Multiple sequence alignment - TraesCS1A01G051100

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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 TraesCS1A01G051100 chr1A 100.000 3455 0 0 1 3455 32544902 32548356 0.000000e+00 6381.0
1 TraesCS1A01G051100 chr1A 88.072 2339 185 37 736 2993 2943273 2945598 0.000000e+00 2687.0
2 TraesCS1A01G051100 chr1A 86.331 139 14 2 3215 3348 3520540 3520402 2.780000e-31 147.0
3 TraesCS1A01G051100 chr1A 84.956 113 10 4 334 439 2949401 2949513 1.310000e-19 108.0
4 TraesCS1A01G051100 chr1D 96.293 2347 73 7 448 2784 33984103 33986445 0.000000e+00 3840.0
5 TraesCS1A01G051100 chr1D 89.942 1899 156 16 770 2639 49764438 49766330 0.000000e+00 2416.0
6 TraesCS1A01G051100 chr1D 92.381 420 24 3 2993 3411 33988051 33988463 2.970000e-165 592.0
7 TraesCS1A01G051100 chr1D 81.944 504 49 16 2514 2980 387269 387767 4.180000e-104 388.0
8 TraesCS1A01G051100 chr1D 94.495 218 12 0 2776 2993 33987790 33988007 1.540000e-88 337.0
9 TraesCS1A01G051100 chr1D 95.798 119 4 1 297 414 33983984 33984102 1.270000e-44 191.0
10 TraesCS1A01G051100 chr1D 94.167 120 3 1 127 246 33983871 33983986 2.740000e-41 180.0
11 TraesCS1A01G051100 chr1D 85.714 175 17 3 3217 3391 388057 388223 9.850000e-41 178.0
12 TraesCS1A01G051100 chr1D 93.023 86 6 0 552 637 49746197 49746282 3.620000e-25 126.0
13 TraesCS1A01G051100 chr1B 88.948 2452 187 27 592 2993 4519078 4516661 0.000000e+00 2950.0
14 TraesCS1A01G051100 chr1B 87.568 2381 201 43 592 2896 4954559 4952198 0.000000e+00 2669.0
15 TraesCS1A01G051100 chr1B 87.315 2365 214 41 592 2896 4110099 4112437 0.000000e+00 2627.0
16 TraesCS1A01G051100 chr1B 87.659 2204 175 47 685 2801 46830354 46828161 0.000000e+00 2473.0
17 TraesCS1A01G051100 chr1B 90.587 1891 128 30 677 2523 70232771 70234655 0.000000e+00 2460.0
18 TraesCS1A01G051100 chr1B 86.687 2291 208 46 706 2910 4597570 4595291 0.000000e+00 2451.0
19 TraesCS1A01G051100 chr1B 86.709 2197 204 44 734 2879 46691989 46694148 0.000000e+00 2359.0
20 TraesCS1A01G051100 chr1B 86.968 1128 107 10 1806 2896 4798955 4797831 0.000000e+00 1232.0
21 TraesCS1A01G051100 chr1B 88.912 487 36 2 2514 2994 3938105 3938579 4.970000e-163 584.0
22 TraesCS1A01G051100 chr1B 81.849 595 58 28 73 626 46690923 46691508 4.060000e-124 455.0
23 TraesCS1A01G051100 chr1B 79.235 732 82 36 103 799 4520098 4519402 2.450000e-121 446.0
24 TraesCS1A01G051100 chr1B 81.755 433 27 23 71 462 4955551 4955130 7.200000e-82 315.0
25 TraesCS1A01G051100 chr1B 81.513 357 36 12 457 791 4109416 4109764 2.040000e-67 267.0
26 TraesCS1A01G051100 chr1B 88.182 220 23 2 2993 3209 4516618 4516399 3.420000e-65 259.0
27 TraesCS1A01G051100 chr1B 77.366 486 50 29 340 796 4143872 4144326 2.070000e-57 233.0
28 TraesCS1A01G051100 chr1B 87.500 184 12 9 3215 3391 4797513 4797334 5.850000e-48 202.0
29 TraesCS1A01G051100 chr1B 86.631 187 13 9 3212 3391 4112743 4112924 2.720000e-46 196.0
30 TraesCS1A01G051100 chr1B 85.207 169 14 6 337 494 46691698 46691866 2.760000e-36 163.0
31 TraesCS1A01G051100 chr1B 94.000 100 5 1 3215 3313 46827693 46827594 2.150000e-32 150.0
32 TraesCS1A01G051100 chr1B 82.209 163 20 8 3215 3370 4951731 4951571 7.780000e-27 132.0
33 TraesCS1A01G051100 chr1B 93.023 86 6 0 552 637 70232695 70232780 3.620000e-25 126.0
34 TraesCS1A01G051100 chr1B 93.846 65 3 1 339 402 4519389 4519325 2.840000e-16 97.1
35 TraesCS1A01G051100 chr1B 91.803 61 5 0 292 352 4543456 4543396 6.140000e-13 86.1
36 TraesCS1A01G051100 chr1B 96.078 51 2 0 292 342 3935789 3935839 2.210000e-12 84.2
37 TraesCS1A01G051100 chr1B 97.778 45 1 0 2993 3037 3938621 3938665 1.030000e-10 78.7
38 TraesCS1A01G051100 chr1B 83.146 89 5 3 3225 3313 4912603 4912525 4.780000e-09 73.1
39 TraesCS1A01G051100 chr6A 87.806 2370 196 35 592 2896 613493540 613495881 0.000000e+00 2689.0
40 TraesCS1A01G051100 chr6A 86.025 1381 124 34 1660 2982 64065216 64063847 0.000000e+00 1417.0
41 TraesCS1A01G051100 chr6A 80.128 312 31 20 148 443 613492552 613492848 1.630000e-48 204.0
42 TraesCS1A01G051100 chr6A 86.740 181 17 6 3215 3391 613496238 613496415 9.780000e-46 195.0
43 TraesCS1A01G051100 chr5B 87.705 2383 186 48 592 2896 60826075 60823722 0.000000e+00 2678.0
44 TraesCS1A01G051100 chr5B 80.463 389 49 17 2476 2856 617172479 617172848 4.390000e-69 272.0
45 TraesCS1A01G051100 chr3D 87.173 2370 209 43 592 2896 560024964 560022625 0.000000e+00 2604.0
46 TraesCS1A01G051100 chr3D 78.663 778 70 49 123 847 560026005 560025271 2.460000e-116 429.0
47 TraesCS1A01G051100 chr3D 93.407 91 5 1 3215 3304 560022313 560022223 2.160000e-27 134.0
48 TraesCS1A01G051100 chr3D 97.368 38 1 0 340 377 560025277 560025240 8.000000e-07 65.8
49 TraesCS1A01G051100 chr5D 87.548 2329 186 45 592 2845 57819449 57821748 0.000000e+00 2599.0
50 TraesCS1A01G051100 chr6D 86.103 2281 217 50 702 2910 53144814 53142562 0.000000e+00 2364.0
51 TraesCS1A01G051100 chr6D 87.167 2104 200 37 597 2660 51068122 51070195 0.000000e+00 2326.0
52 TraesCS1A01G051100 chr6D 87.947 1958 176 32 695 2611 51348818 51350756 0.000000e+00 2254.0
53 TraesCS1A01G051100 chr6D 87.640 1958 185 31 695 2611 51074036 51075977 0.000000e+00 2222.0
54 TraesCS1A01G051100 chr6D 87.589 1958 186 30 695 2611 50949119 50951060 0.000000e+00 2217.0
55 TraesCS1A01G051100 chr6D 92.000 75 4 1 2908 2982 53142542 53142470 1.700000e-18 104.0
56 TraesCS1A01G051100 chr6B 89.115 1920 169 22 616 2523 120355155 120353264 0.000000e+00 2351.0
57 TraesCS1A01G051100 chr6B 88.991 1844 150 30 695 2523 120317446 120315641 0.000000e+00 2231.0
58 TraesCS1A01G051100 chr3B 88.971 136 11 2 734 869 409335227 409335096 7.670000e-37 165.0
59 TraesCS1A01G051100 chrUn 84.956 113 10 4 334 439 325465742 325465854 1.310000e-19 108.0
60 TraesCS1A01G051100 chr7A 78.495 186 11 15 220 402 631983923 631984082 1.020000e-15 95.3
61 TraesCS1A01G051100 chr7B 81.651 109 6 8 221 328 591461109 591461204 1.030000e-10 78.7


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 TraesCS1A01G051100 chr1A 32544902 32548356 3454 False 6381.000000 6381 100.000000 1 3455 1 chr1A.!!$F1 3454
1 TraesCS1A01G051100 chr1A 2943273 2949513 6240 False 1397.500000 2687 86.514000 334 2993 2 chr1A.!!$F2 2659
2 TraesCS1A01G051100 chr1D 49764438 49766330 1892 False 2416.000000 2416 89.942000 770 2639 1 chr1D.!!$F2 1869
3 TraesCS1A01G051100 chr1D 33983871 33988463 4592 False 1028.000000 3840 94.626800 127 3411 5 chr1D.!!$F4 3284
4 TraesCS1A01G051100 chr1D 387269 388223 954 False 283.000000 388 83.829000 2514 3391 2 chr1D.!!$F3 877
5 TraesCS1A01G051100 chr1B 4595291 4597570 2279 True 2451.000000 2451 86.687000 706 2910 1 chr1B.!!$R2 2204
6 TraesCS1A01G051100 chr1B 46827594 46830354 2760 True 1311.500000 2473 90.829500 685 3313 2 chr1B.!!$R7 2628
7 TraesCS1A01G051100 chr1B 70232695 70234655 1960 False 1293.000000 2460 91.805000 552 2523 2 chr1B.!!$F5 1971
8 TraesCS1A01G051100 chr1B 4951571 4955551 3980 True 1038.666667 2669 83.844000 71 3370 3 chr1B.!!$R6 3299
9 TraesCS1A01G051100 chr1B 4109416 4112924 3508 False 1030.000000 2627 85.153000 457 3391 3 chr1B.!!$F3 2934
10 TraesCS1A01G051100 chr1B 46690923 46694148 3225 False 992.333333 2359 84.588333 73 2879 3 chr1B.!!$F4 2806
11 TraesCS1A01G051100 chr1B 4516399 4520098 3699 True 938.025000 2950 87.552750 103 3209 4 chr1B.!!$R4 3106
12 TraesCS1A01G051100 chr1B 4797334 4798955 1621 True 717.000000 1232 87.234000 1806 3391 2 chr1B.!!$R5 1585
13 TraesCS1A01G051100 chr1B 3935789 3938665 2876 False 248.966667 584 94.256000 292 3037 3 chr1B.!!$F2 2745
14 TraesCS1A01G051100 chr6A 64063847 64065216 1369 True 1417.000000 1417 86.025000 1660 2982 1 chr6A.!!$R1 1322
15 TraesCS1A01G051100 chr6A 613492552 613496415 3863 False 1029.333333 2689 84.891333 148 3391 3 chr6A.!!$F1 3243
16 TraesCS1A01G051100 chr5B 60823722 60826075 2353 True 2678.000000 2678 87.705000 592 2896 1 chr5B.!!$R1 2304
17 TraesCS1A01G051100 chr3D 560022223 560026005 3782 True 808.200000 2604 89.152750 123 3304 4 chr3D.!!$R1 3181
18 TraesCS1A01G051100 chr5D 57819449 57821748 2299 False 2599.000000 2599 87.548000 592 2845 1 chr5D.!!$F1 2253
19 TraesCS1A01G051100 chr6D 51068122 51075977 7855 False 2274.000000 2326 87.403500 597 2660 2 chr6D.!!$F3 2063
20 TraesCS1A01G051100 chr6D 51348818 51350756 1938 False 2254.000000 2254 87.947000 695 2611 1 chr6D.!!$F2 1916
21 TraesCS1A01G051100 chr6D 50949119 50951060 1941 False 2217.000000 2217 87.589000 695 2611 1 chr6D.!!$F1 1916
22 TraesCS1A01G051100 chr6D 53142470 53144814 2344 True 1234.000000 2364 89.051500 702 2982 2 chr6D.!!$R1 2280
23 TraesCS1A01G051100 chr6B 120353264 120355155 1891 True 2351.000000 2351 89.115000 616 2523 1 chr6B.!!$R2 1907
24 TraesCS1A01G051100 chr6B 120315641 120317446 1805 True 2231.000000 2231 88.991000 695 2523 1 chr6B.!!$R1 1828

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
54 55 0.179134 GGCGAACTGACGAGCTGTAT 60.179 55.0 0.00 0.0 35.09 2.29 F
64 65 0.373716 CGAGCTGTATTTGTTCCGCC 59.626 55.0 0.00 0.0 0.00 6.13 F
65 66 0.733150 GAGCTGTATTTGTTCCGCCC 59.267 55.0 0.00 0.0 0.00 6.13 F
1264 3497 0.746659 GCAGTTGGACAACAAAGGCT 59.253 50.0 16.58 0.0 43.47 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1244 3477 0.249447 GCCTTTGTTGTCCAACTGCC 60.249 55.000 11.14 0.0 41.67 4.85 R
1264 3497 8.567948 GGAATAGTGAGATGAAAACACAGAAAA 58.432 33.333 0.00 0.0 37.05 2.29 R
2331 4579 4.695455 CCACAATACTCGACAACCAAAGAT 59.305 41.667 0.00 0.0 0.00 2.40 R
3431 8446 0.237498 GCAACCTCCTGTACGTTTGC 59.763 55.000 0.00 0.0 0.00 3.68 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
17 18 2.673341 AGCGAGGTGACGAGCTGA 60.673 61.111 0.00 0.00 44.10 4.26
18 19 2.505118 GCGAGGTGACGAGCTGAC 60.505 66.667 0.00 0.00 35.31 3.51
19 20 2.202362 CGAGGTGACGAGCTGACG 60.202 66.667 0.00 0.00 39.31 4.35
20 21 2.677979 CGAGGTGACGAGCTGACGA 61.678 63.158 1.33 0.00 37.03 4.20
21 22 1.135731 GAGGTGACGAGCTGACGAG 59.864 63.158 1.33 0.00 37.03 4.18
22 23 2.505118 GGTGACGAGCTGACGAGC 60.505 66.667 1.33 0.00 46.64 5.03
31 32 2.311294 GCTGACGAGCTGTGTTTGT 58.689 52.632 0.00 0.00 42.52 2.83
32 33 0.657840 GCTGACGAGCTGTGTTTGTT 59.342 50.000 0.00 0.00 42.52 2.83
33 34 1.333258 GCTGACGAGCTGTGTTTGTTC 60.333 52.381 0.00 0.00 42.52 3.18
34 35 1.261619 CTGACGAGCTGTGTTTGTTCC 59.738 52.381 0.00 0.00 0.00 3.62
35 36 0.232303 GACGAGCTGTGTTTGTTCCG 59.768 55.000 0.00 0.00 0.00 4.30
36 37 1.157870 ACGAGCTGTGTTTGTTCCGG 61.158 55.000 0.00 0.00 0.00 5.14
37 38 1.282875 GAGCTGTGTTTGTTCCGGC 59.717 57.895 0.00 0.00 0.00 6.13
38 39 2.051345 GCTGTGTTTGTTCCGGCG 60.051 61.111 0.00 0.00 0.00 6.46
39 40 2.539338 GCTGTGTTTGTTCCGGCGA 61.539 57.895 9.30 0.00 0.00 5.54
40 41 2.018544 CTGTGTTTGTTCCGGCGAA 58.981 52.632 9.30 0.00 0.00 4.70
52 53 2.049063 GGCGAACTGACGAGCTGT 60.049 61.111 0.00 0.00 35.09 4.40
53 54 1.211969 GGCGAACTGACGAGCTGTA 59.788 57.895 0.00 0.00 35.09 2.74
54 55 0.179134 GGCGAACTGACGAGCTGTAT 60.179 55.000 0.00 0.00 35.09 2.29
55 56 1.630148 GCGAACTGACGAGCTGTATT 58.370 50.000 0.00 0.00 35.09 1.89
56 57 1.993370 GCGAACTGACGAGCTGTATTT 59.007 47.619 0.00 0.00 35.09 1.40
57 58 2.222596 GCGAACTGACGAGCTGTATTTG 60.223 50.000 0.00 0.00 35.09 2.32
58 59 2.987149 CGAACTGACGAGCTGTATTTGT 59.013 45.455 0.00 0.00 35.09 2.83
59 60 3.428870 CGAACTGACGAGCTGTATTTGTT 59.571 43.478 0.00 0.00 35.09 2.83
60 61 4.433022 CGAACTGACGAGCTGTATTTGTTC 60.433 45.833 0.00 0.00 35.09 3.18
61 62 3.326747 ACTGACGAGCTGTATTTGTTCC 58.673 45.455 0.00 0.00 0.00 3.62
62 63 2.333926 TGACGAGCTGTATTTGTTCCG 58.666 47.619 0.00 0.00 0.00 4.30
63 64 1.060698 GACGAGCTGTATTTGTTCCGC 59.939 52.381 0.00 0.00 0.00 5.54
64 65 0.373716 CGAGCTGTATTTGTTCCGCC 59.626 55.000 0.00 0.00 0.00 6.13
65 66 0.733150 GAGCTGTATTTGTTCCGCCC 59.267 55.000 0.00 0.00 0.00 6.13
66 67 1.024579 AGCTGTATTTGTTCCGCCCG 61.025 55.000 0.00 0.00 0.00 6.13
67 68 1.427819 CTGTATTTGTTCCGCCCGC 59.572 57.895 0.00 0.00 0.00 6.13
68 69 1.003112 TGTATTTGTTCCGCCCGCT 60.003 52.632 0.00 0.00 0.00 5.52
69 70 1.022451 TGTATTTGTTCCGCCCGCTC 61.022 55.000 0.00 0.00 0.00 5.03
95 98 4.279982 AGACTAGCTAGGGTTTACACTCC 58.720 47.826 24.35 0.00 0.00 3.85
265 305 3.692791 TCTGATTCGACATGTAGACGG 57.307 47.619 8.29 3.86 36.09 4.79
269 309 4.562082 TGATTCGACATGTAGACGGTTTT 58.438 39.130 8.29 0.00 36.09 2.43
270 310 4.992319 TGATTCGACATGTAGACGGTTTTT 59.008 37.500 8.29 0.00 36.09 1.94
342 402 6.516860 CGGTAGTATCACCCTCATCCTTAAAG 60.517 46.154 0.00 0.00 34.90 1.85
345 405 6.653989 AGTATCACCCTCATCCTTAAAGTTG 58.346 40.000 0.00 0.00 0.00 3.16
414 481 2.373335 TTTTTGCCTAGGGTTGCAGA 57.627 45.000 11.72 0.00 38.95 4.26
484 622 2.230508 CTCATCAGCTGTGGCAAAATGT 59.769 45.455 14.67 0.00 41.70 2.71
683 1792 5.236047 CAGGCTCTGCTTGCTACTTAATTAG 59.764 44.000 0.00 0.00 0.00 1.73
728 2456 8.474831 AGTTTAATTTAATTATGTGCCCTGGAC 58.525 33.333 0.00 0.00 0.00 4.02
804 2952 6.095860 TCAATAAATCTCCATGCTTGTGAAGG 59.904 38.462 0.00 0.00 0.00 3.46
851 3015 6.698766 ACAGAAAAATGCTCAAAGTTCATCAC 59.301 34.615 0.00 0.00 0.00 3.06
998 3229 6.514947 TGCTACAGCTGAATTGAATTTGTTT 58.485 32.000 23.35 0.00 42.66 2.83
1013 3244 4.715534 TTTGTTTGATGGAGGACCTACA 57.284 40.909 9.45 9.45 37.04 2.74
1220 3453 4.567159 GCGAAGAGTGGAAATCGATTACTT 59.433 41.667 11.83 9.93 35.11 2.24
1244 3477 3.545703 GTTGGATACCTGGACATGGAAG 58.454 50.000 0.00 0.00 0.00 3.46
1264 3497 0.746659 GCAGTTGGACAACAAAGGCT 59.253 50.000 16.58 0.00 43.47 4.58
1983 4231 0.895530 ACAGCCTTTACGCTCTAGCA 59.104 50.000 2.44 0.00 42.21 3.49
2331 4579 5.172687 TGGGACATGCACATAAGTTAGAA 57.827 39.130 0.00 0.00 0.00 2.10
2393 4641 1.381056 TGCAGGGTGTTGCCAAGTT 60.381 52.632 0.00 0.00 43.43 2.66
2517 4779 3.569701 AGCCATTAAGTTGTTCAGTGTGG 59.430 43.478 0.00 0.00 0.00 4.17
2589 5321 6.751888 CCTTTACGGCAATGATTTTCCTTTAG 59.248 38.462 0.00 0.00 0.00 1.85
2590 5322 7.362574 CCTTTACGGCAATGATTTTCCTTTAGA 60.363 37.037 0.00 0.00 0.00 2.10
2591 5323 5.310720 ACGGCAATGATTTTCCTTTAGAC 57.689 39.130 0.00 0.00 0.00 2.59
2592 5324 4.764823 ACGGCAATGATTTTCCTTTAGACA 59.235 37.500 0.00 0.00 0.00 3.41
2593 5325 5.106157 ACGGCAATGATTTTCCTTTAGACAG 60.106 40.000 0.00 0.00 0.00 3.51
2595 5327 6.325596 GGCAATGATTTTCCTTTAGACAGTC 58.674 40.000 0.00 0.00 0.00 3.51
2597 5329 7.336931 GGCAATGATTTTCCTTTAGACAGTCTA 59.663 37.037 6.15 6.15 0.00 2.59
2650 5401 9.953565 ATTAATGAAACTTTAGTAGTAGGCACA 57.046 29.630 0.00 0.00 35.54 4.57
2684 5447 5.622770 ATTGTCAACCGTAATTCTGGTTC 57.377 39.130 10.48 3.38 45.10 3.62
2705 5474 9.155785 TGGTTCCTTAATTTCTACCCTCTATAG 57.844 37.037 0.00 0.00 0.00 1.31
3000 7253 0.889306 ACTCCCTCTGTACGTCTTGC 59.111 55.000 0.00 0.00 0.00 4.01
3037 7299 7.509318 AGAGGTAGTAGCATAATTGTGGATGTA 59.491 37.037 4.23 0.00 0.00 2.29
3125 7669 9.999660 ATAGCATATCCATCATATCATGTCTTC 57.000 33.333 0.00 0.00 0.00 2.87
3140 7684 1.066858 GTCTTCGCTCTGGACATCCAA 60.067 52.381 1.50 0.00 46.97 3.53
3236 7912 2.610433 CTCGTTGCATCAGTTCAGCTA 58.390 47.619 0.00 0.00 0.00 3.32
3308 7985 6.966435 TTGCTTTGCTGGCTATTTAATTTC 57.034 33.333 0.00 0.00 0.00 2.17
3402 8417 2.645838 ACATTAGCAATCCGGCAGAT 57.354 45.000 0.00 0.00 36.48 2.90
3411 8426 1.496060 ATCCGGCAGATGTACAGGAA 58.504 50.000 0.33 0.00 32.41 3.36
3412 8427 0.824109 TCCGGCAGATGTACAGGAAG 59.176 55.000 0.33 0.00 0.00 3.46
3413 8428 0.811616 CCGGCAGATGTACAGGAAGC 60.812 60.000 0.33 2.82 0.00 3.86
3414 8429 1.148157 CGGCAGATGTACAGGAAGCG 61.148 60.000 0.33 0.00 0.00 4.68
3415 8430 1.432270 GGCAGATGTACAGGAAGCGC 61.432 60.000 0.00 0.00 0.00 5.92
3416 8431 1.432270 GCAGATGTACAGGAAGCGCC 61.432 60.000 2.29 0.00 0.00 6.53
3417 8432 1.141881 AGATGTACAGGAAGCGCCG 59.858 57.895 2.29 0.00 43.43 6.46
3419 8434 4.752879 TGTACAGGAAGCGCCGCC 62.753 66.667 4.98 5.77 43.43 6.13
3420 8435 4.752879 GTACAGGAAGCGCCGCCA 62.753 66.667 17.26 0.00 43.43 5.69
3440 8455 1.135939 GGCAATCCGGCAAACGTAC 59.864 57.895 0.00 0.00 42.24 3.67
3441 8456 1.579084 GGCAATCCGGCAAACGTACA 61.579 55.000 0.00 0.00 42.24 2.90
3443 8458 0.446222 CAATCCGGCAAACGTACAGG 59.554 55.000 0.00 0.00 42.24 4.00
3444 8459 0.322322 AATCCGGCAAACGTACAGGA 59.678 50.000 0.00 7.32 42.24 3.86
3448 8463 0.601841 CGGCAAACGTACAGGAGGTT 60.602 55.000 0.00 0.00 37.76 3.50
3450 8465 0.237498 GCAAACGTACAGGAGGTTGC 59.763 55.000 5.65 5.65 36.30 4.17
3451 8466 1.588674 CAAACGTACAGGAGGTTGCA 58.411 50.000 0.00 0.00 36.30 4.08
3453 8468 0.756903 AACGTACAGGAGGTTGCAGT 59.243 50.000 0.00 0.00 34.87 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.673341 TCAGCTCGTCACCTCGCT 60.673 61.111 0.00 0.00 0.00 4.93
2 3 2.202362 CGTCAGCTCGTCACCTCG 60.202 66.667 0.00 0.00 0.00 4.63
3 4 1.135731 CTCGTCAGCTCGTCACCTC 59.864 63.158 0.00 0.00 0.00 3.85
4 5 2.983930 GCTCGTCAGCTCGTCACCT 61.984 63.158 0.00 0.00 43.09 4.00
5 6 2.505118 GCTCGTCAGCTCGTCACC 60.505 66.667 0.00 0.00 43.09 4.02
14 15 1.261619 GGAACAAACACAGCTCGTCAG 59.738 52.381 0.00 0.00 0.00 3.51
15 16 1.295792 GGAACAAACACAGCTCGTCA 58.704 50.000 0.00 0.00 0.00 4.35
16 17 0.232303 CGGAACAAACACAGCTCGTC 59.768 55.000 0.00 0.00 0.00 4.20
17 18 1.157870 CCGGAACAAACACAGCTCGT 61.158 55.000 0.00 0.00 0.00 4.18
18 19 1.569493 CCGGAACAAACACAGCTCG 59.431 57.895 0.00 0.00 0.00 5.03
19 20 1.282875 GCCGGAACAAACACAGCTC 59.717 57.895 5.05 0.00 0.00 4.09
20 21 2.542907 CGCCGGAACAAACACAGCT 61.543 57.895 5.05 0.00 0.00 4.24
21 22 2.051345 CGCCGGAACAAACACAGC 60.051 61.111 5.05 0.00 0.00 4.40
22 23 2.018544 TTCGCCGGAACAAACACAG 58.981 52.632 5.05 0.00 0.00 3.66
23 24 4.220413 TTCGCCGGAACAAACACA 57.780 50.000 5.05 0.00 0.00 3.72
31 32 2.257371 CTCGTCAGTTCGCCGGAA 59.743 61.111 5.05 0.00 0.00 4.30
32 33 4.415332 GCTCGTCAGTTCGCCGGA 62.415 66.667 5.05 0.00 0.00 5.14
33 34 4.421479 AGCTCGTCAGTTCGCCGG 62.421 66.667 0.00 0.00 0.00 6.13
34 35 2.523184 TACAGCTCGTCAGTTCGCCG 62.523 60.000 0.00 0.00 0.00 6.46
35 36 0.179134 ATACAGCTCGTCAGTTCGCC 60.179 55.000 0.00 0.00 0.00 5.54
36 37 1.630148 AATACAGCTCGTCAGTTCGC 58.370 50.000 0.00 0.00 0.00 4.70
37 38 2.987149 ACAAATACAGCTCGTCAGTTCG 59.013 45.455 0.00 0.00 0.00 3.95
38 39 4.143094 GGAACAAATACAGCTCGTCAGTTC 60.143 45.833 0.00 0.00 33.89 3.01
39 40 3.746492 GGAACAAATACAGCTCGTCAGTT 59.254 43.478 0.00 0.00 0.00 3.16
40 41 3.326747 GGAACAAATACAGCTCGTCAGT 58.673 45.455 0.00 0.00 0.00 3.41
41 42 2.345641 CGGAACAAATACAGCTCGTCAG 59.654 50.000 0.00 0.00 0.00 3.51
42 43 2.333926 CGGAACAAATACAGCTCGTCA 58.666 47.619 0.00 0.00 0.00 4.35
43 44 1.060698 GCGGAACAAATACAGCTCGTC 59.939 52.381 0.00 0.00 0.00 4.20
44 45 1.076332 GCGGAACAAATACAGCTCGT 58.924 50.000 0.00 0.00 0.00 4.18
45 46 0.373716 GGCGGAACAAATACAGCTCG 59.626 55.000 0.00 0.00 0.00 5.03
46 47 0.733150 GGGCGGAACAAATACAGCTC 59.267 55.000 0.00 0.00 0.00 4.09
47 48 1.024579 CGGGCGGAACAAATACAGCT 61.025 55.000 0.00 0.00 0.00 4.24
48 49 1.427819 CGGGCGGAACAAATACAGC 59.572 57.895 0.00 0.00 0.00 4.40
49 50 1.024579 AGCGGGCGGAACAAATACAG 61.025 55.000 0.00 0.00 0.00 2.74
50 51 1.003112 AGCGGGCGGAACAAATACA 60.003 52.632 0.00 0.00 0.00 2.29
51 52 1.719709 GAGCGGGCGGAACAAATAC 59.280 57.895 0.00 0.00 0.00 1.89
52 53 1.812093 CGAGCGGGCGGAACAAATA 60.812 57.895 0.00 0.00 0.00 1.40
53 54 3.124921 CGAGCGGGCGGAACAAAT 61.125 61.111 0.00 0.00 0.00 2.32
62 63 4.615834 CTAGTCTCGCGAGCGGGC 62.616 72.222 30.97 19.09 40.19 6.13
63 64 4.615834 GCTAGTCTCGCGAGCGGG 62.616 72.222 30.97 21.00 42.03 6.13
66 67 1.572447 CCTAGCTAGTCTCGCGAGC 59.428 63.158 30.97 24.09 44.65 5.03
67 68 0.533308 ACCCTAGCTAGTCTCGCGAG 60.533 60.000 30.03 30.03 0.00 5.03
68 69 0.107312 AACCCTAGCTAGTCTCGCGA 60.107 55.000 19.31 9.26 0.00 5.87
69 70 0.739561 AAACCCTAGCTAGTCTCGCG 59.260 55.000 19.31 0.00 0.00 5.87
95 98 3.591835 GCGGAGGAGAGGAGAGCG 61.592 72.222 0.00 0.00 0.00 5.03
216 246 1.014564 CAACGAACGAAGAGGGAGGC 61.015 60.000 0.14 0.00 0.00 4.70
269 309 8.702163 AGAAAGCGAATCAAAAAGAAAGAAAA 57.298 26.923 0.00 0.00 0.00 2.29
270 310 8.594687 CAAGAAAGCGAATCAAAAAGAAAGAAA 58.405 29.630 0.00 0.00 0.00 2.52
271 311 7.973388 TCAAGAAAGCGAATCAAAAAGAAAGAA 59.027 29.630 0.00 0.00 0.00 2.52
272 312 7.479980 TCAAGAAAGCGAATCAAAAAGAAAGA 58.520 30.769 0.00 0.00 0.00 2.52
273 313 7.684062 TCAAGAAAGCGAATCAAAAAGAAAG 57.316 32.000 0.00 0.00 0.00 2.62
328 384 6.663523 ACATTAACCAACTTTAAGGATGAGGG 59.336 38.462 0.00 0.00 0.00 4.30
342 402 7.151976 AGAATGGCTTTACAACATTAACCAAC 58.848 34.615 0.00 0.00 35.17 3.77
345 405 6.152831 AGGAGAATGGCTTTACAACATTAACC 59.847 38.462 0.00 0.00 35.17 2.85
443 524 1.963515 GTTGAGTTCACAGGGCCAATT 59.036 47.619 6.18 0.00 0.00 2.32
484 622 7.926018 GGCAAGAAAGAAAGTAAGGAAATCAAA 59.074 33.333 0.00 0.00 0.00 2.69
550 698 4.090761 TCTGAACATGAAAACCAGAGCT 57.909 40.909 0.00 0.00 31.15 4.09
804 2952 6.744112 TGTATCCATCCAAAACTTGTGTTTC 58.256 36.000 0.00 0.00 44.70 2.78
869 3043 9.368674 GAATGTGAAGACAGATGGAGATATATG 57.631 37.037 0.00 0.00 34.87 1.78
884 3083 7.700505 TCAGAATAATGCATGAATGTGAAGAC 58.299 34.615 0.00 0.00 0.00 3.01
998 3229 1.062886 CCTCCTGTAGGTCCTCCATCA 60.063 57.143 0.00 0.00 40.94 3.07
1202 3435 6.314784 CAACCAAAGTAATCGATTTCCACTC 58.685 40.000 17.19 1.19 0.00 3.51
1244 3477 0.249447 GCCTTTGTTGTCCAACTGCC 60.249 55.000 11.14 0.00 41.67 4.85
1264 3497 8.567948 GGAATAGTGAGATGAAAACACAGAAAA 58.432 33.333 0.00 0.00 37.05 2.29
2331 4579 4.695455 CCACAATACTCGACAACCAAAGAT 59.305 41.667 0.00 0.00 0.00 2.40
2517 4779 2.548920 GGTGAATCTGGGTCGGATGATC 60.549 54.545 0.00 0.00 28.96 2.92
2589 5321 9.941325 ATCTGGAATTCATCATTATAGACTGTC 57.059 33.333 7.93 0.00 0.00 3.51
2590 5322 9.722184 CATCTGGAATTCATCATTATAGACTGT 57.278 33.333 7.93 0.00 0.00 3.55
2591 5323 9.163899 CCATCTGGAATTCATCATTATAGACTG 57.836 37.037 7.93 0.00 37.39 3.51
2592 5324 7.828223 GCCATCTGGAATTCATCATTATAGACT 59.172 37.037 7.93 0.00 37.39 3.24
2593 5325 7.609146 TGCCATCTGGAATTCATCATTATAGAC 59.391 37.037 7.93 0.00 37.39 2.59
2595 5327 7.933215 TGCCATCTGGAATTCATCATTATAG 57.067 36.000 7.93 0.00 37.39 1.31
2597 5329 6.781014 AGTTGCCATCTGGAATTCATCATTAT 59.219 34.615 7.93 0.00 37.39 1.28
2650 5401 6.870971 ACGGTTGACAATAATACACAAGTT 57.129 33.333 0.00 0.00 0.00 2.66
2684 5447 7.463961 TCGCTATAGAGGGTAGAAATTAAGG 57.536 40.000 3.21 0.00 36.97 2.69
2705 5474 0.935196 CCTACTTATGCCGGTTTCGC 59.065 55.000 1.90 0.00 34.56 4.70
2944 7129 9.732130 ACTATTCTTTTGAGAAGCTATCAAAGT 57.268 29.630 20.22 13.92 44.86 2.66
3000 7253 6.694877 TGCTACTACCTCTGTACACTAATG 57.305 41.667 0.00 0.00 0.00 1.90
3037 7299 9.246670 TCAACTTCATGTCATTTTGGAATCTAT 57.753 29.630 0.00 0.00 0.00 1.98
3114 7658 3.023832 TGTCCAGAGCGAAGACATGATA 58.976 45.455 0.00 0.00 35.67 2.15
3175 7722 8.043710 ACTCTTGATAGGTAAAAAGAGATGTGG 58.956 37.037 16.00 0.00 45.53 4.17
3236 7912 2.821969 CAAGGCAAATGCTGTTCCTACT 59.178 45.455 5.25 0.00 41.70 2.57
3320 8013 3.908382 GTGCGTGTTTCATTTTAGCTCAG 59.092 43.478 0.00 0.00 0.00 3.35
3379 8394 3.625764 TCTGCCGGATTGCTAATGTAAAC 59.374 43.478 5.05 0.00 0.00 2.01
3402 8417 4.752879 GGCGGCGCTTCCTGTACA 62.753 66.667 32.30 0.00 0.00 2.90
3419 8434 1.516821 CGTTTGCCGGATTGCCATG 60.517 57.895 5.05 0.00 0.00 3.66
3420 8435 0.678366 TACGTTTGCCGGATTGCCAT 60.678 50.000 5.05 0.00 42.24 4.40
3424 8439 0.446222 CCTGTACGTTTGCCGGATTG 59.554 55.000 5.05 0.00 42.24 2.67
3425 8440 0.322322 TCCTGTACGTTTGCCGGATT 59.678 50.000 5.05 0.00 42.24 3.01
3427 8442 1.290955 CTCCTGTACGTTTGCCGGA 59.709 57.895 5.05 0.00 42.24 5.14
3428 8443 1.740296 CCTCCTGTACGTTTGCCGG 60.740 63.158 0.00 0.00 42.24 6.13
3430 8445 0.872388 CAACCTCCTGTACGTTTGCC 59.128 55.000 0.00 0.00 0.00 4.52
3431 8446 0.237498 GCAACCTCCTGTACGTTTGC 59.763 55.000 0.00 0.00 0.00 3.68
3432 8447 1.531149 CTGCAACCTCCTGTACGTTTG 59.469 52.381 0.00 0.00 0.00 2.93
3433 8448 1.140252 ACTGCAACCTCCTGTACGTTT 59.860 47.619 0.00 0.00 0.00 3.60
3434 8449 0.756903 ACTGCAACCTCCTGTACGTT 59.243 50.000 0.00 0.00 0.00 3.99
3435 8450 0.756903 AACTGCAACCTCCTGTACGT 59.243 50.000 0.00 0.00 0.00 3.57
3436 8451 3.606886 AACTGCAACCTCCTGTACG 57.393 52.632 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.