGAAAGTTTGTAACAAACGA 57.899 29.630 7.31 0.00 35.42 3.85
2192 2736 1.140312 TGTTCTCAGGGCTCTGGTTT 58.860 50.000 15.13 0.00 41.23 3.27
2193 2737 0.398318 GTGTTCTCAGGGCTCTGGTT 59.602 55.000 15.13 0.00 41.23 3.67
2195 2739 1.298014 GGTGTTCTCAGGGCTCTGG 59.702 63.158 15.13 4.61 41.23 3.86
2227 2771 6.169094 CAGCTTAAACATCAAGAGGAGAAGA 58.831 40.000 0.00 0.00 0.00 2.87
2309 2853 4.248859 GCAGAGAAGCAAGTGAGACAATA 58.751 43.478 0.00 0.00 0.00 1.90
2350 2894 4.104831 AGGCTAAAAGCTCCCTTTCTCTA 58.895 43.478 0.00 0.00 40.30 2.43
2410 5591 3.565307 ACAAAACCATTTCAGGAGCTGA 58.435 40.909 0.00 0.00 38.87 4.26
2423 5604 3.924114 TTGAGAGACAGGACAAAACCA 57.076 42.857 0.00 0.00 0.00 3.67
2575 7182 9.991906 CCTTGATTTGGCAATATGAATCTAAAT 57.008 29.630 0.00 0.00 31.48 1.40
2626 7233 9.309516 TCGAACTAGTTAATATTGTTAGGCTTG 57.690 33.333 8.42 0.00 0.00 4.01
2825 7432 0.537188 ATGTTGGGAGCGGTAGACAG 59.463 55.000 0.00 0.00 0.00 3.51
2834 7441 4.765339 GGGTATAAATGGTATGTTGGGAGC 59.235 45.833 0.00 0.00 0.00 4.70
2889 7496 4.207165 CACCCTTCTCACTTCTGGAAAAA 58.793 43.478 0.00 0.00 0.00 1.94
2900 7507 1.003233 GGACAGCCACCCTTCTCAC 60.003 63.158 0.00 0.00 0.00 3.51
2959 7566 9.475620 TCCTTATAGAAGAAGATAGTTGACACA 57.524 33.333 0.00 0.00 34.25 3.72
2960 7567 9.738832 GTCCTTATAGAAGAAGATAGTTGACAC 57.261 37.037 0.00 0.00 34.25 3.67
2978 7585 1.789523 AGCTGGCGAAGGTCCTTATA 58.210 50.000 3.42 0.00 27.29 0.98
3062 7670 0.566176 ACGAAGAGGGGATATGGGGA 59.434 55.000 0.00 0.00 0.00 4.81
3080 7688 3.860641 CCAATTGGCCTTCCATTTGTAC 58.139 45.455 12.53 0.00 45.45 2.90
3118 7726 3.116096 TGTAGTGATAGTGAAGGGGCT 57.884 47.619 0.00 0.00 0.00 5.19
3139 7747 6.433716 TCAATTCACAGATGGCAAATTGTCTA 59.566 34.615 15.73 0.15 38.10 2.59
3154 7762 4.380233 GCCTTGAACCTGATCAATTCACAG 60.380 45.833 17.55 16.38 38.55 3.66
3292 7902 9.696917 AGCTTTGATTGGTAAATTTTTAGTCAG 57.303 29.630 0.00 0.00 0.00 3.51
3295 7905 9.639601 GCTAGCTTTGATTGGTAAATTTTTAGT 57.360 29.630 7.70 0.00 0.00 2.24
3334 7944 5.911752 TCCTTTGCATTTTGACAAGCTTAA 58.088 33.333 0.00 0.00 0.00 1.85
3513 8173 8.798859 ATAAAATGATGTTAGAGTTGCTCTGT 57.201 30.769 8.75 0.00 41.37 3.41
3616 8276 6.663093 ACCAAAAGAACATGCATATTACTCCA 59.337 34.615 0.00 0.00 0.00 3.86
3617 8277 6.974622 CACCAAAAGAACATGCATATTACTCC 59.025 38.462 0.00 0.00 0.00 3.85
3710 8370 3.545703 AGACACCAAAGTTCACCTTCAG 58.454 45.455 0.00 0.00 31.27 3.02
3733 8393 1.547675 GCCAACATCTTCACCTCCCAA 60.548 52.381 0.00 0.00 0.00 4.12
3949 8609 1.210478 TCCTTCCAGAACCTAGCATGC 59.790 52.381 10.51 10.51 0.00 4.06
3965 8625 2.286523 CGACTGGACTGGCCTCCTT 61.287 63.158 12.06 0.00 37.63 3.36
4045 8705 4.181578 CCACGTACTTGAGGAATTCGAAT 58.818 43.478 4.39 4.39 0.00 3.34
4048 8708 1.659098 GCCACGTACTTGAGGAATTCG 59.341 52.381 0.00 0.00 0.00 3.34
4141 8801 3.084039 GTTTGCCATCTCATTCACCTCA 58.916 45.455 0.00 0.00 0.00 3.86
4171 8831 1.942657 CATGGCTGAAATAGTGGACGG 59.057 52.381 0.00 0.00 0.00 4.79
4269 8929 0.534203 TCACCAGCGAAAAGGGTCAC 60.534 55.000 0.00 0.00 31.03 3.67
4296 8956 2.265367 TCAGGAGAACACATAGCCCAA 58.735 47.619 0.00 0.00 0.00 4.12
4298 8958 2.224402 GGATCAGGAGAACACATAGCCC 60.224 54.545 0.00 0.00 0.00 5.19
4517 9180 7.169645 GCTAGAGATTGAGTTCATTTAGCTCTG 59.830 40.741 9.27 0.00 36.46 3.35
4523 9186 7.065085 GCTTGTGCTAGAGATTGAGTTCATTTA 59.935 37.037 0.00 0.00 36.03 1.40
4546 9209 0.548510 GGCTTCTAGGATGGTGGCTT 59.451 55.000 0.00 0.00 0.00 4.35
4593 9257 5.221661 CCCAGTAGTTACATCCCCAATAGTC 60.222 48.000 0.00 0.00 0.00 2.59
4599 9263 2.653543 ACCCAGTAGTTACATCCCCA 57.346 50.000 0.00 0.00 0.00 4.96
4600 9264 5.012458 GGTTATACCCAGTAGTTACATCCCC 59.988 48.000 0.00 0.00 30.04 4.81
4601 9265 6.106648 GGTTATACCCAGTAGTTACATCCC 57.893 45.833 0.00 0.00 30.04 3.85
4616 9280 1.752833 CTCCTGGGCGGGTTATACC 59.247 63.158 0.00 0.00 37.60 2.73
4617 9281 1.752833 CCTCCTGGGCGGGTTATAC 59.247 63.158 0.00 0.00 0.00 1.47
4618 9282 4.306245 CCTCCTGGGCGGGTTATA 57.694 61.111 0.00 0.00 0.00 0.98
4628 9292 2.976284 TATAACCCGGCCCCTCCTGG 62.976 65.000 0.00 0.00 44.15 4.45
4629 9293 1.460689 TATAACCCGGCCCCTCCTG 60.461 63.158 0.00 0.00 0.00 3.86
4630 9294 1.460882 GTATAACCCGGCCCCTCCT 60.461 63.158 0.00 0.00 0.00 3.69
4631 9295 2.523285 GGTATAACCCGGCCCCTCC 61.523 68.421 0.00 0.00 30.04 4.30
4632 9296 2.875804 CGGTATAACCCGGCCCCTC 61.876 68.421 0.00 0.00 44.32 4.30
4633 9297 2.845795 CGGTATAACCCGGCCCCT 60.846 66.667 0.00 0.00 44.32 4.79
4640 9304 0.253894 AACCACCAGCGGTATAACCC 59.746 55.000 0.00 0.00 38.76 4.11
4641 9305 1.741145 CAAACCACCAGCGGTATAACC 59.259 52.381 0.00 0.00 38.76 2.85
4642 9306 2.429478 ACAAACCACCAGCGGTATAAC 58.571 47.619 0.00 0.00 38.76 1.89
4643 9307 2.863132 ACAAACCACCAGCGGTATAA 57.137 45.000 0.00 0.00 38.76 0.98
4644 9308 2.863132 AACAAACCACCAGCGGTATA 57.137 45.000 0.00 0.00 38.76 1.47
4645 9309 2.863132 TAACAAACCACCAGCGGTAT 57.137 45.000 0.00 0.00 38.76 2.73
4646 9310 2.038689 TCATAACAAACCACCAGCGGTA 59.961 45.455 0.00 0.00 38.76 4.02
4647 9311 1.202830 TCATAACAAACCACCAGCGGT 60.203 47.619 0.00 0.00 42.71 5.68
4648 9312 1.199097 GTCATAACAAACCACCAGCGG 59.801 52.381 0.00 0.00 0.00 5.52
4649 9313 1.876799 TGTCATAACAAACCACCAGCG 59.123 47.619 0.00 0.00 30.70 5.18
4653 9317 7.253166 ATGGGCTTTGTCATAACAAACCACC 62.253 44.000 6.06 2.68 46.17 4.61
4654 9318 4.262420 ATGGGCTTTGTCATAACAAACCAC 60.262 41.667 6.06 0.00 46.17 4.16
4659 9323 7.178274 ACATCTTTATGGGCTTTGTCATAACAA 59.822 33.333 0.00 0.00 39.29 2.83
4660 9324 6.663093 ACATCTTTATGGGCTTTGTCATAACA 59.337 34.615 0.00 0.00 36.10 2.41
4661 9325 7.100458 ACATCTTTATGGGCTTTGTCATAAC 57.900 36.000 0.00 0.00 36.10 1.89
4662 9326 7.178274 ACAACATCTTTATGGGCTTTGTCATAA 59.822 33.333 0.00 0.00 37.43 1.90
4663 9327 6.663093 ACAACATCTTTATGGGCTTTGTCATA 59.337 34.615 0.00 0.00 37.43 2.15
4664 9328 5.481473 ACAACATCTTTATGGGCTTTGTCAT 59.519 36.000 0.00 0.00 37.43 3.06
4665 9329 4.832266 ACAACATCTTTATGGGCTTTGTCA 59.168 37.500 0.00 0.00 37.43 3.58
4666 9330 5.048083 TCACAACATCTTTATGGGCTTTGTC 60.048 40.000 0.00 0.00 37.43 3.18
4667 9331 4.832266 TCACAACATCTTTATGGGCTTTGT 59.168 37.500 0.00 0.00 37.43 2.83
4668 9332 5.163513 GTCACAACATCTTTATGGGCTTTG 58.836 41.667 0.00 0.00 37.43 2.77
4669 9333 4.832266 TGTCACAACATCTTTATGGGCTTT 59.168 37.500 0.00 0.00 37.43 3.51
4670 9334 4.406456 TGTCACAACATCTTTATGGGCTT 58.594 39.130 0.00 0.00 37.43 4.35
4671 9335 4.012374 CTGTCACAACATCTTTATGGGCT 58.988 43.478 0.00 0.00 37.43 5.19
4672 9336 3.428045 GCTGTCACAACATCTTTATGGGC 60.428 47.826 0.00 0.00 37.43 5.36
4673 9337 3.129287 GGCTGTCACAACATCTTTATGGG 59.871 47.826 0.00 0.00 37.43 4.00
4674 9338 4.012374 AGGCTGTCACAACATCTTTATGG 58.988 43.478 0.00 0.00 37.43 2.74
4675 9339 4.696877 TCAGGCTGTCACAACATCTTTATG 59.303 41.667 15.27 0.00 39.17 1.90
4676 9340 4.910195 TCAGGCTGTCACAACATCTTTAT 58.090 39.130 15.27 0.00 34.13 1.40
4677 9341 4.350368 TCAGGCTGTCACAACATCTTTA 57.650 40.909 15.27 0.00 34.13 1.85
4678 9342 3.213206 TCAGGCTGTCACAACATCTTT 57.787 42.857 15.27 0.00 34.13 2.52
4679 9343 2.936919 TCAGGCTGTCACAACATCTT 57.063 45.000 15.27 0.00 34.13 2.40
4680 9344 2.936919 TTCAGGCTGTCACAACATCT 57.063 45.000 15.27 0.00 34.13 2.90
4681 9345 4.510038 AAATTCAGGCTGTCACAACATC 57.490 40.909 15.27 0.00 34.13 3.06
4682 9346 4.501915 CCAAAATTCAGGCTGTCACAACAT 60.502 41.667 15.27 0.00 34.13 2.71
4683 9347 3.181477 CCAAAATTCAGGCTGTCACAACA 60.181 43.478 15.27 0.00 0.00 3.33
4743 9407 4.983671 AGCCACGAAAAAGAAAAACTCT 57.016 36.364 0.00 0.00 35.13 3.24
4832 9497 4.540099 TGAAAATGACAGGGTCTAGGGAAT 59.460 41.667 0.00 0.00 33.15 3.01
5089 9755 3.756933 AATGGCACTTGCTTCACAATT 57.243 38.095 0.38 0.00 41.70 2.32
5106 9772 6.991531 TGAGGTCAATTGGAAAAAGGAAAATG 59.008 34.615 5.42 0.00 0.00 2.32
5167 9833 1.417145 AGGTTGCATTTTGGCATGTGT 59.583 42.857 0.00 0.00 44.48 3.72


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

AutoCloner maintained by Alex Coulton.