Multiple sequence alignment - TraesCS7A01G082200

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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 TraesCS7A01G082200 chr7A 100.000 5792 0 0 1 5792 47449292 47443501 0.000000e+00 10696.0
1 TraesCS7A01G082200 chr7A 100.000 41 0 0 1 41 375879147 375879187 6.220000e-10 76.8
2 TraesCS7A01G082200 chr7D 93.653 2379 102 21 1 2342 45230986 45228620 0.000000e+00 3511.0
3 TraesCS7A01G082200 chr7D 91.294 2148 142 21 3097 5238 45192125 45190017 0.000000e+00 2889.0
4 TraesCS7A01G082200 chr7D 95.027 1669 62 5 2343 4007 45228542 45226891 0.000000e+00 2603.0
5 TraesCS7A01G082200 chr7D 91.512 1237 86 10 4009 5236 45226727 45225501 0.000000e+00 1685.0
6 TraesCS7A01G082200 chr7D 89.706 68 5 2 1087 1154 45222405 45222340 1.030000e-12 86.1
7 TraesCS7A01G082200 chr4A 88.895 1882 145 28 40 1875 656781279 656779416 0.000000e+00 2259.0
8 TraesCS7A01G082200 chr4A 87.053 1259 104 30 3005 4235 656778242 656777015 0.000000e+00 1367.0
9 TraesCS7A01G082200 chr4A 89.564 757 72 5 4482 5236 656776642 656775891 0.000000e+00 953.0
10 TraesCS7A01G082200 chr4A 95.760 566 12 3 5237 5792 97759902 97759339 0.000000e+00 902.0
11 TraesCS7A01G082200 chr4A 86.408 618 55 15 3005 3604 656769633 656769027 0.000000e+00 649.0
12 TraesCS7A01G082200 chr4A 84.187 683 70 21 2348 3017 656778917 656778260 3.810000e-176 628.0
13 TraesCS7A01G082200 chr4A 90.888 428 32 2 1916 2342 656779418 656778997 8.420000e-158 568.0
14 TraesCS7A01G082200 chr4A 100.000 41 0 0 1 41 656782635 656782595 6.220000e-10 76.8
15 TraesCS7A01G082200 chrUn 88.842 1882 146 27 40 1875 275538115 275539978 0.000000e+00 2254.0
16 TraesCS7A01G082200 chrUn 87.262 1311 111 27 603 1875 411628459 411627167 0.000000e+00 1445.0
17 TraesCS7A01G082200 chrUn 87.716 1213 100 27 3005 4199 274358058 274356877 0.000000e+00 1369.0
18 TraesCS7A01G082200 chrUn 87.387 1213 104 27 3005 4199 291877126 291878307 0.000000e+00 1347.0
19 TraesCS7A01G082200 chrUn 87.387 1213 104 27 3005 4199 295663428 295664609 0.000000e+00 1347.0
20 TraesCS7A01G082200 chrUn 89.828 757 70 5 4482 5236 355410630 355411381 0.000000e+00 965.0
21 TraesCS7A01G082200 chrUn 89.828 757 70 5 4482 5236 430531989 430531238 0.000000e+00 965.0
22 TraesCS7A01G082200 chrUn 84.187 683 70 21 2348 3017 359896656 359895999 3.810000e-176 628.0
23 TraesCS7A01G082200 chrUn 93.902 410 25 0 40 449 231460889 231461298 2.290000e-173 619.0
24 TraesCS7A01G082200 chrUn 87.257 565 42 14 3681 4235 413088309 413087765 8.250000e-173 617.0
25 TraesCS7A01G082200 chrUn 91.121 428 31 2 1916 2342 275539976 275540397 1.810000e-159 573.0
26 TraesCS7A01G082200 chrUn 90.888 428 32 2 1916 2342 359897157 359896736 8.420000e-158 568.0
27 TraesCS7A01G082200 chrUn 90.888 428 32 2 1916 2342 444818865 444819286 8.420000e-158 568.0
28 TraesCS7A01G082200 chrUn 88.174 482 37 11 3718 4199 282246308 282245847 1.820000e-154 556.0
29 TraesCS7A01G082200 chrUn 88.174 482 37 11 3718 4199 378521498 378521037 1.820000e-154 556.0
30 TraesCS7A01G082200 chrUn 88.591 447 45 6 1434 1875 444818422 444818867 6.600000e-149 538.0
31 TraesCS7A01G082200 chrUn 91.553 367 31 0 4482 4848 413087368 413087002 1.860000e-139 507.0
32 TraesCS7A01G082200 chrUn 87.443 438 36 9 3005 3426 275540810 275541244 2.430000e-133 486.0
33 TraesCS7A01G082200 chrUn 87.443 438 36 9 3005 3426 359895981 359895547 2.430000e-133 486.0
34 TraesCS7A01G082200 chrUn 87.435 382 42 6 1499 1875 359897535 359897155 8.910000e-118 435.0
35 TraesCS7A01G082200 chrUn 94.375 160 9 0 2858 3017 274358235 274358076 4.480000e-61 246.0
36 TraesCS7A01G082200 chrUn 93.902 164 8 2 2851 3014 291876944 291877105 4.480000e-61 246.0
37 TraesCS7A01G082200 chrUn 93.902 164 8 2 2851 3014 295663246 295663407 4.480000e-61 246.0
38 TraesCS7A01G082200 chrUn 93.233 133 9 0 40 172 418475690 418475822 4.580000e-46 196.0
39 TraesCS7A01G082200 chrUn 92.029 138 11 0 2345 2482 275540474 275540611 1.650000e-45 195.0
40 TraesCS7A01G082200 chrUn 100.000 41 0 0 1 41 231459535 231459575 6.220000e-10 76.8
41 TraesCS7A01G082200 chrUn 100.000 41 0 0 1 41 275536781 275536821 6.220000e-10 76.8
42 TraesCS7A01G082200 chrUn 100.000 41 0 0 1 41 398232654 398232614 6.220000e-10 76.8
43 TraesCS7A01G082200 chr6D 78.774 1696 245 58 2344 3959 451173830 451175490 0.000000e+00 1031.0
44 TraesCS7A01G082200 chr6D 82.082 932 136 22 1431 2342 451172836 451173756 0.000000e+00 767.0
45 TraesCS7A01G082200 chr6D 76.596 517 84 20 846 1335 451172273 451172779 3.470000e-62 250.0
46 TraesCS7A01G082200 chr5A 94.633 559 11 4 5233 5790 4295716 4296256 0.000000e+00 848.0
47 TraesCS7A01G082200 chr5A 92.743 565 13 7 5239 5792 537246981 537246434 0.000000e+00 791.0
48 TraesCS7A01G082200 chr5A 92.334 574 15 7 5231 5792 704823779 704824335 0.000000e+00 789.0
49 TraesCS7A01G082200 chr2A 93.885 556 16 4 5238 5792 567161473 567160935 0.000000e+00 822.0
50 TraesCS7A01G082200 chr2A 93.537 557 17 4 5238 5792 547712960 547713499 0.000000e+00 811.0
51 TraesCS7A01G082200 chr2A 92.806 556 22 3 5238 5792 567052351 567051813 0.000000e+00 789.0
52 TraesCS7A01G082200 chr2A 92.500 560 20 6 5238 5792 65282613 65283155 0.000000e+00 782.0
53 TraesCS7A01G082200 chr3A 93.606 563 9 5 5238 5790 726855051 726854506 0.000000e+00 815.0
54 TraesCS7A01G082200 chr3A 92.920 565 13 5 5238 5792 532941867 532942414 0.000000e+00 797.0
55 TraesCS7A01G082200 chr3A 92.179 537 28 7 5239 5763 455476131 455475597 0.000000e+00 747.0
56 TraesCS7A01G082200 chr6B 79.466 1198 157 47 2344 3481 685342600 685343768 0.000000e+00 767.0
57 TraesCS7A01G082200 chr6B 81.646 790 124 16 1562 2342 685341749 685342526 2.280000e-178 636.0
58 TraesCS7A01G082200 chr6B 76.923 494 73 27 857 1326 685341023 685341499 5.800000e-60 243.0
59 TraesCS7A01G082200 chr6B 87.931 116 11 3 1431 1543 685341574 685341689 3.640000e-27 134.0
60 TraesCS7A01G082200 chr1A 91.636 538 24 7 5230 5763 258201185 258200665 0.000000e+00 725.0
61 TraesCS7A01G082200 chr6A 81.360 794 123 18 1563 2342 596902698 596903480 1.770000e-174 623.0
62 TraesCS7A01G082200 chr6A 87.273 110 11 3 1431 1537 596902526 596902635 7.880000e-24 122.0
63 TraesCS7A01G082200 chr5B 83.022 536 66 18 5239 5763 192661660 192661139 4.090000e-126 462.0
64 TraesCS7A01G082200 chr3D 93.939 231 13 1 5238 5467 569884788 569884558 1.190000e-91 348.0
65 TraesCS7A01G082200 chr2B 93.562 233 13 2 5237 5467 790135426 790135658 4.300000e-91 346.0
66 TraesCS7A01G082200 chr3B 78.804 184 32 5 4973 5154 686126473 686126651 3.670000e-22 117.0


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 TraesCS7A01G082200 chr7A 47443501 47449292 5791 True 10696.000000 10696 100.000000 1 5792 1 chr7A.!!$R1 5791
1 TraesCS7A01G082200 chr7D 45190017 45192125 2108 True 2889.000000 2889 91.294000 3097 5238 1 chr7D.!!$R1 2141
2 TraesCS7A01G082200 chr7D 45222340 45230986 8646 True 1971.275000 3511 92.474500 1 5236 4 chr7D.!!$R2 5235
3 TraesCS7A01G082200 chr4A 656775891 656782635 6744 True 975.300000 2259 90.097833 1 5236 6 chr4A.!!$R3 5235
4 TraesCS7A01G082200 chr4A 97759339 97759902 563 True 902.000000 902 95.760000 5237 5792 1 chr4A.!!$R1 555
5 TraesCS7A01G082200 chr4A 656769027 656769633 606 True 649.000000 649 86.408000 3005 3604 1 chr4A.!!$R2 599
6 TraesCS7A01G082200 chrUn 411627167 411628459 1292 True 1445.000000 1445 87.262000 603 1875 1 chrUn.!!$R4 1272
7 TraesCS7A01G082200 chrUn 355410630 355411381 751 False 965.000000 965 89.828000 4482 5236 1 chrUn.!!$F1 754
8 TraesCS7A01G082200 chrUn 430531238 430531989 751 True 965.000000 965 89.828000 4482 5236 1 chrUn.!!$R5 754
9 TraesCS7A01G082200 chrUn 274356877 274358235 1358 True 807.500000 1369 91.045500 2858 4199 2 chrUn.!!$R6 1341
10 TraesCS7A01G082200 chrUn 291876944 291878307 1363 False 796.500000 1347 90.644500 2851 4199 2 chrUn.!!$F5 1348
11 TraesCS7A01G082200 chrUn 295663246 295664609 1363 False 796.500000 1347 90.644500 2851 4199 2 chrUn.!!$F6 1348
12 TraesCS7A01G082200 chrUn 275536781 275541244 4463 False 716.960000 2254 91.887000 1 3426 5 chrUn.!!$F4 3425
13 TraesCS7A01G082200 chrUn 413087002 413088309 1307 True 562.000000 617 89.405000 3681 4848 2 chrUn.!!$R8 1167
14 TraesCS7A01G082200 chrUn 444818422 444819286 864 False 553.000000 568 89.739500 1434 2342 2 chrUn.!!$F7 908
15 TraesCS7A01G082200 chrUn 359895547 359897535 1988 True 529.250000 628 87.488250 1499 3426 4 chrUn.!!$R7 1927
16 TraesCS7A01G082200 chrUn 231459535 231461298 1763 False 347.900000 619 96.951000 1 449 2 chrUn.!!$F3 448
17 TraesCS7A01G082200 chr6D 451172273 451175490 3217 False 682.666667 1031 79.150667 846 3959 3 chr6D.!!$F1 3113
18 TraesCS7A01G082200 chr5A 4295716 4296256 540 False 848.000000 848 94.633000 5233 5790 1 chr5A.!!$F1 557
19 TraesCS7A01G082200 chr5A 537246434 537246981 547 True 791.000000 791 92.743000 5239 5792 1 chr5A.!!$R1 553
20 TraesCS7A01G082200 chr5A 704823779 704824335 556 False 789.000000 789 92.334000 5231 5792 1 chr5A.!!$F2 561
21 TraesCS7A01G082200 chr2A 567160935 567161473 538 True 822.000000 822 93.885000 5238 5792 1 chr2A.!!$R2 554
22 TraesCS7A01G082200 chr2A 547712960 547713499 539 False 811.000000 811 93.537000 5238 5792 1 chr2A.!!$F2 554
23 TraesCS7A01G082200 chr2A 567051813 567052351 538 True 789.000000 789 92.806000 5238 5792 1 chr2A.!!$R1 554
24 TraesCS7A01G082200 chr2A 65282613 65283155 542 False 782.000000 782 92.500000 5238 5792 1 chr2A.!!$F1 554
25 TraesCS7A01G082200 chr3A 726854506 726855051 545 True 815.000000 815 93.606000 5238 5790 1 chr3A.!!$R2 552
26 TraesCS7A01G082200 chr3A 532941867 532942414 547 False 797.000000 797 92.920000 5238 5792 1 chr3A.!!$F1 554
27 TraesCS7A01G082200 chr3A 455475597 455476131 534 True 747.000000 747 92.179000 5239 5763 1 chr3A.!!$R1 524
28 TraesCS7A01G082200 chr6B 685341023 685343768 2745 False 445.000000 767 81.491500 857 3481 4 chr6B.!!$F1 2624
29 TraesCS7A01G082200 chr1A 258200665 258201185 520 True 725.000000 725 91.636000 5230 5763 1 chr1A.!!$R1 533
30 TraesCS7A01G082200 chr6A 596902526 596903480 954 False 372.500000 623 84.316500 1431 2342 2 chr6A.!!$F1 911
31 TraesCS7A01G082200 chr5B 192661139 192661660 521 True 462.000000 462 83.022000 5239 5763 1 chr5B.!!$R1 524

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
245 1565 0.685785 TGGTGGAAAGCCTTGTGCAA 60.686 50.000 0.00 0.0 44.83 4.08 F
582 1903 1.762957 ACTCTCCGGTTACCCATGATG 59.237 52.381 0.00 0.0 0.00 3.07 F
1901 3409 0.315886 TTAAGCAGAGCCGACGTCAA 59.684 50.000 17.16 0.0 0.00 3.18 F
2500 4102 0.378610 GAGTAGAATGCAAAGCGGGC 59.621 55.000 0.00 0.0 0.00 6.13 F
4355 6350 0.040157 GCTGCTTTGCACATTCGACA 60.040 50.000 0.00 0.0 33.79 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 3354 1.669795 GCATCTTTTGCCTTTCCCACG 60.670 52.381 0.0 0.0 46.15 4.94 R
2500 4102 1.929836 GAGTGCTTCTAACGGATGCTG 59.070 52.381 0.0 0.0 43.06 4.41 R
3835 5562 0.764890 CCCACAGGTTGAGGAAGTCA 59.235 55.000 0.0 0.0 28.90 3.41 R
4375 6370 0.179020 CCCGCATTATCTCCTTGCCA 60.179 55.000 0.0 0.0 32.76 4.92 R
5514 7719 0.034477 GGAAATGAGCGAGGGGGAAA 60.034 55.000 0.0 0.0 0.00 3.13 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
107 1427 9.178758 ACAATAATTTTCTTACTGACCCTCATC 57.821 33.333 0.00 0.00 0.00 2.92
153 1473 7.672983 ACATATCTTGTACAACAGAGTTTGG 57.327 36.000 3.59 0.00 36.57 3.28
176 1496 0.732538 GCGGCTTGAATTGTTTCCGG 60.733 55.000 0.00 0.00 37.55 5.14
207 1527 2.946329 AGTCTAGTGATGTGTCTAGGCG 59.054 50.000 0.00 0.00 41.82 5.52
245 1565 0.685785 TGGTGGAAAGCCTTGTGCAA 60.686 50.000 0.00 0.00 44.83 4.08
259 1579 3.663995 TGTGCAATGTGGAAGGATTTG 57.336 42.857 0.00 0.00 0.00 2.32
309 1629 8.492673 TTTTTGCAGTATATCAGGAAGTGTAG 57.507 34.615 0.00 0.00 0.00 2.74
367 1687 9.239551 GATTGGTATTGTAGGTTAGGTTTCTTT 57.760 33.333 0.00 0.00 0.00 2.52
433 1753 6.603237 TGTTTCGGTGCAGATTATTAGATG 57.397 37.500 0.00 0.00 0.00 2.90
456 1777 4.127907 GGAAGGTGAAGTTCTCGAAACTT 58.872 43.478 19.04 19.04 42.62 2.66
556 1877 9.143631 CACCCTTTCAATTAAATCTTGATGTTC 57.856 33.333 0.00 0.00 32.94 3.18
582 1903 1.762957 ACTCTCCGGTTACCCATGATG 59.237 52.381 0.00 0.00 0.00 3.07
597 1918 3.070590 CCATGATGGCAGATCTGTACTGA 59.929 47.826 23.38 4.80 37.54 3.41
630 1959 5.855740 ATACCTCTGTTTCCTACTGCTAC 57.144 43.478 0.00 0.00 0.00 3.58
674 2004 5.713025 ACAACGAAGAGCCTACGTTAATAA 58.287 37.500 0.00 0.00 45.95 1.40
675 2005 6.335777 ACAACGAAGAGCCTACGTTAATAAT 58.664 36.000 0.00 0.00 45.95 1.28
676 2006 6.474751 ACAACGAAGAGCCTACGTTAATAATC 59.525 38.462 0.00 0.00 45.95 1.75
677 2007 6.140303 ACGAAGAGCCTACGTTAATAATCA 57.860 37.500 0.00 0.00 36.91 2.57
678 2008 6.567050 ACGAAGAGCCTACGTTAATAATCAA 58.433 36.000 0.00 0.00 36.91 2.57
679 2009 7.208080 ACGAAGAGCCTACGTTAATAATCAAT 58.792 34.615 0.00 0.00 36.91 2.57
680 2010 8.355169 ACGAAGAGCCTACGTTAATAATCAATA 58.645 33.333 0.00 0.00 36.91 1.90
710 2040 3.518634 TGAAGGTTTTTGTGTTGAGGC 57.481 42.857 0.00 0.00 0.00 4.70
749 2079 7.348080 TGATAGTTAGACCGTCATCTTTGAT 57.652 36.000 0.40 0.00 33.56 2.57
750 2080 7.203218 TGATAGTTAGACCGTCATCTTTGATG 58.797 38.462 0.40 1.45 38.41 3.07
815 2161 5.892160 ACATCAGATCTCCACAACAATTG 57.108 39.130 3.24 3.24 0.00 2.32
822 2168 7.280876 TCAGATCTCCACAACAATTGTTATAGC 59.719 37.037 22.87 8.29 43.23 2.97
909 2262 4.209911 GGTTATTTCTATTACGCACCGGAC 59.790 45.833 9.46 0.00 0.00 4.79
1194 2570 4.353777 TGGACTACTTCTATCAGGCACTT 58.646 43.478 0.00 0.00 34.60 3.16
1359 2744 2.098614 TCCTGTGTCTCTCTCTGCATC 58.901 52.381 0.00 0.00 0.00 3.91
1372 2757 3.056250 TCTCTGCATCTCTTTCCAGTGTC 60.056 47.826 0.00 0.00 0.00 3.67
1400 2785 5.183228 TGCCTGAATGTTTAGGTTAGTAGC 58.817 41.667 5.59 0.00 36.44 3.58
1430 2815 5.993055 TGATTTCAGGTGCTGATTATGAGA 58.007 37.500 0.00 0.00 40.39 3.27
1432 2817 7.058525 TGATTTCAGGTGCTGATTATGAGATT 58.941 34.615 0.00 0.00 40.39 2.40
1644 3136 3.722295 CACGACCGCACGCCATTT 61.722 61.111 0.00 0.00 36.70 2.32
1725 3226 9.635520 ATCTGAATTGAAAATTTGAGCTTACTG 57.364 29.630 0.00 0.00 0.00 2.74
1756 3257 3.823304 AGAGTGAAAGACATCCTTTTGGC 59.177 43.478 0.00 0.00 44.63 4.52
1764 3265 5.612725 AGACATCCTTTTGGCTTGAAAAA 57.387 34.783 0.00 0.00 40.12 1.94
1859 3363 2.841215 TCAGGTTAACACGTGGGAAAG 58.159 47.619 21.57 7.03 38.99 2.62
1901 3409 0.315886 TTAAGCAGAGCCGACGTCAA 59.684 50.000 17.16 0.00 0.00 3.18
1928 3440 3.320541 CCGCCTGGCCAATCATTAAATTA 59.679 43.478 14.12 0.00 0.00 1.40
2163 3675 2.760650 TCTGATGGTATGCGAGTGAACT 59.239 45.455 0.00 0.00 0.00 3.01
2169 3681 2.673368 GGTATGCGAGTGAACTTTCCTG 59.327 50.000 0.00 0.00 0.00 3.86
2357 3957 5.106869 GGTAAGTACGTGATGCATTTGTTGA 60.107 40.000 0.00 0.00 0.00 3.18
2393 3993 9.573133 TGTCTGATAATTAGCACGATATACATG 57.427 33.333 0.00 0.00 0.00 3.21
2417 4017 9.950680 ATGTGTTTACATCTGTTCTTTAAGTTG 57.049 29.630 0.00 0.00 44.00 3.16
2496 4098 2.159462 GGCACTGAGTAGAATGCAAAGC 60.159 50.000 0.00 0.00 39.92 3.51
2500 4102 0.378610 GAGTAGAATGCAAAGCGGGC 59.621 55.000 0.00 0.00 0.00 6.13
2584 4186 4.865925 CGGTTTGTACCATCGACTTCATTA 59.134 41.667 0.00 0.00 45.31 1.90
2697 4308 6.723977 AGGCCAGAGGTTATTCTCTATAGAAG 59.276 42.308 5.01 0.00 44.79 2.85
2741 4352 9.579932 AAGAAAATAGTCTGAAACTGAATTCCT 57.420 29.630 2.27 0.00 39.11 3.36
2750 4361 5.385198 TGAAACTGAATTCCTTTGCCTACT 58.615 37.500 2.27 0.00 0.00 2.57
2751 4362 6.539173 TGAAACTGAATTCCTTTGCCTACTA 58.461 36.000 2.27 0.00 0.00 1.82
2752 4363 6.655003 TGAAACTGAATTCCTTTGCCTACTAG 59.345 38.462 2.27 0.00 0.00 2.57
2782 4393 4.705110 TTTCTCATGTTTCTCTGGGTGA 57.295 40.909 0.00 0.00 0.00 4.02
2799 4411 3.118371 GGGTGATCTGTAGGTTAAGGTGG 60.118 52.174 0.00 0.00 0.00 4.61
2839 4472 7.761249 GCATCTTTTAAGGAAAATATGTGTGCT 59.239 33.333 9.08 0.00 39.53 4.40
2893 4526 6.379988 ACCAAAAGACACACTAAAATGGAAGT 59.620 34.615 0.00 0.00 0.00 3.01
2952 4585 3.187637 GCCGTTTACAATCAGTTACAGCA 59.812 43.478 0.00 0.00 0.00 4.41
3020 4688 4.965119 ACTTCCAATTTCATCGTTAGCC 57.035 40.909 0.00 0.00 0.00 3.93
3078 4750 6.035327 GCATGATTTAGCAATGTTTCTTGTCC 59.965 38.462 0.00 0.00 0.00 4.02
3091 4763 6.434596 TGTTTCTTGTCCGAATGTGTATTTG 58.565 36.000 0.00 0.00 0.00 2.32
3100 4773 5.870433 TCCGAATGTGTATTTGTTGTCGTAT 59.130 36.000 0.00 0.00 0.00 3.06
3101 4774 6.369340 TCCGAATGTGTATTTGTTGTCGTATT 59.631 34.615 0.00 0.00 0.00 1.89
3499 5205 5.961843 CGACAAAGCTAGCATGTAATCAAAG 59.038 40.000 21.66 7.78 0.00 2.77
3517 5236 0.606401 AGTCACCACCCAGCAAATCG 60.606 55.000 0.00 0.00 0.00 3.34
3539 5258 5.696270 TCGTTAAATCATATGCGCTGAATCT 59.304 36.000 9.73 0.00 0.00 2.40
3778 5505 2.672996 GTGGTCCGTGGCATTGCT 60.673 61.111 8.82 0.00 0.00 3.91
3823 5550 3.644399 GAAGACGTGGTCGGAGGGC 62.644 68.421 0.00 0.00 41.85 5.19
3835 5562 1.375326 GGAGGGCCACGACTTCTTT 59.625 57.895 6.18 0.00 0.00 2.52
3899 5626 6.387041 AGTACATATACGAGTTGCTAGCAA 57.613 37.500 26.06 26.06 36.33 3.91
4028 5917 7.684529 ACTCCAGAATTCTGTCAGAGTAAATT 58.315 34.615 29.35 14.69 39.51 1.82
4033 5922 9.092876 CAGAATTCTGTCAGAGTAAATTCTACC 57.907 37.037 24.65 2.12 42.04 3.18
4055 5944 6.721321 ACCGTTGTGAACTTACTTACATTTG 58.279 36.000 0.00 0.00 0.00 2.32
4219 6118 2.548920 CGGATTAGGTCATCCCTTGCTC 60.549 54.545 0.00 0.00 42.73 4.26
4316 6258 7.714377 AGAGATTCAGAATGTAACCATAAGCTG 59.286 37.037 0.00 0.00 37.40 4.24
4355 6350 0.040157 GCTGCTTTGCACATTCGACA 60.040 50.000 0.00 0.00 33.79 4.35
4375 6370 2.044806 ATATCAGGAGCGCGCCCTTT 62.045 55.000 30.59 23.83 0.00 3.11
4423 6418 6.326064 ACAGTAAGCATCTGAATCTCAGGTAT 59.674 38.462 3.92 0.00 44.39 2.73
4427 6422 4.040217 AGCATCTGAATCTCAGGTATGGTC 59.960 45.833 3.92 0.00 44.39 4.02
4428 6423 4.802248 GCATCTGAATCTCAGGTATGGTCC 60.802 50.000 3.92 0.00 44.39 4.46
4461 6468 5.279556 GCTACTAACTCCTTTTGTCAGGTCT 60.280 44.000 0.00 0.00 35.15 3.85
4470 6477 6.936279 TCCTTTTGTCAGGTCTAGTTCATAG 58.064 40.000 0.00 0.00 35.15 2.23
4650 6700 0.739462 CCGCAACGGTTCTCTATGCA 60.739 55.000 0.00 0.00 42.73 3.96
4758 6808 2.054453 GTTCATGGCTTCCCAGGGC 61.054 63.158 0.00 0.00 46.24 5.19
4894 6945 9.079833 CAGAATAATGCTTGTAATTTGTGAAGG 57.920 33.333 0.00 0.00 0.00 3.46
4895 6946 8.806146 AGAATAATGCTTGTAATTTGTGAAGGT 58.194 29.630 0.00 0.00 0.00 3.50
4919 6970 5.531634 TGAATTTTCAGCATTCCTGTTCAC 58.468 37.500 0.00 0.00 42.38 3.18
4944 6999 2.851263 AAATTCGTGTGTGCCCTCTA 57.149 45.000 0.00 0.00 0.00 2.43
4955 7010 1.004440 GCCCTCTATCGGCCATGAC 60.004 63.158 2.24 0.00 40.78 3.06
4956 7011 1.758440 GCCCTCTATCGGCCATGACA 61.758 60.000 2.24 0.00 40.78 3.58
5040 7096 0.038526 CCGTTGGAGTACTTGTCGCT 60.039 55.000 0.00 0.00 0.00 4.93
5160 7216 2.599645 ATCTTCCTCGGCAAGCGCAT 62.600 55.000 11.47 0.00 41.24 4.73
5165 7221 3.425938 CTCGGCAAGCGCATTCGTC 62.426 63.158 11.47 0.00 41.24 4.20
5166 7222 4.520846 CGGCAAGCGCATTCGTCC 62.521 66.667 11.47 0.25 41.24 4.79
5174 7230 1.813753 CGCATTCGTCCACCGGAAT 60.814 57.895 9.46 0.00 37.11 3.01
5315 7439 0.673644 ACGAGGATGGGCGTCTTTTG 60.674 55.000 0.00 0.00 35.59 2.44
5514 7719 3.227276 CCAGTATCGCCCGCTCCT 61.227 66.667 0.00 0.00 0.00 3.69
5515 7720 2.797278 CCAGTATCGCCCGCTCCTT 61.797 63.158 0.00 0.00 0.00 3.36
5516 7721 1.144057 CAGTATCGCCCGCTCCTTT 59.856 57.895 0.00 0.00 0.00 3.11
5517 7722 0.876342 CAGTATCGCCCGCTCCTTTC 60.876 60.000 0.00 0.00 0.00 2.62
5518 7723 1.594564 GTATCGCCCGCTCCTTTCC 60.595 63.158 0.00 0.00 0.00 3.13
5519 7724 2.803817 TATCGCCCGCTCCTTTCCC 61.804 63.158 0.00 0.00 0.00 3.97
5523 7728 3.798511 CCCGCTCCTTTCCCCCTC 61.799 72.222 0.00 0.00 0.00 4.30
5524 7729 4.162690 CCGCTCCTTTCCCCCTCG 62.163 72.222 0.00 0.00 0.00 4.63
5525 7730 4.840005 CGCTCCTTTCCCCCTCGC 62.840 72.222 0.00 0.00 0.00 5.03
5526 7731 3.403558 GCTCCTTTCCCCCTCGCT 61.404 66.667 0.00 0.00 0.00 4.93
5527 7732 2.904131 CTCCTTTCCCCCTCGCTC 59.096 66.667 0.00 0.00 0.00 5.03
5528 7733 1.990060 CTCCTTTCCCCCTCGCTCA 60.990 63.158 0.00 0.00 0.00 4.26
5557 7762 1.659794 GCTCGAGCCCTCATCTCTC 59.340 63.158 27.22 0.00 34.31 3.20
5558 7763 0.823356 GCTCGAGCCCTCATCTCTCT 60.823 60.000 27.22 0.00 34.31 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 1372 6.682537 ACCATATCCCAATACAAAGGAACAT 58.317 36.000 0.00 0.00 32.26 2.71
61 1381 7.969690 ATTGTCAAAACCATATCCCAATACA 57.030 32.000 0.00 0.00 0.00 2.29
107 1427 8.712285 ATGTTTCAGATTTTAATGCATGAAGG 57.288 30.769 0.00 0.00 0.00 3.46
138 1458 2.092211 CGCGATCCAAACTCTGTTGTAC 59.908 50.000 0.00 0.00 0.00 2.90
153 1473 2.177173 GAAACAATTCAAGCCGCGATC 58.823 47.619 8.23 0.00 35.54 3.69
176 1496 5.934625 ACACATCACTAGACTGAACCAATTC 59.065 40.000 0.00 0.00 35.18 2.17
207 1527 6.266558 TCCACCATCTAGCTAAGAAGATTCTC 59.733 42.308 0.00 0.00 37.89 2.87
245 1565 3.259123 GCCTTGAACAAATCCTTCCACAT 59.741 43.478 0.00 0.00 0.00 3.21
259 1579 9.807649 AAGAACATAAATATCATTGCCTTGAAC 57.192 29.630 0.00 0.00 0.00 3.18
309 1629 5.475719 GGGCAAAAACTAAAATACAGGTCC 58.524 41.667 0.00 0.00 0.00 4.46
367 1687 5.650703 TCAAATGTAGTCAGAGACGGTATCA 59.349 40.000 5.47 0.00 37.67 2.15
415 1735 4.271696 TCCCATCTAATAATCTGCACCG 57.728 45.455 0.00 0.00 0.00 4.94
433 1753 2.806818 GTTTCGAGAACTTCACCTTCCC 59.193 50.000 4.02 0.00 0.00 3.97
456 1777 6.316890 GTGACAAACCAACTACTTTACCTCAA 59.683 38.462 0.00 0.00 0.00 3.02
476 1797 2.543848 GTCGCACAAGAATTCTGTGACA 59.456 45.455 27.68 16.75 42.48 3.58
556 1877 2.770699 GGTAACCGGAGAGTCATACG 57.229 55.000 9.46 0.00 0.00 3.06
630 1959 3.254166 GTCCATTATGTGCCTAATGCCTG 59.746 47.826 5.63 0.00 37.64 4.85
640 1969 3.485877 GCTCTTCGTTGTCCATTATGTGC 60.486 47.826 0.00 0.00 0.00 4.57
749 2079 2.696707 ACTTTTGACACCTACGTCTCCA 59.303 45.455 0.00 0.00 36.82 3.86
750 2080 3.005578 AGACTTTTGACACCTACGTCTCC 59.994 47.826 0.00 0.00 36.82 3.71
751 2081 4.240175 AGACTTTTGACACCTACGTCTC 57.760 45.455 0.00 0.00 36.82 3.36
752 2082 4.667519 AAGACTTTTGACACCTACGTCT 57.332 40.909 0.00 0.00 36.82 4.18
753 2083 5.176406 GGTAAAGACTTTTGACACCTACGTC 59.824 44.000 5.61 0.00 36.40 4.34
815 2161 4.644103 TCAGTAAGGACCACGCTATAAC 57.356 45.455 0.00 0.00 0.00 1.89
822 2168 1.012486 GCGGTTCAGTAAGGACCACG 61.012 60.000 0.00 0.00 32.95 4.94
870 2223 2.270352 AACCGAATTTCAGTGAGGCA 57.730 45.000 0.00 0.00 0.00 4.75
984 2342 0.530744 CCATTGCTGCATTGAGCTGT 59.469 50.000 22.19 0.00 45.94 4.40
1359 2744 2.746362 GGCATCAAGACACTGGAAAGAG 59.254 50.000 0.00 0.00 0.00 2.85
1372 2757 5.649782 AACCTAAACATTCAGGCATCAAG 57.350 39.130 0.00 0.00 35.14 3.02
1400 2785 2.031420 CAGCACCTGAAATCAGTGTGTG 60.031 50.000 21.97 17.26 42.17 3.82
1425 2810 7.937700 TCTACCCCTGAAAAGATAATCTCAT 57.062 36.000 0.00 0.00 0.00 2.90
1426 2811 7.202130 CCATCTACCCCTGAAAAGATAATCTCA 60.202 40.741 0.00 0.00 0.00 3.27
1428 2813 6.851836 TCCATCTACCCCTGAAAAGATAATCT 59.148 38.462 0.00 0.00 0.00 2.40
1430 2815 7.465900 TTCCATCTACCCCTGAAAAGATAAT 57.534 36.000 0.00 0.00 0.00 1.28
1432 2817 6.183361 CCATTCCATCTACCCCTGAAAAGATA 60.183 42.308 0.00 0.00 0.00 1.98
1725 3226 7.327214 AGGATGTCTTTCACTCTGAATCTTAC 58.673 38.462 0.00 0.00 36.11 2.34
1850 3354 1.669795 GCATCTTTTGCCTTTCCCACG 60.670 52.381 0.00 0.00 46.15 4.94
1959 3471 6.694411 CCATTGTGACAAGTTCTGAAAAAGAG 59.306 38.462 3.74 0.00 35.91 2.85
2212 3730 4.447138 TGTAGCTTTCCCAGGAGAAAAA 57.553 40.909 0.00 0.00 35.41 1.94
2393 3993 9.783256 AACAACTTAAAGAACAGATGTAAACAC 57.217 29.630 0.00 0.00 0.00 3.32
2417 4017 8.231161 GGAAGAACAGAAGAAGCAAGTATTAAC 58.769 37.037 0.00 0.00 0.00 2.01
2420 4020 6.429385 CAGGAAGAACAGAAGAAGCAAGTATT 59.571 38.462 0.00 0.00 0.00 1.89
2421 4021 5.936956 CAGGAAGAACAGAAGAAGCAAGTAT 59.063 40.000 0.00 0.00 0.00 2.12
2500 4102 1.929836 GAGTGCTTCTAACGGATGCTG 59.070 52.381 0.00 0.00 43.06 4.41
2508 4110 5.871524 TGTCAATCTGATGAGTGCTTCTAAC 59.128 40.000 0.00 0.00 38.09 2.34
2648 4255 2.291365 CATCGATTGATCCAGGCAACA 58.709 47.619 0.00 0.00 32.33 3.33
2654 4261 2.414806 CCTCTGCATCGATTGATCCAG 58.585 52.381 7.49 7.49 41.05 3.86
2732 4343 7.731054 AGATACTAGTAGGCAAAGGAATTCAG 58.269 38.462 8.85 0.00 0.00 3.02
2777 4388 3.118371 CCACCTTAACCTACAGATCACCC 60.118 52.174 0.00 0.00 0.00 4.61
2778 4389 3.518303 ACCACCTTAACCTACAGATCACC 59.482 47.826 0.00 0.00 0.00 4.02
2779 4390 4.820894 ACCACCTTAACCTACAGATCAC 57.179 45.455 0.00 0.00 0.00 3.06
2782 4393 5.546499 TCTGAAACCACCTTAACCTACAGAT 59.454 40.000 0.00 0.00 0.00 2.90
2799 4411 9.294030 CCTTAAAAGATGCACATATTCTGAAAC 57.706 33.333 0.00 0.00 0.00 2.78
2893 4526 2.293122 CAGCCCGTTTCATCAGTTTCAA 59.707 45.455 0.00 0.00 0.00 2.69
3020 4688 4.624015 ACCATGTGACAAAATTCTGCAAG 58.376 39.130 0.00 0.00 0.00 4.01
3051 4720 7.101054 ACAAGAAACATTGCTAAATCATGCAT 58.899 30.769 0.00 0.00 39.07 3.96
3078 4750 8.429739 AAAATACGACAACAAATACACATTCG 57.570 30.769 0.00 0.00 0.00 3.34
3499 5205 0.889186 ACGATTTGCTGGGTGGTGAC 60.889 55.000 0.00 0.00 0.00 3.67
3517 5236 7.355017 TCAAGATTCAGCGCATATGATTTAAC 58.645 34.615 11.47 0.00 0.00 2.01
3539 5258 1.870402 ACGTGCAATCGATGTGTTCAA 59.130 42.857 0.00 0.00 34.70 2.69
3778 5505 4.329545 GGGAACAGCAGCGGGTGA 62.330 66.667 22.78 0.00 45.29 4.02
3823 5550 3.060602 GAGGAAGTCAAAGAAGTCGTGG 58.939 50.000 0.00 0.00 0.00 4.94
3835 5562 0.764890 CCCACAGGTTGAGGAAGTCA 59.235 55.000 0.00 0.00 28.90 3.41
3899 5626 3.692406 GAGCACGAACTCCCCGGT 61.692 66.667 0.00 0.00 0.00 5.28
4028 5917 6.389830 TGTAAGTAAGTTCACAACGGTAGA 57.610 37.500 0.00 0.00 36.23 2.59
4033 5922 8.120465 AGTTCAAATGTAAGTAAGTTCACAACG 58.880 33.333 0.00 0.00 36.23 4.10
4055 5944 4.015872 TCACCCTACAATCCACAAGTTC 57.984 45.455 0.00 0.00 0.00 3.01
4219 6118 5.108405 CCGAAGAACGTTTACTTGCAAATTG 60.108 40.000 0.46 0.00 40.78 2.32
4235 6134 4.320275 GGATCCAAACTTGAACCGAAGAAC 60.320 45.833 6.95 0.00 0.00 3.01
4267 6208 2.034053 GCGGTTTCAGGATTGACAAACA 59.966 45.455 0.00 0.00 31.71 2.83
4272 6213 3.119101 TCTCTAGCGGTTTCAGGATTGAC 60.119 47.826 0.00 0.00 31.71 3.18
4316 6258 9.578439 AAGCAGCTGTGATTTTTAGAATAAATC 57.422 29.630 16.64 0.00 40.66 2.17
4355 6350 2.031163 GGGCGCGCTCCTGATATT 59.969 61.111 32.29 0.00 0.00 1.28
4375 6370 0.179020 CCCGCATTATCTCCTTGCCA 60.179 55.000 0.00 0.00 32.76 4.92
4427 6422 1.521681 GTTAGTAGCAGCAGGGCGG 60.522 63.158 0.00 0.00 39.27 6.13
4428 6423 0.528684 GAGTTAGTAGCAGCAGGGCG 60.529 60.000 0.00 0.00 39.27 6.13
4461 6468 7.346175 TGGGTTATTCCTTGTAGCTATGAACTA 59.654 37.037 0.00 0.00 36.25 2.24
4470 6477 4.781934 ACAGATGGGTTATTCCTTGTAGC 58.218 43.478 0.00 0.00 36.25 3.58
4521 6571 1.080354 ACCCGGGAAGATCACCTCA 59.920 57.895 32.02 0.00 0.00 3.86
4581 6631 3.502164 CCTCATTGGGATCGGCTTT 57.498 52.632 0.00 0.00 0.00 3.51
4635 6685 2.831685 TGTGTGCATAGAGAACCGTT 57.168 45.000 0.00 0.00 0.00 4.44
4650 6700 1.338107 TCACCTCCGACTTGATGTGT 58.662 50.000 0.00 0.00 33.97 3.72
4758 6808 1.602377 GACGGAACTTGGGTGTTGAAG 59.398 52.381 0.00 0.00 0.00 3.02
4894 6945 5.984926 TGAACAGGAATGCTGAAAATTCAAC 59.015 36.000 9.20 0.00 36.64 3.18
4895 6946 5.984926 GTGAACAGGAATGCTGAAAATTCAA 59.015 36.000 9.20 0.00 36.64 2.69
4919 6970 4.555262 AGGGCACACACGAATTTAATTTG 58.445 39.130 3.54 3.54 0.00 2.32
4944 6999 2.824936 TGAACAATTTGTCATGGCCGAT 59.175 40.909 1.83 0.00 0.00 4.18
4955 7010 4.217118 AGCTTGCCTAGACTGAACAATTTG 59.783 41.667 0.00 0.00 0.00 2.32
4956 7011 4.401925 AGCTTGCCTAGACTGAACAATTT 58.598 39.130 0.00 0.00 0.00 1.82
5165 7221 1.032114 GGGCTTCAAGATTCCGGTGG 61.032 60.000 0.00 0.00 0.00 4.61
5166 7222 1.032114 GGGGCTTCAAGATTCCGGTG 61.032 60.000 0.00 0.00 0.00 4.94
5299 7423 1.408822 GGATCAAAAGACGCCCATCCT 60.409 52.381 0.00 0.00 0.00 3.24
5514 7719 0.034477 GGAAATGAGCGAGGGGGAAA 60.034 55.000 0.00 0.00 0.00 3.13
5515 7720 1.607612 GGAAATGAGCGAGGGGGAA 59.392 57.895 0.00 0.00 0.00 3.97
5516 7721 2.375345 GGGAAATGAGCGAGGGGGA 61.375 63.158 0.00 0.00 0.00 4.81
5517 7722 2.193248 GGGAAATGAGCGAGGGGG 59.807 66.667 0.00 0.00 0.00 5.40
5518 7723 2.193248 GGGGAAATGAGCGAGGGG 59.807 66.667 0.00 0.00 0.00 4.79
5519 7724 2.193248 GGGGGAAATGAGCGAGGG 59.807 66.667 0.00 0.00 0.00 4.30
5520 7725 1.147153 GAGGGGGAAATGAGCGAGG 59.853 63.158 0.00 0.00 0.00 4.63
5521 7726 1.227380 CGAGGGGGAAATGAGCGAG 60.227 63.158 0.00 0.00 0.00 5.03
5522 7727 2.900273 CGAGGGGGAAATGAGCGA 59.100 61.111 0.00 0.00 0.00 4.93
5523 7728 2.897350 GCGAGGGGGAAATGAGCG 60.897 66.667 0.00 0.00 0.00 5.03
5524 7729 1.524849 GAGCGAGGGGGAAATGAGC 60.525 63.158 0.00 0.00 0.00 4.26
5525 7730 1.227380 CGAGCGAGGGGGAAATGAG 60.227 63.158 0.00 0.00 0.00 2.90
5526 7731 1.676678 CTCGAGCGAGGGGGAAATGA 61.677 60.000 11.83 0.00 38.51 2.57
5527 7732 1.227380 CTCGAGCGAGGGGGAAATG 60.227 63.158 11.83 0.00 38.51 2.32
5528 7733 3.095347 GCTCGAGCGAGGGGGAAAT 62.095 63.158 23.61 0.00 42.19 2.17
5557 7762 5.246429 GGGTTAGGTATTATGTGGGAGAGAG 59.754 48.000 0.00 0.00 0.00 3.20
5558 7763 5.102783 AGGGTTAGGTATTATGTGGGAGAGA 60.103 44.000 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.