Multiple sequence alignment - TraesCS2A01G328400

Loading Multiple Alignment...

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 TraesCS2A01G328400 chr2A 100.000 4223 0 0 1 4223 559837574 559833352 0.000000e+00 7799.0
1 TraesCS2A01G328400 chr2A 93.673 980 61 1 2933 3912 559778046 559777068 0.000000e+00 1465.0
2 TraesCS2A01G328400 chr2A 86.801 1341 137 20 1 1332 559779351 559778042 0.000000e+00 1459.0
3 TraesCS2A01G328400 chr2A 86.080 1056 100 21 2977 4016 559704427 559703403 0.000000e+00 1092.0
4 TraesCS2A01G328400 chr2A 92.695 616 41 1 720 1331 559741263 559740648 0.000000e+00 885.0
5 TraesCS2A01G328400 chr2A 84.974 772 83 13 1 742 559742823 559742055 0.000000e+00 752.0
6 TraesCS2A01G328400 chr2A 94.357 443 15 3 1333 1773 559835077 559834643 0.000000e+00 671.0
7 TraesCS2A01G328400 chr2A 94.357 443 15 3 2498 2932 559836242 559835802 0.000000e+00 671.0
8 TraesCS2A01G328400 chr2A 84.457 682 75 17 1807 2462 564075702 564075026 0.000000e+00 643.0
9 TraesCS2A01G328400 chr2A 95.349 301 10 2 3923 4223 559776783 559776487 3.820000e-130 475.0
10 TraesCS2A01G328400 chr2D 90.889 1339 90 8 1 1332 427924619 427925932 0.000000e+00 1768.0
11 TraesCS2A01G328400 chr2D 90.957 1338 83 10 1 1332 427943847 427945152 0.000000e+00 1766.0
12 TraesCS2A01G328400 chr2D 91.475 1220 85 15 2933 4144 427910179 427911387 0.000000e+00 1659.0
13 TraesCS2A01G328400 chr2D 90.519 1234 105 9 1 1222 427905287 427906520 0.000000e+00 1620.0
14 TraesCS2A01G328400 chr2D 90.339 1180 106 5 159 1332 427909006 427910183 0.000000e+00 1541.0
15 TraesCS2A01G328400 chr2D 86.519 1350 131 23 1 1331 427783722 427785039 0.000000e+00 1437.0
16 TraesCS2A01G328400 chr2D 90.153 914 73 12 3238 4144 427927958 427928861 0.000000e+00 1173.0
17 TraesCS2A01G328400 chr2D 89.655 841 59 13 2934 3747 427945149 427945988 0.000000e+00 1046.0
18 TraesCS2A01G328400 chr2D 94.855 311 16 0 2933 3243 427925928 427926238 1.770000e-133 486.0
19 TraesCS2A01G328400 chr2D 88.038 418 37 6 2938 3343 427785041 427785457 2.280000e-132 483.0
20 TraesCS2A01G328400 chr2D 79.147 211 22 9 3806 4016 427785622 427785810 4.430000e-25 126.0
21 TraesCS2A01G328400 chr2D 97.222 72 2 0 4152 4223 427911557 427911628 5.730000e-24 122.0
22 TraesCS2A01G328400 chr2D 97.222 72 2 0 4152 4223 427929031 427929102 5.730000e-24 122.0
23 TraesCS2A01G328400 chr2B 87.803 1361 119 13 1 1332 504769247 504770589 0.000000e+00 1550.0
24 TraesCS2A01G328400 chr2B 86.852 1369 111 23 1 1332 512358783 512357447 0.000000e+00 1467.0
25 TraesCS2A01G328400 chr2B 88.586 1139 83 13 2933 4062 512357451 512356351 0.000000e+00 1339.0
26 TraesCS2A01G328400 chr2B 91.489 846 62 5 2933 3771 504770585 504771427 0.000000e+00 1155.0
27 TraesCS2A01G328400 chr2B 86.765 884 100 10 3 876 512365135 512364259 0.000000e+00 968.0
28 TraesCS2A01G328400 chr2B 88.220 747 60 9 1730 2462 773559861 773560593 0.000000e+00 867.0
29 TraesCS2A01G328400 chr2B 87.586 290 28 4 3774 4062 504771981 504772263 3.150000e-86 329.0
30 TraesCS2A01G328400 chr7A 88.221 798 62 9 1732 2506 78567652 78566864 0.000000e+00 924.0
31 TraesCS2A01G328400 chr7A 84.178 651 59 16 1821 2456 643774716 643775337 3.640000e-165 592.0
32 TraesCS2A01G328400 chr7A 83.634 666 63 16 1807 2456 643775967 643776602 6.080000e-163 584.0
33 TraesCS2A01G328400 chr6A 89.243 753 61 6 1730 2468 448648254 448647508 0.000000e+00 924.0
34 TraesCS2A01G328400 chr6A 80.592 608 61 28 2112 2668 317156623 317156022 2.350000e-112 416.0
35 TraesCS2A01G328400 chr6A 85.608 403 39 9 1978 2362 187728917 187729318 5.080000e-109 405.0
36 TraesCS2A01G328400 chr4A 88.331 737 64 14 1730 2452 22533725 22534453 0.000000e+00 865.0
37 TraesCS2A01G328400 chr4A 86.486 555 55 7 1734 2284 441825533 441824995 3.640000e-165 592.0
38 TraesCS2A01G328400 chr4A 86.444 450 53 8 1727 2171 244914321 244914767 1.770000e-133 486.0
39 TraesCS2A01G328400 chr4A 87.407 135 6 10 2567 2694 625092833 625092703 1.220000e-30 145.0
40 TraesCS2A01G328400 chr1A 87.370 768 57 13 1730 2476 31815926 31815178 0.000000e+00 845.0
41 TraesCS2A01G328400 chr7B 87.635 647 51 10 1828 2451 658023537 658024177 0.000000e+00 725.0
42 TraesCS2A01G328400 chr5B 89.251 521 41 6 1730 2241 592748076 592747562 4.600000e-179 638.0
43 TraesCS2A01G328400 chr5B 86.712 444 37 11 1978 2406 319312857 319312421 1.370000e-129 473.0
44 TraesCS2A01G328400 chr5B 85.654 237 19 4 2230 2452 592741528 592741293 7.060000e-58 235.0
45 TraesCS2A01G328400 chr6B 93.824 421 17 3 1333 1745 151910802 151911221 3.580000e-175 625.0
46 TraesCS2A01G328400 chr6B 90.150 467 36 5 1333 1792 151909580 151910043 2.170000e-167 599.0
47 TraesCS2A01G328400 chr6B 92.027 439 14 8 2483 2904 151910787 151911221 7.820000e-167 597.0
48 TraesCS2A01G328400 chr6B 89.882 425 25 7 2497 2906 151909579 151910000 8.040000e-147 531.0
49 TraesCS2A01G328400 chr6D 85.769 527 59 10 1978 2502 343477182 343477694 1.030000e-150 544.0
50 TraesCS2A01G328400 chr6D 96.610 59 2 0 2448 2506 367105434 367105376 9.660000e-17 99.0
51 TraesCS2A01G328400 chr5A 87.257 463 37 14 1730 2179 133508110 133507657 3.770000e-140 508.0
52 TraesCS2A01G328400 chr7D 84.162 543 56 15 1978 2506 627818042 627818568 2.270000e-137 499.0
53 TraesCS2A01G328400 chr5D 87.359 443 36 6 1978 2406 18158608 18159044 1.360000e-134 490.0
54 TraesCS2A01G328400 chr5D 85.981 214 12 10 2449 2658 23109727 23109926 3.310000e-51 213.0
55 TraesCS2A01G328400 chr5D 86.957 138 8 7 2527 2658 23108660 23108793 3.400000e-31 147.0
56 TraesCS2A01G328400 chr4D 82.993 588 47 18 2102 2650 351689235 351688662 2.280000e-132 483.0
57 TraesCS2A01G328400 chr4D 93.141 277 13 3 1333 1604 238023996 238024271 6.580000e-108 401.0
58 TraesCS2A01G328400 chr4D 92.419 277 12 4 2498 2768 238023996 238024269 1.840000e-103 387.0
59 TraesCS2A01G328400 chr1D 86.456 443 40 6 1978 2406 14314454 14314018 6.390000e-128 468.0
60 TraesCS2A01G328400 chr1D 80.000 285 37 17 2448 2721 395094621 395094896 4.310000e-45 193.0
61 TraesCS2A01G328400 chr3B 88.852 305 29 4 2165 2468 94484220 94483920 1.850000e-98 370.0
62 TraesCS2A01G328400 chr3B 95.161 62 3 0 2447 2508 36434285 36434346 9.660000e-17 99.0
63 TraesCS2A01G328400 chr3D 82.036 167 16 11 2448 2606 390047465 390047305 3.430000e-26 130.0
64 TraesCS2A01G328400 chr3D 80.838 167 18 11 2448 2606 390045632 390045472 7.420000e-23 119.0
65 TraesCS2A01G328400 chr3D 77.647 170 23 15 2454 2609 69914210 69914042 5.820000e-14 89.8
66 TraesCS2A01G328400 chrUn 80.272 147 21 8 2448 2590 126797668 126797810 2.080000e-18 104.0
67 TraesCS2A01G328400 chrUn 93.846 65 4 0 1422 1486 146408994 146408930 9.660000e-17 99.0
68 TraesCS2A01G328400 chrUn 93.333 60 4 0 1427 1486 146421475 146421416 5.820000e-14 89.8


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 TraesCS2A01G328400 chr2A 559833352 559837574 4222 True 3047.000000 7799 96.238000 1 4223 3 chr2A.!!$R5 4222
1 TraesCS2A01G328400 chr2A 559776487 559779351 2864 True 1133.000000 1465 91.941000 1 4223 3 chr2A.!!$R4 4222
2 TraesCS2A01G328400 chr2A 559703403 559704427 1024 True 1092.000000 1092 86.080000 2977 4016 1 chr2A.!!$R1 1039
3 TraesCS2A01G328400 chr2A 559740648 559742823 2175 True 818.500000 885 88.834500 1 1331 2 chr2A.!!$R3 1330
4 TraesCS2A01G328400 chr2A 564075026 564075702 676 True 643.000000 643 84.457000 1807 2462 1 chr2A.!!$R2 655
5 TraesCS2A01G328400 chr2D 427943847 427945988 2141 False 1406.000000 1766 90.306000 1 3747 2 chr2D.!!$F4 3746
6 TraesCS2A01G328400 chr2D 427905287 427911628 6341 False 1235.500000 1659 92.388750 1 4223 4 chr2D.!!$F2 4222
7 TraesCS2A01G328400 chr2D 427924619 427929102 4483 False 887.250000 1768 93.279750 1 4223 4 chr2D.!!$F3 4222
8 TraesCS2A01G328400 chr2D 427783722 427785810 2088 False 682.000000 1437 84.568000 1 4016 3 chr2D.!!$F1 4015
9 TraesCS2A01G328400 chr2B 512356351 512358783 2432 True 1403.000000 1467 87.719000 1 4062 2 chr2B.!!$R2 4061
10 TraesCS2A01G328400 chr2B 504769247 504772263 3016 False 1011.333333 1550 88.959333 1 4062 3 chr2B.!!$F2 4061
11 TraesCS2A01G328400 chr2B 512364259 512365135 876 True 968.000000 968 86.765000 3 876 1 chr2B.!!$R1 873
12 TraesCS2A01G328400 chr2B 773559861 773560593 732 False 867.000000 867 88.220000 1730 2462 1 chr2B.!!$F1 732
13 TraesCS2A01G328400 chr7A 78566864 78567652 788 True 924.000000 924 88.221000 1732 2506 1 chr7A.!!$R1 774
14 TraesCS2A01G328400 chr7A 643774716 643776602 1886 False 588.000000 592 83.906000 1807 2456 2 chr7A.!!$F1 649
15 TraesCS2A01G328400 chr6A 448647508 448648254 746 True 924.000000 924 89.243000 1730 2468 1 chr6A.!!$R2 738
16 TraesCS2A01G328400 chr6A 317156022 317156623 601 True 416.000000 416 80.592000 2112 2668 1 chr6A.!!$R1 556
17 TraesCS2A01G328400 chr4A 22533725 22534453 728 False 865.000000 865 88.331000 1730 2452 1 chr4A.!!$F1 722
18 TraesCS2A01G328400 chr4A 441824995 441825533 538 True 592.000000 592 86.486000 1734 2284 1 chr4A.!!$R1 550
19 TraesCS2A01G328400 chr1A 31815178 31815926 748 True 845.000000 845 87.370000 1730 2476 1 chr1A.!!$R1 746
20 TraesCS2A01G328400 chr7B 658023537 658024177 640 False 725.000000 725 87.635000 1828 2451 1 chr7B.!!$F1 623
21 TraesCS2A01G328400 chr5B 592747562 592748076 514 True 638.000000 638 89.251000 1730 2241 1 chr5B.!!$R3 511
22 TraesCS2A01G328400 chr6B 151909579 151911221 1642 False 588.000000 625 91.470750 1333 2906 4 chr6B.!!$F1 1573
23 TraesCS2A01G328400 chr6D 343477182 343477694 512 False 544.000000 544 85.769000 1978 2502 1 chr6D.!!$F1 524
24 TraesCS2A01G328400 chr7D 627818042 627818568 526 False 499.000000 499 84.162000 1978 2506 1 chr7D.!!$F1 528
25 TraesCS2A01G328400 chr4D 351688662 351689235 573 True 483.000000 483 82.993000 2102 2650 1 chr4D.!!$R1 548


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
881 5320 0.773644 AAAAGGAGGAGGAGCAGCAA 59.226 50.0 0.00 0.00 0.00 3.91 F
1019 5462 0.178998 ATGGCTAATCTGGCAGCAGG 60.179 55.0 10.34 1.03 45.49 4.85 F
2914 8984 0.096976 GCACGCACACACATATGGAC 59.903 55.0 7.80 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2273 6991 0.528470 GCTACAAGCAGACGAGGAGT 59.472 55.000 0.0 0.0 41.89 3.85 R
2924 8994 0.882927 GAACCTGCACCGTGTTAGCA 60.883 55.000 0.0 0.0 36.72 3.49 R
4088 12776 2.038952 ACAGCAAAGTGAGCAGGTCATA 59.961 45.455 5.4 0.0 37.56 2.15 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
63 65 7.661968 TCTCTCAATTATCTGAATTAGGGACG 58.338 38.462 0.00 0.00 0.00 4.79
75 77 3.317455 TTAGGGACGTAGGGAATGCTA 57.683 47.619 0.00 0.00 0.00 3.49
147 149 3.446310 TTTAGAGCGCCGACATCATTA 57.554 42.857 2.29 0.00 0.00 1.90
235 242 9.578576 AAAAATAGCATGTATGGTCTCATATGT 57.421 29.630 1.90 0.00 38.06 2.29
249 257 7.833682 TGGTCTCATATGTGATAAAAATGTGGT 59.166 33.333 10.47 0.00 32.98 4.16
261 269 5.534207 AAAAATGTGGTGTGTCATCATGT 57.466 34.783 0.00 0.00 0.00 3.21
350 360 7.374754 GCGACAAATTAAATCAACGCACATATA 59.625 33.333 0.00 0.00 43.35 0.86
364 374 7.421530 ACGCACATATATTTAACAGTCATCC 57.578 36.000 0.00 0.00 0.00 3.51
420 430 6.127980 TGTTCCTTACGAAAACACAAATCACA 60.128 34.615 0.00 0.00 30.39 3.58
436 446 7.120285 CACAAATCACATCCTTATCAACTGTCT 59.880 37.037 0.00 0.00 0.00 3.41
447 457 3.213206 TCAACTGTCTGAAAGCCATGT 57.787 42.857 0.00 0.00 0.00 3.21
478 488 1.344763 ACAACTTACTCTTCTGCCGCT 59.655 47.619 0.00 0.00 0.00 5.52
495 526 3.610821 GCCGCTTACTTGTTTCGGAAAAT 60.611 43.478 4.46 0.00 42.43 1.82
529 560 1.899814 TCCATTTAGTCAGAGGCGTGT 59.100 47.619 0.00 0.00 0.00 4.49
546 578 3.119673 GCGTGTCTCTCTCAATTCTCTGA 60.120 47.826 0.00 0.00 0.00 3.27
601 636 1.069358 GAAGCCTAGATCAACCTCCCG 59.931 57.143 0.00 0.00 0.00 5.14
621 662 9.144298 CCTCCCGCTCTTATATTAGGAATATTA 57.856 37.037 0.00 0.00 35.72 0.98
701 4307 2.618709 AGACGAAACTGAAAAAGGCCAG 59.381 45.455 5.01 0.00 36.53 4.85
804 5226 2.953093 TTGACACCCCCTATCTGGTA 57.047 50.000 0.00 0.00 32.32 3.25
815 5241 5.030147 CCCCTATCTGGTATGCCATACTTA 58.970 45.833 14.18 3.95 45.05 2.24
848 5281 4.454678 CTTCCTTGCTAACTGCCATGATA 58.545 43.478 0.00 0.00 42.00 2.15
881 5320 0.773644 AAAAGGAGGAGGAGCAGCAA 59.226 50.000 0.00 0.00 0.00 3.91
901 5340 3.231298 CCCCCGGATCTGAGTTCC 58.769 66.667 0.73 0.00 0.00 3.62
916 5355 1.858910 AGTTCCCCCATGGCATAATCA 59.141 47.619 6.09 0.00 0.00 2.57
1019 5462 0.178998 ATGGCTAATCTGGCAGCAGG 60.179 55.000 10.34 1.03 45.49 4.85
1295 5738 2.307768 CCAGGAGAAGGCATACTACGA 58.692 52.381 0.00 0.00 0.00 3.43
1381 5824 2.057922 CCCTAGCTCTCCTCTCTCTCT 58.942 57.143 0.00 0.00 0.00 3.10
1391 5834 4.473196 TCTCCTCTCTCTCTTTCTCTAGCA 59.527 45.833 0.00 0.00 0.00 3.49
1411 5854 1.416401 ACGAACCAAGCAGAAGAAGGA 59.584 47.619 0.00 0.00 0.00 3.36
1418 5861 3.244700 CCAAGCAGAAGAAGGAAGGAAGA 60.245 47.826 0.00 0.00 0.00 2.87
1420 5863 4.284829 AGCAGAAGAAGGAAGGAAGAAG 57.715 45.455 0.00 0.00 0.00 2.85
1421 5864 3.906846 AGCAGAAGAAGGAAGGAAGAAGA 59.093 43.478 0.00 0.00 0.00 2.87
1422 5865 4.000325 GCAGAAGAAGGAAGGAAGAAGAC 59.000 47.826 0.00 0.00 0.00 3.01
1426 5869 5.245977 AGAAGAAGGAAGGAAGAAGACAGAG 59.754 44.000 0.00 0.00 0.00 3.35
1457 5904 3.966215 TTTTTCCAGGCGCTCGAG 58.034 55.556 8.45 8.45 0.00 4.04
1469 5916 2.811317 CTCGAGCGCCACTTCCAC 60.811 66.667 2.29 0.00 0.00 4.02
1475 5922 3.414700 CGCCACTTCCACGAGCAC 61.415 66.667 0.00 0.00 0.00 4.40
1496 5943 0.600255 AACTCGTCAAACCTCGCCAG 60.600 55.000 0.00 0.00 0.00 4.85
1541 5988 2.370445 CCTGGGAGACGCTGGGAAT 61.370 63.158 0.00 0.00 33.17 3.01
1564 6013 2.358737 CCACGTCCTCCACCAAGC 60.359 66.667 0.00 0.00 0.00 4.01
1570 6019 1.461268 TCCTCCACCAAGCAGGACA 60.461 57.895 1.83 0.00 41.22 4.02
1646 6095 1.298713 CGAGCCCTCAACGATCTCG 60.299 63.158 0.00 0.00 46.33 4.04
1749 6199 4.312231 GCACGCACGCACACACAT 62.312 61.111 0.00 0.00 0.00 3.21
1916 6366 3.183776 TACACGACGAGCACGCACA 62.184 57.895 0.00 0.00 43.96 4.57
1922 6372 2.355126 CGAGCACGCACACAGTCT 60.355 61.111 0.00 0.00 0.00 3.24
1983 6447 4.980805 GCCTTCGTCACGCCACCA 62.981 66.667 0.00 0.00 0.00 4.17
2080 6622 4.389576 CGCAAACAGGTCCAGCGC 62.390 66.667 0.00 0.00 41.95 5.92
2081 6623 4.043200 GCAAACAGGTCCAGCGCC 62.043 66.667 2.29 0.00 0.00 6.53
2082 6624 2.281761 CAAACAGGTCCAGCGCCT 60.282 61.111 2.29 0.00 36.66 5.52
2083 6625 2.032681 AAACAGGTCCAGCGCCTC 59.967 61.111 2.29 0.00 33.31 4.70
2084 6626 3.883744 AAACAGGTCCAGCGCCTCG 62.884 63.158 2.29 0.00 33.31 4.63
2187 6888 2.046285 GCTTATTGCCCTGCACCGT 61.046 57.895 0.00 0.00 38.71 4.83
2202 6903 3.722295 CGTTGCGCCGTCAACCAT 61.722 61.111 4.18 0.00 42.37 3.55
2273 6991 2.915659 ACGCAGGTCCTCCACGAA 60.916 61.111 11.45 0.00 38.39 3.85
2552 8606 3.629398 GCTCTCCTCTCTCTCTTTCTCTG 59.371 52.174 0.00 0.00 0.00 3.35
2669 8728 2.032290 GTCAAACCTCGCCAGTTACAAC 60.032 50.000 0.00 0.00 0.00 3.32
2736 8795 1.461268 TCCTCCACCAAGCAGGACA 60.461 57.895 1.83 0.00 41.22 4.02
2740 8799 2.515398 CACCAAGCAGGACACCCA 59.485 61.111 1.83 0.00 41.22 4.51
2804 8870 1.153549 GCGAGCCCTCAACGATCTT 60.154 57.895 0.00 0.00 0.00 2.40
2884 8954 3.653009 CACACACGCACCAGCCTG 61.653 66.667 0.00 0.00 37.52 4.85
2908 8978 4.312231 GCACGCACGCACACACAT 62.312 61.111 0.00 0.00 0.00 3.21
2909 8979 2.949030 GCACGCACGCACACACATA 61.949 57.895 0.00 0.00 0.00 2.29
2910 8980 1.787215 CACGCACGCACACACATAT 59.213 52.632 0.00 0.00 0.00 1.78
2911 8981 0.518969 CACGCACGCACACACATATG 60.519 55.000 0.00 0.00 0.00 1.78
2912 8982 1.060779 CGCACGCACACACATATGG 59.939 57.895 7.80 0.00 0.00 2.74
2913 8983 1.357991 CGCACGCACACACATATGGA 61.358 55.000 7.80 0.00 0.00 3.41
2914 8984 0.096976 GCACGCACACACATATGGAC 59.903 55.000 7.80 0.00 0.00 4.02
2915 8985 1.437625 CACGCACACACATATGGACA 58.562 50.000 7.80 0.00 0.00 4.02
2916 8986 2.009051 CACGCACACACATATGGACAT 58.991 47.619 7.80 0.00 0.00 3.06
2917 8987 3.194062 CACGCACACACATATGGACATA 58.806 45.455 7.80 0.00 0.00 2.29
2918 8988 3.245990 CACGCACACACATATGGACATAG 59.754 47.826 7.80 0.00 0.00 2.23
2919 8989 2.221749 CGCACACACATATGGACATAGC 59.778 50.000 7.80 3.26 0.00 2.97
2920 8990 3.470709 GCACACACATATGGACATAGCT 58.529 45.455 7.80 0.00 0.00 3.32
2921 8991 3.879295 GCACACACATATGGACATAGCTT 59.121 43.478 7.80 0.00 0.00 3.74
2922 8992 4.260907 GCACACACATATGGACATAGCTTG 60.261 45.833 7.80 0.00 0.00 4.01
2923 8993 3.879295 ACACACATATGGACATAGCTTGC 59.121 43.478 7.80 0.00 0.00 4.01
2924 8994 4.132336 CACACATATGGACATAGCTTGCT 58.868 43.478 7.80 0.00 0.00 3.91
2925 8995 4.024302 CACACATATGGACATAGCTTGCTG 60.024 45.833 7.80 0.00 0.00 4.41
2926 8996 3.058432 CACATATGGACATAGCTTGCTGC 60.058 47.826 7.80 0.00 43.29 5.25
2935 9005 3.655481 GCTTGCTGCTAACACGGT 58.345 55.556 0.00 0.00 38.95 4.83
3010 9080 1.115467 CTGGCGGATGAAGGAGTACT 58.885 55.000 0.00 0.00 0.00 2.73
3021 9091 2.310779 AGGAGTACTGGCTCAACAGA 57.689 50.000 0.00 0.00 40.97 3.41
3121 9192 3.933722 CGCTGATCCCTCCGCCAT 61.934 66.667 0.00 0.00 0.00 4.40
3227 9304 4.176752 GCTGGGGAACTAGGGCGG 62.177 72.222 0.00 0.00 39.75 6.13
3336 11146 2.957402 TTCAGTTCTGGATTGTGCCT 57.043 45.000 0.00 0.00 0.00 4.75
3343 11153 1.554617 TCTGGATTGTGCCTTCGATCA 59.445 47.619 0.00 0.00 31.73 2.92
3359 11169 2.223203 CGATCAAGTTGAGGCAGATTGC 60.223 50.000 11.91 0.00 44.08 3.56
3387 11197 5.211454 TGTAGTTCGTCGATCGTTGTTTTA 58.789 37.500 15.94 0.39 40.80 1.52
3391 11201 5.403166 AGTTCGTCGATCGTTGTTTTAATCA 59.597 36.000 15.94 0.00 40.80 2.57
3431 11241 7.386851 TCTGTTGCTTAGACATAGCTTTAGTT 58.613 34.615 0.00 0.00 39.38 2.24
3458 11284 5.772825 ATGACTTTGCTATGTTTGTGTGT 57.227 34.783 0.00 0.00 0.00 3.72
3461 11287 5.586643 TGACTTTGCTATGTTTGTGTGTGTA 59.413 36.000 0.00 0.00 0.00 2.90
3528 11358 7.710044 TGATTGTGCTCATTGTGTTTGTATTTT 59.290 29.630 0.00 0.00 0.00 1.82
3560 11390 9.932207 TGCTTCATTTGAGTCAATAAAAATCAT 57.068 25.926 6.36 0.00 0.00 2.45
3598 11429 9.947433 AAAATTATGATCCATCTTCTTTGCAAA 57.053 25.926 12.14 12.14 0.00 3.68
3611 11442 8.627208 TCTTCTTTGCAAAATCTATCAGAACT 57.373 30.769 13.84 0.00 0.00 3.01
3749 11606 1.534729 ATTGGTCTCCGTTTCTTGGC 58.465 50.000 0.00 0.00 0.00 4.52
3854 12267 5.358160 AGCTTACAATAATTGCTTCTGGGTC 59.642 40.000 0.00 0.00 0.00 4.46
3874 12287 2.486203 TCGCACGAGTTATTTTTGGCAT 59.514 40.909 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 149 5.276461 TGCATACATCTATCCGACAAAGT 57.724 39.130 0.00 0.00 0.00 2.66
200 207 8.612619 ACCATACATGCTATTTTTAAAGAGACG 58.387 33.333 1.28 0.00 28.93 4.18
213 220 7.486407 TCACATATGAGACCATACATGCTAT 57.514 36.000 10.38 0.00 38.02 2.97
235 242 6.890979 TGATGACACACCACATTTTTATCA 57.109 33.333 0.00 0.00 0.00 2.15
249 257 1.545582 TGAGCTCGACATGATGACACA 59.454 47.619 9.64 0.00 0.00 3.72
261 269 2.025155 GACAACCCTAGATGAGCTCGA 58.975 52.381 9.64 0.00 0.00 4.04
313 321 5.866335 TTAATTTGTCGCCGAACAATACT 57.134 34.783 0.00 0.00 38.83 2.12
350 360 5.116882 GCTTACGAGGGATGACTGTTAAAT 58.883 41.667 0.00 0.00 0.00 1.40
403 413 5.514274 AAGGATGTGATTTGTGTTTTCGT 57.486 34.783 0.00 0.00 0.00 3.85
420 430 5.189180 GGCTTTCAGACAGTTGATAAGGAT 58.811 41.667 0.00 0.00 0.00 3.24
436 446 2.607499 ACCAAATCCACATGGCTTTCA 58.393 42.857 0.00 0.00 40.51 2.69
447 457 7.444183 CAGAAGAGTAAGTTGTTACCAAATCCA 59.556 37.037 0.00 0.00 39.65 3.41
456 466 3.006537 AGCGGCAGAAGAGTAAGTTGTTA 59.993 43.478 1.45 0.00 0.00 2.41
478 488 6.702716 AGGTTGATTTTCCGAAACAAGTAA 57.297 33.333 0.00 0.00 0.00 2.24
495 526 8.754991 TGACTAAATGGAGTTTTTAAGGTTGA 57.245 30.769 0.00 0.00 0.00 3.18
518 549 0.036875 TGAGAGAGACACGCCTCTGA 59.963 55.000 7.23 0.00 43.11 3.27
529 560 8.790718 CCAAAATTTTCAGAGAATTGAGAGAGA 58.209 33.333 0.00 0.00 0.00 3.10
546 578 6.594744 AGCATTTCTTGAGTCCCAAAATTTT 58.405 32.000 0.00 0.00 33.76 1.82
701 4307 1.343465 TGAAAAGAGGGTCAGACCGAC 59.657 52.381 13.80 9.72 44.57 4.79
715 4321 6.429078 TGATCAAGAGTGTCCAATCTGAAAAG 59.571 38.462 0.00 0.00 35.75 2.27
804 5226 4.475016 AGGTTCCAGAAGTAAGTATGGCAT 59.525 41.667 4.88 4.88 32.63 4.40
848 5281 3.134804 CCTCCTTTTGTAGATGGGACGAT 59.865 47.826 0.00 0.00 0.00 3.73
901 5340 3.569491 AGAGTTTGATTATGCCATGGGG 58.431 45.455 15.13 0.00 37.18 4.96
916 5355 2.711009 TGTTGGGTGGATCAGAGAGTTT 59.289 45.455 0.00 0.00 0.00 2.66
1019 5462 1.232621 GGGTTGGAACACGTAGCCAC 61.233 60.000 3.02 0.50 39.29 5.01
1089 5532 3.009115 CCGGGGAGGAAGAAGCCA 61.009 66.667 0.00 0.00 45.00 4.75
1151 5594 1.544759 GGTTTTTCGGGAAGGAGAGCA 60.545 52.381 0.00 0.00 0.00 4.26
1287 5730 2.550101 GCCCTCGCCGTCGTAGTAT 61.550 63.158 0.00 0.00 36.96 2.12
1381 5824 2.224185 TGCTTGGTTCGTGCTAGAGAAA 60.224 45.455 0.00 0.00 0.00 2.52
1391 5834 1.416401 TCCTTCTTCTGCTTGGTTCGT 59.584 47.619 0.00 0.00 0.00 3.85
1411 5854 2.297597 CGTGTCCTCTGTCTTCTTCCTT 59.702 50.000 0.00 0.00 0.00 3.36
1418 5861 0.900647 CCTCCCGTGTCCTCTGTCTT 60.901 60.000 0.00 0.00 0.00 3.01
1420 5863 1.186267 AACCTCCCGTGTCCTCTGTC 61.186 60.000 0.00 0.00 0.00 3.51
1421 5864 0.763223 AAACCTCCCGTGTCCTCTGT 60.763 55.000 0.00 0.00 0.00 3.41
1422 5865 0.396811 AAAACCTCCCGTGTCCTCTG 59.603 55.000 0.00 0.00 0.00 3.35
1475 5922 1.615107 GGCGAGGTTTGACGAGTTCG 61.615 60.000 0.00 0.00 46.33 3.95
1482 5929 1.873698 TGTAACTGGCGAGGTTTGAC 58.126 50.000 0.00 0.00 0.00 3.18
1492 5939 2.538449 CCGTATGATCGTTGTAACTGGC 59.462 50.000 0.00 0.00 0.00 4.85
1496 5943 1.862827 GCCCCGTATGATCGTTGTAAC 59.137 52.381 0.00 0.00 0.00 2.50
1541 5988 1.987855 GTGGAGGACGTGGGGATCA 60.988 63.158 0.00 0.00 0.00 2.92
1646 6095 0.463833 GGATCACGGGATTGGTGGAC 60.464 60.000 0.00 0.00 36.09 4.02
1653 6102 2.191981 AGTTAGGGGATCACGGGATT 57.808 50.000 0.00 0.00 32.67 3.01
1654 6103 2.970640 GTTAGTTAGGGGATCACGGGAT 59.029 50.000 0.00 0.00 36.13 3.85
1687 6136 4.082523 GGACCCAGCTAGCGTGCA 62.083 66.667 9.55 0.00 34.99 4.57
1717 6166 3.233980 TGCGTGAGTCAGGCTGGT 61.234 61.111 31.34 1.82 44.26 4.00
1718 6167 2.740055 GTGCGTGAGTCAGGCTGG 60.740 66.667 31.34 5.27 44.26 4.85
1749 6199 6.056090 TGTTAGTAACAAGCCATGTCCATA 57.944 37.500 13.36 0.00 42.99 2.74
1907 6357 2.029666 GGAGACTGTGTGCGTGCT 59.970 61.111 0.00 0.00 0.00 4.40
1916 6366 4.988716 TCGGGCCGTGGAGACTGT 62.989 66.667 27.32 0.00 0.00 3.55
2187 6888 2.395360 GCTATGGTTGACGGCGCAA 61.395 57.895 10.83 9.89 0.00 4.85
2202 6903 2.656646 CGTGGAGGTGCTGTGCTA 59.343 61.111 0.00 0.00 0.00 3.49
2273 6991 0.528470 GCTACAAGCAGACGAGGAGT 59.472 55.000 0.00 0.00 41.89 3.85
2287 7036 2.813474 GATGCCGTGCACGCTACA 60.813 61.111 33.17 27.71 43.04 2.74
2463 8479 4.016706 ACAAGGTTCGAGGGGCGG 62.017 66.667 0.00 0.00 41.33 6.13
2506 8552 1.676678 GCTAGACAGGATCGGGCACA 61.677 60.000 0.00 0.00 32.43 4.57
2552 8606 2.282180 TTCTGCTTGGTTCGGGCC 60.282 61.111 0.00 0.00 0.00 5.80
2658 8717 2.538449 CCGTATGATCGTTGTAACTGGC 59.462 50.000 0.00 0.00 0.00 4.85
2669 8728 3.194968 AGGTATAAAGCCCCGTATGATCG 59.805 47.826 0.00 0.00 0.00 3.69
2740 8799 4.162690 GGCCAGAGCGGACCGATT 62.163 66.667 20.50 4.23 36.36 3.34
2904 8974 3.058432 GCAGCAAGCTATGTCCATATGTG 60.058 47.826 1.24 0.00 41.15 3.21
2905 8975 3.144506 GCAGCAAGCTATGTCCATATGT 58.855 45.455 1.24 0.00 41.15 2.29
2906 8976 3.826236 GCAGCAAGCTATGTCCATATG 57.174 47.619 0.00 0.00 41.15 1.78
2918 8988 1.207593 CACCGTGTTAGCAGCAAGC 59.792 57.895 0.00 0.00 46.19 4.01
2919 8989 1.207593 GCACCGTGTTAGCAGCAAG 59.792 57.895 0.00 0.00 0.00 4.01
2920 8990 1.524849 TGCACCGTGTTAGCAGCAA 60.525 52.632 0.00 0.00 33.75 3.91
2921 8991 2.110006 TGCACCGTGTTAGCAGCA 59.890 55.556 0.00 0.00 33.75 4.41
2924 8994 0.882927 GAACCTGCACCGTGTTAGCA 60.883 55.000 0.00 0.00 36.72 3.49
2925 8995 1.866925 GAACCTGCACCGTGTTAGC 59.133 57.895 0.00 0.00 0.00 3.09
2926 8996 1.897398 GCGAACCTGCACCGTGTTAG 61.897 60.000 0.00 0.00 34.15 2.34
2927 8997 1.957186 GCGAACCTGCACCGTGTTA 60.957 57.895 0.00 0.00 34.15 2.41
2928 8998 3.276846 GCGAACCTGCACCGTGTT 61.277 61.111 0.00 0.00 34.15 3.32
2931 9001 3.980989 TACGCGAACCTGCACCGT 61.981 61.111 15.93 0.00 36.07 4.83
2932 9002 3.475774 GTACGCGAACCTGCACCG 61.476 66.667 15.93 0.00 34.15 4.94
2933 9003 3.116531 GGTACGCGAACCTGCACC 61.117 66.667 15.93 4.17 36.53 5.01
3010 9080 2.250939 CCGCGTTTCTGTTGAGCCA 61.251 57.895 4.92 0.00 0.00 4.75
3336 11146 3.616956 ATCTGCCTCAACTTGATCGAA 57.383 42.857 0.00 0.00 0.00 3.71
3343 11153 2.590821 ACAAGCAATCTGCCTCAACTT 58.409 42.857 0.00 0.00 46.52 2.66
3359 11169 3.231965 ACGATCGACGAACTACAACAAG 58.768 45.455 24.34 0.00 45.77 3.16
3387 11197 6.884280 ACAGAAGAAAACTCCGAAATGATT 57.116 33.333 0.00 0.00 0.00 2.57
3391 11201 4.580580 AGCAACAGAAGAAAACTCCGAAAT 59.419 37.500 0.00 0.00 0.00 2.17
3431 11241 7.647318 CACACAAACATAGCAAAGTCATACAAA 59.353 33.333 0.00 0.00 0.00 2.83
3458 11284 0.886938 CACGGCCACACCAACATACA 60.887 55.000 2.24 0.00 39.03 2.29
3461 11287 2.192861 CACACGGCCACACCAACAT 61.193 57.895 2.24 0.00 39.03 2.71
3528 11358 5.771153 TTGACTCAAATGAAGCATCAACA 57.229 34.783 0.00 0.00 39.49 3.33
3598 11429 6.212388 ACACCTCTGAACAGTTCTGATAGATT 59.788 38.462 19.88 5.02 37.08 2.40
3749 11606 6.870439 TCGCTTCAGTCCAATTCATATATCTG 59.130 38.462 0.00 0.00 0.00 2.90
3780 11637 3.914435 TGGAGTAGTTTCCCTTAGCCTTT 59.086 43.478 0.00 0.00 36.35 3.11
3854 12267 2.323939 TGCCAAAAATAACTCGTGCG 57.676 45.000 0.00 0.00 0.00 5.34
3899 12312 8.893563 AATATTTTGGACTTATGGGTCTTGAA 57.106 30.769 0.00 0.00 36.55 2.69
4088 12776 2.038952 ACAGCAAAGTGAGCAGGTCATA 59.961 45.455 5.40 0.00 37.56 2.15



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

AutoCloner maintained by Alex Coulton.