Multiple sequence alignment - TraesCS3A01G517800

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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 TraesCS3A01G517800 chr3A 100.000 6581 0 0 1 6581 734837532 734844112 0.000000e+00 12153.0
1 TraesCS3A01G517800 chr3A 98.670 4888 61 2 1698 6581 734884609 734889496 0.000000e+00 8663.0
2 TraesCS3A01G517800 chr3A 99.079 543 5 0 1 543 734817661 734818203 0.000000e+00 976.0
3 TraesCS3A01G517800 chr3A 98.000 200 4 0 5612 5811 308203805 308203606 1.360000e-91 348.0
4 TraesCS3A01G517800 chr3A 97.990 199 4 0 5612 5810 585158773 585158575 4.880000e-91 346.0
5 TraesCS3A01G517800 chr3A 90.909 121 9 2 5839 5958 662883235 662883116 1.900000e-35 161.0
6 TraesCS3A01G517800 chr3D 92.410 3913 182 61 461 4333 604683581 604687418 0.000000e+00 5474.0
7 TraesCS3A01G517800 chr3D 91.713 543 41 3 5072 5611 604687651 604688192 0.000000e+00 750.0
8 TraesCS3A01G517800 chr3D 92.276 492 35 3 5933 6421 569277490 569276999 0.000000e+00 695.0
9 TraesCS3A01G517800 chr3D 94.077 439 24 2 7 445 604683071 604683507 0.000000e+00 665.0
10 TraesCS3A01G517800 chr3D 94.444 144 7 1 6439 6581 308779304 308779161 3.090000e-53 220.0
11 TraesCS3A01G517800 chr3B 92.464 2070 98 29 2276 4326 812459143 812461173 0.000000e+00 2905.0
12 TraesCS3A01G517800 chr3B 93.390 1059 56 7 4562 5611 812461189 812462242 0.000000e+00 1555.0
13 TraesCS3A01G517800 chr3B 93.139 787 45 8 1443 2224 812458362 812459144 0.000000e+00 1146.0
14 TraesCS3A01G517800 chr3B 93.318 434 25 4 6008 6439 806959817 806960248 7.200000e-179 638.0
15 TraesCS3A01G517800 chr3B 91.917 433 32 3 6008 6439 56916616 56916186 2.630000e-168 603.0
16 TraesCS3A01G517800 chr3B 88.757 507 19 14 835 1331 812457885 812458363 2.640000e-163 586.0
17 TraesCS3A01G517800 chr3B 82.267 344 58 3 2 344 775734633 775734974 1.790000e-75 294.0
18 TraesCS3A01G517800 chr3B 95.139 144 6 1 6439 6581 402458531 402458674 6.640000e-55 226.0
19 TraesCS3A01G517800 chr3B 84.305 223 20 4 4355 4562 427853598 427853820 3.110000e-48 204.0
20 TraesCS3A01G517800 chr5A 84.583 1414 156 41 2957 4333 623024452 623023064 0.000000e+00 1347.0
21 TraesCS3A01G517800 chr5A 94.700 434 20 3 5838 6269 430986357 430985925 0.000000e+00 671.0
22 TraesCS3A01G517800 chr5A 86.947 475 61 1 5122 5595 623022742 623022268 3.490000e-147 532.0
23 TraesCS3A01G517800 chr5A 85.176 425 54 7 1761 2178 623025738 623025316 1.700000e-115 427.0
24 TraesCS3A01G517800 chr5A 95.833 216 8 1 1020 1234 623026433 623026218 1.360000e-91 348.0
25 TraesCS3A01G517800 chr5D 84.459 1422 146 43 2957 4333 498732208 498730817 0.000000e+00 1332.0
26 TraesCS3A01G517800 chr5D 85.393 712 89 14 4891 5595 498730683 498729980 0.000000e+00 725.0
27 TraesCS3A01G517800 chr5D 86.260 393 47 6 1787 2178 498733460 498733074 2.840000e-113 420.0
28 TraesCS3A01G517800 chr5D 96.535 202 7 0 1020 1221 498734183 498733982 1.060000e-87 335.0
29 TraesCS3A01G517800 chr5D 78.694 291 60 2 1 290 551089220 551088931 6.730000e-45 193.0
30 TraesCS3A01G517800 chr5D 81.172 239 16 3 4356 4565 444858381 444858619 1.470000e-36 165.0
31 TraesCS3A01G517800 chr5B 83.885 1421 160 42 2957 4332 618284722 618283326 0.000000e+00 1291.0
32 TraesCS3A01G517800 chr5B 86.158 708 81 15 4895 5595 618283189 618282492 0.000000e+00 749.0
33 TraesCS3A01G517800 chr5B 94.651 430 17 3 6015 6440 335412050 335412477 0.000000e+00 662.0
34 TraesCS3A01G517800 chr5B 85.176 425 54 7 1761 2178 618286005 618285583 1.700000e-115 427.0
35 TraesCS3A01G517800 chr5B 96.535 202 7 0 1020 1221 618286909 618286708 1.060000e-87 335.0
36 TraesCS3A01G517800 chr5B 82.500 320 48 8 42 357 36473413 36473728 2.340000e-69 274.0
37 TraesCS3A01G517800 chr5B 94.406 143 7 1 6440 6581 455275953 455276095 1.110000e-52 219.0
38 TraesCS3A01G517800 chr5B 90.833 120 9 2 5838 5956 689197030 689196912 6.830000e-35 159.0
39 TraesCS3A01G517800 chr5B 80.252 238 17 8 4355 4562 129011181 129010944 1.140000e-32 152.0
40 TraesCS3A01G517800 chr5B 80.252 238 17 8 4355 4562 129012411 129012174 1.140000e-32 152.0
41 TraesCS3A01G517800 chr6A 95.606 751 24 6 5839 6581 614469332 614470081 0.000000e+00 1195.0
42 TraesCS3A01G517800 chr6A 95.181 747 30 3 5839 6581 598680780 598681524 0.000000e+00 1175.0
43 TraesCS3A01G517800 chr6A 98.000 200 4 0 5612 5811 607089168 607089367 1.360000e-91 348.0
44 TraesCS3A01G517800 chr6A 98.000 200 4 0 5612 5811 607224354 607224553 1.360000e-91 348.0
45 TraesCS3A01G517800 chr7D 91.106 877 32 9 2732 3605 499627403 499626570 0.000000e+00 1146.0
46 TraesCS3A01G517800 chr7D 94.340 689 29 5 3639 4326 499626571 499625892 0.000000e+00 1048.0
47 TraesCS3A01G517800 chr7D 97.826 46 1 0 4562 4607 499625876 499625831 5.470000e-11 80.5
48 TraesCS3A01G517800 chr4B 88.864 880 48 25 2726 3602 642737041 642737873 0.000000e+00 1037.0
49 TraesCS3A01G517800 chr4B 93.198 691 36 6 3638 4326 642737873 642738554 0.000000e+00 1005.0
50 TraesCS3A01G517800 chr4B 92.517 147 10 1 6436 6581 165816420 165816566 6.690000e-50 209.0
51 TraesCS3A01G517800 chr4B 82.418 182 12 4 4355 4516 450944877 450944696 2.470000e-29 141.0
52 TraesCS3A01G517800 chr4B 97.826 46 1 0 4562 4607 642738570 642738615 5.470000e-11 80.5
53 TraesCS3A01G517800 chr7A 90.539 761 33 6 2843 3602 109230790 109230068 0.000000e+00 970.0
54 TraesCS3A01G517800 chr7A 92.319 690 40 7 3638 4326 61493011 61492334 0.000000e+00 968.0
55 TraesCS3A01G517800 chr7A 92.387 683 42 5 3644 4326 109230063 109229391 0.000000e+00 965.0
56 TraesCS3A01G517800 chr7A 90.132 760 36 6 2843 3602 61493731 61493011 0.000000e+00 952.0
57 TraesCS3A01G517800 chr7A 99.000 200 2 0 5612 5811 353071894 353071695 6.270000e-95 359.0
58 TraesCS3A01G517800 chr7A 93.277 119 5 3 5834 5949 246272234 246272352 8.770000e-39 172.0
59 TraesCS3A01G517800 chr7A 97.826 46 1 0 4562 4607 61492318 61492273 5.470000e-11 80.5
60 TraesCS3A01G517800 chr7A 97.826 46 1 0 4562 4607 109229375 109229330 5.470000e-11 80.5
61 TraesCS3A01G517800 chr2B 92.407 619 19 2 2985 3602 30335319 30334728 0.000000e+00 857.0
62 TraesCS3A01G517800 chr2B 94.291 508 20 4 3638 4145 30334728 30334230 0.000000e+00 769.0
63 TraesCS3A01G517800 chr2B 90.909 517 38 7 5934 6448 82501925 82502434 0.000000e+00 686.0
64 TraesCS3A01G517800 chr2B 83.488 539 58 20 2571 3098 710834755 710835273 2.150000e-129 473.0
65 TraesCS3A01G517800 chr2B 82.263 327 53 5 1 326 758876723 758876401 1.810000e-70 278.0
66 TraesCS3A01G517800 chr2B 91.837 196 16 0 4131 4326 30334045 30333850 2.340000e-69 274.0
67 TraesCS3A01G517800 chr2B 88.128 219 15 2 4355 4562 627255644 627255426 3.940000e-62 250.0
68 TraesCS3A01G517800 chr2B 97.391 115 3 0 4563 4677 30333833 30333719 5.210000e-46 196.0
69 TraesCS3A01G517800 chr2B 96.226 106 4 0 5839 5944 799982046 799981941 2.440000e-39 174.0
70 TraesCS3A01G517800 chrUn 100.000 385 0 0 2373 2757 480790319 480790703 0.000000e+00 712.0
71 TraesCS3A01G517800 chrUn 85.204 196 15 4 4375 4560 26606062 26606253 8.710000e-44 189.0
72 TraesCS3A01G517800 chr2A 86.056 502 58 5 2467 2963 17648286 17647792 4.520000e-146 529.0
73 TraesCS3A01G517800 chr2A 80.663 543 55 28 2569 3102 434076438 434076939 6.230000e-100 375.0
74 TraesCS3A01G517800 chr6D 85.265 509 61 7 2461 2963 7261900 7262400 4.550000e-141 512.0
75 TraesCS3A01G517800 chr1B 83.488 539 58 20 2571 3098 635793024 635793542 2.150000e-129 473.0
76 TraesCS3A01G517800 chr1B 93.252 163 10 1 4355 4516 574137193 574137031 8.530000e-59 239.0
77 TraesCS3A01G517800 chr1B 93.750 112 4 3 5839 5948 175901363 175901253 1.470000e-36 165.0
78 TraesCS3A01G517800 chr4A 84.358 358 47 6 2 357 717816979 717816629 6.320000e-90 342.0
79 TraesCS3A01G517800 chr4A 97.487 199 5 0 5612 5810 59087450 59087252 2.270000e-89 340.0
80 TraesCS3A01G517800 chr4A 97.000 200 6 0 5611 5810 263281135 263281334 2.940000e-88 337.0
81 TraesCS3A01G517800 chr4A 80.495 364 62 9 2 362 631023176 631022819 3.020000e-68 270.0
82 TraesCS3A01G517800 chr4A 95.139 144 6 1 6439 6581 615513937 615514080 6.640000e-55 226.0
83 TraesCS3A01G517800 chr1A 97.500 200 5 0 5612 5811 441604855 441604656 6.320000e-90 342.0
84 TraesCS3A01G517800 chr1A 81.073 317 56 3 2 318 67463451 67463139 3.940000e-62 250.0
85 TraesCS3A01G517800 chr7B 87.215 219 17 4 4355 4562 654584753 654584535 8.530000e-59 239.0
86 TraesCS3A01G517800 chr2D 94.444 144 7 1 6439 6581 547216487 547216630 3.090000e-53 220.0
87 TraesCS3A01G517800 chr6B 96.000 100 3 1 4355 4453 504730329 504730428 1.900000e-35 161.0
88 TraesCS3A01G517800 chr1D 96.000 100 3 1 4355 4453 32149023 32149122 1.900000e-35 161.0


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 TraesCS3A01G517800 chr3A 734837532 734844112 6580 False 12153.000000 12153 100.000000 1 6581 1 chr3A.!!$F2 6580
1 TraesCS3A01G517800 chr3A 734884609 734889496 4887 False 8663.000000 8663 98.670000 1698 6581 1 chr3A.!!$F3 4883
2 TraesCS3A01G517800 chr3A 734817661 734818203 542 False 976.000000 976 99.079000 1 543 1 chr3A.!!$F1 542
3 TraesCS3A01G517800 chr3D 604683071 604688192 5121 False 2296.333333 5474 92.733333 7 5611 3 chr3D.!!$F1 5604
4 TraesCS3A01G517800 chr3B 812457885 812462242 4357 False 1548.000000 2905 91.937500 835 5611 4 chr3B.!!$F5 4776
5 TraesCS3A01G517800 chr5A 623022268 623026433 4165 True 663.500000 1347 88.134750 1020 5595 4 chr5A.!!$R2 4575
6 TraesCS3A01G517800 chr5D 498729980 498734183 4203 True 703.000000 1332 88.161750 1020 5595 4 chr5D.!!$R2 4575
7 TraesCS3A01G517800 chr5B 618282492 618286909 4417 True 700.500000 1291 87.938500 1020 5595 4 chr5B.!!$R3 4575
8 TraesCS3A01G517800 chr6A 614469332 614470081 749 False 1195.000000 1195 95.606000 5839 6581 1 chr6A.!!$F4 742
9 TraesCS3A01G517800 chr6A 598680780 598681524 744 False 1175.000000 1175 95.181000 5839 6581 1 chr6A.!!$F1 742
10 TraesCS3A01G517800 chr7D 499625831 499627403 1572 True 758.166667 1146 94.424000 2732 4607 3 chr7D.!!$R1 1875
11 TraesCS3A01G517800 chr4B 642737041 642738615 1574 False 707.500000 1037 93.296000 2726 4607 3 chr4B.!!$F2 1881
12 TraesCS3A01G517800 chr7A 109229330 109230790 1460 True 671.833333 970 93.584000 2843 4607 3 chr7A.!!$R3 1764
13 TraesCS3A01G517800 chr7A 61492273 61493731 1458 True 666.833333 968 93.425667 2843 4607 3 chr7A.!!$R2 1764
14 TraesCS3A01G517800 chr2B 82501925 82502434 509 False 686.000000 686 90.909000 5934 6448 1 chr2B.!!$F1 514
15 TraesCS3A01G517800 chr2B 30333719 30335319 1600 True 524.000000 857 93.981500 2985 4677 4 chr2B.!!$R4 1692
16 TraesCS3A01G517800 chr2B 710834755 710835273 518 False 473.000000 473 83.488000 2571 3098 1 chr2B.!!$F2 527
17 TraesCS3A01G517800 chr2A 434076438 434076939 501 False 375.000000 375 80.663000 2569 3102 1 chr2A.!!$F1 533
18 TraesCS3A01G517800 chr6D 7261900 7262400 500 False 512.000000 512 85.265000 2461 2963 1 chr6D.!!$F1 502
19 TraesCS3A01G517800 chr1B 635793024 635793542 518 False 473.000000 473 83.488000 2571 3098 1 chr1B.!!$F1 527

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
891 963 0.250513 AAAGTCCTTAGCAGCCTCGG 59.749 55.000 0.00 0.00 0.00 4.63 F
1245 1328 0.322546 CCCTTCCCTTTCTTCCACCG 60.323 60.000 0.00 0.00 0.00 4.94 F
1250 1333 0.391793 CCCTTTCTTCCACCGCTCTC 60.392 60.000 0.00 0.00 0.00 3.20 F
1251 1334 0.610687 CCTTTCTTCCACCGCTCTCT 59.389 55.000 0.00 0.00 0.00 3.10 F
1495 1805 1.142667 TGAAATCGGCTGCCCATATGA 59.857 47.619 14.12 4.22 0.00 2.15 F
1685 2003 2.553904 GCTGGGATGATGGACCAATAGG 60.554 54.545 0.00 0.00 42.21 2.57 F
4469 5501 3.039202 GCCAGCCGTTGTGATTCCG 62.039 63.158 0.00 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2268 2659 4.574599 AAGGTAAGAGCAACAGCTTTTG 57.425 40.909 8.28 8.28 39.10 2.44 R
2894 3312 4.511527 ACATCACAAACAGGATAGAGCAG 58.488 43.478 0.00 0.00 0.00 4.24 R
3445 4220 4.202419 TGCTACTGGTTTCCTTCTGCTTTA 60.202 41.667 0.00 0.00 0.00 1.85 R
3642 4436 1.056660 GAGGGTCCACACAAGAGGAA 58.943 55.000 0.00 0.00 36.22 3.36 R
4491 5523 0.600255 ACGAAGGAAACAGACGCCTG 60.600 55.000 0.00 0.00 45.76 4.85 R
4496 5528 3.545426 CGGTTTTGACGAAGGAAACAGAC 60.545 47.826 0.00 0.00 35.53 3.51 R
5644 6702 0.621082 ACAAAAGCTAGGGAGGAGGC 59.379 55.000 0.00 0.00 0.00 4.70 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
181 182 3.640029 ACCTCTCCGAGTAAGACACAAAA 59.360 43.478 0.00 0.00 0.00 2.44
459 460 9.491675 TTGTAGTACATTTCATCCGTTAAAAGA 57.508 29.630 3.28 0.00 0.00 2.52
531 590 0.541063 TGGCAAGACTACCTCCGACA 60.541 55.000 0.00 0.00 0.00 4.35
549 613 4.923281 CCGACAAGATGCGATATATCACAA 59.077 41.667 13.11 0.00 0.00 3.33
576 644 1.555075 TCCAGGAAGAAAGATGGTCCG 59.445 52.381 0.00 0.00 35.19 4.79
577 645 1.555075 CCAGGAAGAAAGATGGTCCGA 59.445 52.381 0.00 0.00 35.19 4.55
684 752 2.283351 CGTCAAACTTTCGAAACTCCGT 59.717 45.455 6.47 0.16 0.00 4.69
687 755 3.554324 TCAAACTTTCGAAACTCCGTCTG 59.446 43.478 6.47 0.77 0.00 3.51
705 773 5.343058 CCGTCTGCTAATGTGTTTTCAAATG 59.657 40.000 0.00 0.00 0.00 2.32
711 779 9.462174 CTGCTAATGTGTTTTCAAATGTTTAGA 57.538 29.630 0.00 0.00 0.00 2.10
818 887 8.980481 ATATTTAGGAACTTCCGACATGATTT 57.020 30.769 0.00 0.00 42.75 2.17
820 889 6.494893 TTAGGAACTTCCGACATGATTTTG 57.505 37.500 0.00 0.00 42.75 2.44
823 892 4.917415 GGAACTTCCGACATGATTTTGTTG 59.083 41.667 0.00 0.00 0.00 3.33
825 894 5.514274 ACTTCCGACATGATTTTGTTGTT 57.486 34.783 0.00 0.00 30.29 2.83
826 895 5.280945 ACTTCCGACATGATTTTGTTGTTG 58.719 37.500 0.00 0.00 30.29 3.33
827 896 3.637432 TCCGACATGATTTTGTTGTTGC 58.363 40.909 0.00 0.00 30.29 4.17
828 897 3.067320 TCCGACATGATTTTGTTGTTGCA 59.933 39.130 0.00 0.00 30.29 4.08
829 898 3.801050 CCGACATGATTTTGTTGTTGCAA 59.199 39.130 0.00 0.00 30.29 4.08
830 899 4.084952 CCGACATGATTTTGTTGTTGCAAG 60.085 41.667 0.00 0.00 30.29 4.01
831 900 4.503734 CGACATGATTTTGTTGTTGCAAGT 59.496 37.500 0.00 0.00 0.00 3.16
832 901 5.685068 CGACATGATTTTGTTGTTGCAAGTA 59.315 36.000 0.00 0.00 0.00 2.24
833 902 6.129378 CGACATGATTTTGTTGTTGCAAGTAG 60.129 38.462 0.00 0.00 0.00 2.57
891 963 0.250513 AAAGTCCTTAGCAGCCTCGG 59.749 55.000 0.00 0.00 0.00 4.63
899 971 2.167398 TAGCAGCCTCGGGTGTTGAC 62.167 60.000 15.72 0.41 44.52 3.18
901 973 1.669115 CAGCCTCGGGTGTTGACTG 60.669 63.158 6.97 0.00 38.64 3.51
902 974 1.837051 AGCCTCGGGTGTTGACTGA 60.837 57.895 0.00 0.00 0.00 3.41
1222 1304 2.032681 GGCTCAACGGCAAGGTCT 59.967 61.111 0.00 0.00 38.25 3.85
1235 1317 2.941583 GGTCTGCCCCCTTCCCTT 60.942 66.667 0.00 0.00 0.00 3.95
1236 1318 2.548547 GGTCTGCCCCCTTCCCTTT 61.549 63.158 0.00 0.00 0.00 3.11
1239 1322 0.776080 TCTGCCCCCTTCCCTTTCTT 60.776 55.000 0.00 0.00 0.00 2.52
1242 1325 1.800229 GCCCCCTTCCCTTTCTTCCA 61.800 60.000 0.00 0.00 0.00 3.53
1245 1328 0.322546 CCCTTCCCTTTCTTCCACCG 60.323 60.000 0.00 0.00 0.00 4.94
1250 1333 0.391793 CCCTTTCTTCCACCGCTCTC 60.392 60.000 0.00 0.00 0.00 3.20
1251 1334 0.610687 CCTTTCTTCCACCGCTCTCT 59.389 55.000 0.00 0.00 0.00 3.10
1253 1336 2.342179 CTTTCTTCCACCGCTCTCTTC 58.658 52.381 0.00 0.00 0.00 2.87
1279 1362 3.336676 TCTTCTTCCCTTTCCCTTTCCT 58.663 45.455 0.00 0.00 0.00 3.36
1428 1738 2.117156 CCAGCAGGAGCCGATTTGG 61.117 63.158 0.00 0.00 43.56 3.28
1455 1765 3.414700 CTGTGCCAGTCGCCGTTC 61.415 66.667 0.00 0.00 36.24 3.95
1495 1805 1.142667 TGAAATCGGCTGCCCATATGA 59.857 47.619 14.12 4.22 0.00 2.15
1620 1933 9.796120 CCTTTTTCTGTTTGTTAATGTTGTCTA 57.204 29.630 0.00 0.00 0.00 2.59
1636 1949 8.879342 ATGTTGTCTACAGTTAGCATCTATTC 57.121 34.615 0.00 0.00 40.83 1.75
1640 1953 8.167605 TGTCTACAGTTAGCATCTATTCCTAC 57.832 38.462 0.00 0.00 0.00 3.18
1643 1956 9.727859 TCTACAGTTAGCATCTATTCCTACTAG 57.272 37.037 0.00 0.00 0.00 2.57
1685 2003 2.553904 GCTGGGATGATGGACCAATAGG 60.554 54.545 0.00 0.00 42.21 2.57
1691 2021 4.841246 GGATGATGGACCAATAGGAGTAGT 59.159 45.833 0.00 0.00 38.69 2.73
2233 2624 4.000988 ACATTCGTTGTTGAGGGTGATAC 58.999 43.478 0.00 0.00 33.74 2.24
2268 2659 4.473477 ACAAGTGGACTGTTATCCTAGC 57.527 45.455 0.00 0.00 39.75 3.42
2894 3312 7.133891 ACATTATGTAGCAACACTCTGTTTC 57.866 36.000 0.00 0.00 38.77 2.78
3445 4220 4.892934 TGCTTTGTGGAATTAGGTCAGTTT 59.107 37.500 0.00 0.00 0.00 2.66
3571 4356 6.699642 ACTTGTTTTTGGCACATATTGTACAC 59.300 34.615 0.00 0.00 39.30 2.90
4469 5501 3.039202 GCCAGCCGTTGTGATTCCG 62.039 63.158 0.00 0.00 0.00 4.30
5070 6124 1.305802 TACCGGAGTGGATGGTGCT 60.306 57.895 9.46 0.00 42.00 4.40
5475 6533 2.812358 ACCAAAAATTCAAGGGCGAC 57.188 45.000 0.00 0.00 0.00 5.19
5614 6672 1.899814 TGACTGGTTTGATACTCGGCT 59.100 47.619 0.00 0.00 0.00 5.52
5892 6950 1.459450 CCGGTCAATTTTCGTCCCAT 58.541 50.000 0.00 0.00 0.00 4.00
5995 7060 2.101640 ACCAAAACCAATTGAGCCCT 57.898 45.000 7.12 0.00 31.84 5.19
6021 7086 3.189287 CCATGAAACGAAACCAGAGGAAG 59.811 47.826 0.00 0.00 0.00 3.46
6044 7110 1.308326 CCCCCTCGACTCCTCTCTT 59.692 63.158 0.00 0.00 0.00 2.85
6067 7133 5.032846 TGATCTGTTTCCTAGGGACTGAAT 58.967 41.667 20.93 13.63 41.52 2.57
6192 7262 2.346541 CCGTCTCTCCAGCAGCTCA 61.347 63.158 0.00 0.00 0.00 4.26
6193 7263 1.588597 CGTCTCTCCAGCAGCTCAA 59.411 57.895 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
348 349 3.690139 GGGAGATCGTTTTCTTTCTTCCC 59.310 47.826 0.00 0.00 28.89 3.97
531 590 8.169977 ACCAAATTTGTGATATATCGCATCTT 57.830 30.769 25.49 18.93 45.59 2.40
549 613 4.774200 CCATCTTTCTTCCTGGACCAAATT 59.226 41.667 0.00 0.00 0.00 1.82
595 663 7.446106 TGTGGACCCTAACACTTATATTGAT 57.554 36.000 0.00 0.00 38.39 2.57
612 680 1.981256 ACCTTTGTGTGATGTGGACC 58.019 50.000 0.00 0.00 0.00 4.46
684 752 9.462174 CTAAACATTTGAAAACACATTAGCAGA 57.538 29.630 0.00 0.00 0.00 4.26
804 873 4.148696 GCAACAACAAAATCATGTCGGAAG 59.851 41.667 0.00 0.00 31.81 3.46
805 874 4.047822 GCAACAACAAAATCATGTCGGAA 58.952 39.130 0.00 0.00 31.81 4.30
818 887 7.217200 AGAATCTACTCTACTTGCAACAACAA 58.783 34.615 0.00 0.00 0.00 2.83
820 889 7.659652 AAGAATCTACTCTACTTGCAACAAC 57.340 36.000 0.00 0.00 0.00 3.32
862 934 4.744570 TGCTAAGGACTTTGACTACGATG 58.255 43.478 0.00 0.00 0.00 3.84
955 1035 2.371259 GGAGGGAGTGAGGAAGGGC 61.371 68.421 0.00 0.00 0.00 5.19
1059 1141 2.034179 CCAGTACTTGATCACCGCGATA 59.966 50.000 8.23 0.00 33.17 2.92
1222 1304 1.774300 GAAGAAAGGGAAGGGGGCA 59.226 57.895 0.00 0.00 0.00 5.36
1235 1317 1.633774 AGAAGAGAGCGGTGGAAGAA 58.366 50.000 0.00 0.00 0.00 2.52
1236 1318 1.546476 GAAGAAGAGAGCGGTGGAAGA 59.454 52.381 0.00 0.00 0.00 2.87
1239 1322 1.546476 GAAGAAGAAGAGAGCGGTGGA 59.454 52.381 0.00 0.00 0.00 4.02
1242 1325 3.161866 AGAAGAAGAAGAAGAGAGCGGT 58.838 45.455 0.00 0.00 0.00 5.68
1245 1328 4.222810 AGGGAAGAAGAAGAAGAAGAGAGC 59.777 45.833 0.00 0.00 0.00 4.09
1250 1333 5.007034 GGGAAAGGGAAGAAGAAGAAGAAG 58.993 45.833 0.00 0.00 0.00 2.85
1251 1334 4.665483 AGGGAAAGGGAAGAAGAAGAAGAA 59.335 41.667 0.00 0.00 0.00 2.52
1253 1336 4.649267 AGGGAAAGGGAAGAAGAAGAAG 57.351 45.455 0.00 0.00 0.00 2.85
1279 1362 1.374252 GAGGCGAGCGTGAGGAAAA 60.374 57.895 0.00 0.00 0.00 2.29
1349 1432 0.179089 CGGATCACTGCAGGAAGGAG 60.179 60.000 19.93 1.22 42.18 3.69
1443 1753 0.443869 CAAATCAGAACGGCGACTGG 59.556 55.000 26.84 14.41 35.20 4.00
1449 1759 3.065371 CAGTAATCCCAAATCAGAACGGC 59.935 47.826 0.00 0.00 0.00 5.68
1455 1765 7.921786 TTTCACTACAGTAATCCCAAATCAG 57.078 36.000 0.00 0.00 0.00 2.90
1495 1805 3.582208 GCAGGTCCTGATCCAGATCTAAT 59.418 47.826 23.77 0.00 38.60 1.73
1576 1888 2.576615 AGGTGTCTTTTGGCTTCTGTC 58.423 47.619 0.00 0.00 0.00 3.51
1605 1918 8.615878 ATGCTAACTGTAGACAACATTAACAA 57.384 30.769 0.00 0.00 37.50 2.83
1634 1947 5.279506 GCAGGCAGCAATATACTAGTAGGAA 60.280 44.000 8.85 0.00 44.79 3.36
1636 1949 4.499183 GCAGGCAGCAATATACTAGTAGG 58.501 47.826 8.85 0.00 44.79 3.18
1640 1953 2.989840 GACGCAGGCAGCAATATACTAG 59.010 50.000 1.96 0.00 46.13 2.57
1643 1956 1.581934 TGACGCAGGCAGCAATATAC 58.418 50.000 1.96 0.00 46.13 1.47
1685 2003 7.868906 AGACCTGATGTAGAACTAACTACTC 57.131 40.000 0.00 0.00 42.01 2.59
1691 2021 8.311836 CCAGTTAAAGACCTGATGTAGAACTAA 58.688 37.037 0.00 0.00 0.00 2.24
2233 2624 5.934625 AGTCCACTTGTAGCAGAAATACTTG 59.065 40.000 0.00 0.00 0.00 3.16
2268 2659 4.574599 AAGGTAAGAGCAACAGCTTTTG 57.425 40.909 8.28 8.28 39.10 2.44
2894 3312 4.511527 ACATCACAAACAGGATAGAGCAG 58.488 43.478 0.00 0.00 0.00 4.24
3445 4220 4.202419 TGCTACTGGTTTCCTTCTGCTTTA 60.202 41.667 0.00 0.00 0.00 1.85
3642 4436 1.056660 GAGGGTCCACACAAGAGGAA 58.943 55.000 0.00 0.00 36.22 3.36
4491 5523 0.600255 ACGAAGGAAACAGACGCCTG 60.600 55.000 0.00 0.00 45.76 4.85
4496 5528 3.545426 CGGTTTTGACGAAGGAAACAGAC 60.545 47.826 0.00 0.00 35.53 3.51
5070 6124 8.731275 ACGTTGGTTTCATTATCAGATCAATA 57.269 30.769 0.00 0.00 0.00 1.90
5475 6533 2.537625 GCTGCAGATGAAGTAGCTAACG 59.462 50.000 20.43 0.00 40.85 3.18
5614 6672 5.517322 TTTTTAAGCCGCCAAAAGAACTA 57.483 34.783 0.00 0.00 0.00 2.24
5644 6702 0.621082 ACAAAAGCTAGGGAGGAGGC 59.379 55.000 0.00 0.00 0.00 4.70
6044 7110 4.061131 TCAGTCCCTAGGAAACAGATCA 57.939 45.455 11.48 0.00 31.38 2.92
6192 7262 1.002502 GTGGGCTAGGGTTTCGCTT 60.003 57.895 0.00 0.00 0.00 4.68
6193 7263 2.669240 GTGGGCTAGGGTTTCGCT 59.331 61.111 0.00 0.00 0.00 4.93


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

AutoCloner maintained by Alex Coulton.