Multiple sequence alignment - TraesCS2A01G209800

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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 TraesCS2A01G209800 chr2A 100.000 4601 0 0 1 4601 193878902 193874302 0.000000e+00 8497.0
1 TraesCS2A01G209800 chr2A 76.375 309 38 20 4122 4405 38543148 38543446 2.890000e-27 134.0
2 TraesCS2A01G209800 chr2B 92.503 1974 107 19 1 1967 236170348 236168409 0.000000e+00 2787.0
3 TraesCS2A01G209800 chr2B 92.275 932 38 8 2436 3351 236167948 236167035 0.000000e+00 1291.0
4 TraesCS2A01G209800 chr2B 90.203 541 27 12 3317 3835 236167038 236166502 0.000000e+00 682.0
5 TraesCS2A01G209800 chr2B 93.831 308 16 2 2049 2355 236168250 236167945 1.170000e-125 460.0
6 TraesCS2A01G209800 chr2B 95.745 94 3 1 2344 2437 303097358 303097266 2.870000e-32 150.0
7 TraesCS2A01G209800 chr2D 90.807 892 47 14 2994 3869 179353051 179352179 0.000000e+00 1160.0
8 TraesCS2A01G209800 chr2D 86.245 727 66 17 643 1354 179355477 179354770 0.000000e+00 758.0
9 TraesCS2A01G209800 chr2D 87.082 658 60 17 1 645 179356210 179355565 0.000000e+00 721.0
10 TraesCS2A01G209800 chr2D 92.200 500 34 2 2437 2935 179353543 179353048 0.000000e+00 702.0
11 TraesCS2A01G209800 chr2D 92.593 351 16 5 4000 4344 179334965 179334619 3.200000e-136 496.0
12 TraesCS2A01G209800 chr2D 96.923 260 8 0 4342 4601 179334509 179334250 1.970000e-118 436.0
13 TraesCS2A01G209800 chr2D 93.966 116 4 1 3870 3985 179351965 179351853 6.120000e-39 172.0
14 TraesCS2A01G209800 chr2D 93.750 112 7 0 2049 2160 179353989 179353878 7.920000e-38 169.0
15 TraesCS2A01G209800 chr2D 83.230 161 14 10 4217 4372 618179649 618179497 8.030000e-28 135.0
16 TraesCS2A01G209800 chr2D 97.297 37 1 0 3978 4014 179335015 179334979 3.840000e-06 63.9
17 TraesCS2A01G209800 chr7A 80.323 310 41 15 2626 2925 6597638 6597937 2.790000e-52 217.0
18 TraesCS2A01G209800 chr7A 88.060 67 8 0 1008 1074 6848516 6848450 3.820000e-11 80.5
19 TraesCS2A01G209800 chr4A 80.887 293 31 18 2638 2925 737096787 737097059 1.680000e-49 207.0
20 TraesCS2A01G209800 chr4A 76.855 337 51 22 4217 4537 684126978 684126653 1.020000e-36 165.0
21 TraesCS2A01G209800 chr4A 100.000 88 0 0 2352 2439 605646982 605646895 3.680000e-36 163.0
22 TraesCS2A01G209800 chr4A 76.142 197 28 15 4325 4515 88521098 88521281 8.200000e-13 86.1
23 TraesCS2A01G209800 chr4A 88.060 67 8 0 1008 1074 737094890 737094956 3.820000e-11 80.5
24 TraesCS2A01G209800 chr7D 79.310 290 43 12 2638 2925 5379367 5379093 2.190000e-43 187.0
25 TraesCS2A01G209800 chr7D 94.286 105 4 1 2335 2437 311872831 311872935 4.760000e-35 159.0
26 TraesCS2A01G209800 chr7D 90.769 65 6 0 1000 1064 5308750 5308814 2.280000e-13 87.9
27 TraesCS2A01G209800 chr7D 88.060 67 8 0 1008 1074 5381137 5381071 3.820000e-11 80.5
28 TraesCS2A01G209800 chr7B 95.327 107 0 4 2349 2451 715301933 715302038 1.020000e-36 165.0
29 TraesCS2A01G209800 chr3B 97.917 96 1 1 2345 2440 816514521 816514615 1.020000e-36 165.0
30 TraesCS2A01G209800 chr3B 81.699 153 16 10 4219 4367 25247590 25247734 2.910000e-22 117.0
31 TraesCS2A01G209800 chr1A 96.907 97 2 1 2348 2444 504269083 504269178 1.320000e-35 161.0
32 TraesCS2A01G209800 chr1B 95.876 97 3 1 2344 2440 332837884 332837979 6.160000e-34 156.0
33 TraesCS2A01G209800 chr1B 91.071 112 6 3 2351 2460 624302705 624302596 1.030000e-31 148.0
34 TraesCS2A01G209800 chr6D 94.118 102 4 2 2349 2450 26359304 26359205 2.220000e-33 154.0
35 TraesCS2A01G209800 chr6B 75.281 356 67 16 4248 4592 165103455 165103110 2.870000e-32 150.0
36 TraesCS2A01G209800 chr6B 74.719 356 69 16 4248 4592 165051128 165050783 6.210000e-29 139.0
37 TraesCS2A01G209800 chr6B 90.698 43 3 1 1031 1072 620909321 620909279 6.430000e-04 56.5
38 TraesCS2A01G209800 chr3A 78.469 209 32 12 4327 4531 67436718 67436917 1.740000e-24 124.0
39 TraesCS2A01G209800 chr3A 73.926 326 62 22 4219 4531 621986338 621986023 4.870000e-20 110.0
40 TraesCS2A01G209800 chr4D 75.472 265 39 16 4328 4590 47565150 47565390 6.300000e-19 106.0


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 TraesCS2A01G209800 chr2A 193874302 193878902 4600 True 8497.000000 8497 100.000000 1 4601 1 chr2A.!!$R1 4600
1 TraesCS2A01G209800 chr2B 236166502 236170348 3846 True 1305.000000 2787 92.203000 1 3835 4 chr2B.!!$R2 3834
2 TraesCS2A01G209800 chr2D 179351853 179356210 4357 True 613.666667 1160 90.675000 1 3985 6 chr2D.!!$R3 3984
3 TraesCS2A01G209800 chr2D 179334250 179335015 765 True 331.966667 496 95.604333 3978 4601 3 chr2D.!!$R2 623

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
474 487 2.159085 CCTAGCTCAAGGAACGTAAGGG 60.159 54.545 0.00 0.0 39.81 3.95 F
1267 1387 1.620819 AGCCGATTGCCAGACTATAGG 59.379 52.381 4.43 0.0 42.71 2.57 F
1503 1624 0.095417 GCCTGTCGATGAGCGTTTTC 59.905 55.000 0.00 0.0 41.80 2.29 F
2002 2263 0.464036 TCCCTCGCGAAGTGCAATAT 59.536 50.000 11.33 0.0 46.97 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1336 1457 0.036875 GACAAAGCTGGCTACCTGGT 59.963 55.000 4.05 4.05 34.79 4.00 R
2531 2980 1.133025 GCACCATCCAACAGATTTCCG 59.867 52.381 0.00 0.00 30.59 4.30 R
3151 3605 1.279271 CTGGGGTTCAAGGGTACTCAG 59.721 57.143 0.00 0.00 0.00 3.35 R
3732 4235 1.151668 GCACATTGCTCTCTTCACGT 58.848 50.000 0.00 0.00 40.96 4.49 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 51 3.326747 GCGACTTGGATGTAGTTCTGTT 58.673 45.455 0.00 0.00 0.00 3.16
53 55 5.542779 GACTTGGATGTAGTTCTGTTCACT 58.457 41.667 0.00 0.00 0.00 3.41
108 110 6.617784 TGGGTGGTAGGTATTCTGAATTGATA 59.382 38.462 8.38 0.00 0.00 2.15
238 240 3.428532 AGACATGCTCTTCAATTTGGCT 58.571 40.909 0.00 0.00 0.00 4.75
239 241 4.592942 AGACATGCTCTTCAATTTGGCTA 58.407 39.130 0.00 0.00 0.00 3.93
312 315 9.693739 CCTGAGATTCATATGTAGGAGTAGTAT 57.306 37.037 1.90 0.00 0.00 2.12
345 348 5.436175 TCTTCCATTGAAAGTTGTGACTCA 58.564 37.500 0.00 0.00 34.21 3.41
421 424 5.894298 AGAGGCAATTCTACATGATACCA 57.106 39.130 0.00 0.00 0.00 3.25
474 487 2.159085 CCTAGCTCAAGGAACGTAAGGG 60.159 54.545 0.00 0.00 39.81 3.95
495 508 6.081356 AGGGGAATTTACATTGTTTCTTCCA 58.919 36.000 18.09 0.00 33.85 3.53
568 581 2.930950 AGTTTGGTAGCAGCTCAACAA 58.069 42.857 0.00 0.00 0.00 2.83
570 583 3.316308 AGTTTGGTAGCAGCTCAACAAAG 59.684 43.478 15.50 0.00 0.00 2.77
668 771 8.635765 ATCAAGTTTGTGTTATAGTCAATGGT 57.364 30.769 0.00 0.00 0.00 3.55
895 1007 8.511321 TGAGTTTTACTATTGTATTGTGCCAAG 58.489 33.333 0.00 0.00 0.00 3.61
898 1017 6.995511 TTACTATTGTATTGTGCCAAGGAC 57.004 37.500 0.00 0.00 0.00 3.85
1107 1227 9.729281 CCCCTAAGTTTGTAGTTGTTATTTCTA 57.271 33.333 0.00 0.00 0.00 2.10
1127 1247 3.959535 ATTTCGGTTGTCAATTGCCAT 57.040 38.095 0.00 0.00 0.00 4.40
1170 1290 3.365220 GCACGAAGACACTCTGTAATGAC 59.635 47.826 0.00 0.00 0.00 3.06
1267 1387 1.620819 AGCCGATTGCCAGACTATAGG 59.379 52.381 4.43 0.00 42.71 2.57
1276 1396 6.420913 TTGCCAGACTATAGGATTTAGGAC 57.579 41.667 4.43 0.00 0.00 3.85
1336 1457 5.883673 ACAGTAACAGAAAAGTAGCAACCAA 59.116 36.000 0.00 0.00 0.00 3.67
1337 1458 6.183360 ACAGTAACAGAAAAGTAGCAACCAAC 60.183 38.462 0.00 0.00 0.00 3.77
1338 1459 4.649088 AACAGAAAAGTAGCAACCAACC 57.351 40.909 0.00 0.00 0.00 3.77
1339 1460 3.626930 ACAGAAAAGTAGCAACCAACCA 58.373 40.909 0.00 0.00 0.00 3.67
1363 1484 0.884704 GCCAGCTTTGTCGACCAGAA 60.885 55.000 14.12 4.59 0.00 3.02
1371 1492 1.719529 TGTCGACCAGAAACCCCTTA 58.280 50.000 14.12 0.00 0.00 2.69
1402 1523 6.258068 CGACCAACCTGAATATTAGGAGAAAC 59.742 42.308 14.32 5.70 38.71 2.78
1503 1624 0.095417 GCCTGTCGATGAGCGTTTTC 59.905 55.000 0.00 0.00 41.80 2.29
1507 1628 3.616821 CCTGTCGATGAGCGTTTTCATTA 59.383 43.478 0.00 0.00 37.90 1.90
1514 1635 6.960992 TCGATGAGCGTTTTCATTATTCTTTG 59.039 34.615 0.00 0.00 37.90 2.77
1549 1670 4.751767 TTCCCTTGTGCAGTTTGATTTT 57.248 36.364 0.00 0.00 0.00 1.82
1577 1698 2.233271 CTTGCCAGGTTTGTGACATCT 58.767 47.619 0.00 0.00 0.00 2.90
1599 1720 9.190858 CATCTCTTGAATGCAGAAGTACTATAC 57.809 37.037 0.00 0.00 0.00 1.47
1607 1728 6.369059 TGCAGAAGTACTATACGTTACTCC 57.631 41.667 0.00 0.00 0.00 3.85
1647 1864 1.726853 GGGATGACGACTTCCTTGTG 58.273 55.000 16.85 0.00 39.41 3.33
1648 1865 1.002087 GGGATGACGACTTCCTTGTGT 59.998 52.381 16.85 0.00 39.41 3.72
1733 1950 8.408043 TGACATCACAGATAAAACCTGAAAAT 57.592 30.769 0.00 0.00 35.69 1.82
1922 2146 4.744136 ATTATGATGCATCAGCGAGTTG 57.256 40.909 31.36 0.00 46.23 3.16
1942 2166 4.591321 TGGCCAAGAACTTATTCCTCAT 57.409 40.909 0.61 0.00 35.18 2.90
1967 2228 4.250464 TCCGTTGTGTTCTGATTCCATAC 58.750 43.478 0.00 0.00 0.00 2.39
1989 2250 5.126067 ACCTTGATTTGAATATGTCCCTCG 58.874 41.667 0.00 0.00 0.00 4.63
1991 2252 3.130633 TGATTTGAATATGTCCCTCGCG 58.869 45.455 0.00 0.00 0.00 5.87
2002 2263 0.464036 TCCCTCGCGAAGTGCAATAT 59.536 50.000 11.33 0.00 46.97 1.28
2134 2438 9.033481 CACATTTTTCATTTGCTCTTGTTTCTA 57.967 29.630 0.00 0.00 0.00 2.10
2228 2652 7.394144 AGGGATTAAAGTGATATAGTGGCTT 57.606 36.000 0.00 0.00 0.00 4.35
2229 2653 7.816411 AGGGATTAAAGTGATATAGTGGCTTT 58.184 34.615 0.00 0.00 34.35 3.51
2253 2677 3.814504 TTTCTCAAGCCCCAAAGAGAT 57.185 42.857 0.00 0.00 37.03 2.75
2332 2781 4.708177 TGAGCTACATTCTTGGCTATTCC 58.292 43.478 0.00 0.00 35.01 3.01
2348 2797 6.055588 GGCTATTCCATACTGAACTTAGCAA 58.944 40.000 0.00 0.00 35.78 3.91
2350 2799 7.308229 GGCTATTCCATACTGAACTTAGCAATG 60.308 40.741 0.00 0.00 35.78 2.82
2351 2800 7.227512 GCTATTCCATACTGAACTTAGCAATGT 59.772 37.037 0.00 0.00 34.89 2.71
2352 2801 9.764363 CTATTCCATACTGAACTTAGCAATGTA 57.236 33.333 0.00 0.00 0.00 2.29
2353 2802 7.843490 TTCCATACTGAACTTAGCAATGTAC 57.157 36.000 0.00 0.00 0.00 2.90
2354 2803 7.182817 TCCATACTGAACTTAGCAATGTACT 57.817 36.000 0.00 0.00 0.00 2.73
2355 2804 7.265673 TCCATACTGAACTTAGCAATGTACTC 58.734 38.462 0.00 0.00 0.00 2.59
2356 2805 6.480320 CCATACTGAACTTAGCAATGTACTCC 59.520 42.308 0.00 0.00 0.00 3.85
2357 2806 4.833390 ACTGAACTTAGCAATGTACTCCC 58.167 43.478 0.00 0.00 0.00 4.30
2358 2807 4.532521 ACTGAACTTAGCAATGTACTCCCT 59.467 41.667 0.00 0.00 0.00 4.20
2359 2808 5.086104 TGAACTTAGCAATGTACTCCCTC 57.914 43.478 0.00 0.00 0.00 4.30
2360 2809 4.081087 TGAACTTAGCAATGTACTCCCTCC 60.081 45.833 0.00 0.00 0.00 4.30
2361 2810 2.431057 ACTTAGCAATGTACTCCCTCCG 59.569 50.000 0.00 0.00 0.00 4.63
2362 2811 2.154567 TAGCAATGTACTCCCTCCGT 57.845 50.000 0.00 0.00 0.00 4.69
2363 2812 1.276622 AGCAATGTACTCCCTCCGTT 58.723 50.000 0.00 0.00 0.00 4.44
2364 2813 1.207329 AGCAATGTACTCCCTCCGTTC 59.793 52.381 0.00 0.00 0.00 3.95
2365 2814 1.742750 GCAATGTACTCCCTCCGTTCC 60.743 57.143 0.00 0.00 0.00 3.62
2366 2815 1.553248 CAATGTACTCCCTCCGTTCCA 59.447 52.381 0.00 0.00 0.00 3.53
2367 2816 1.946984 ATGTACTCCCTCCGTTCCAA 58.053 50.000 0.00 0.00 0.00 3.53
2368 2817 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
2369 2818 2.048601 TGTACTCCCTCCGTTCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
2370 2819 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
2371 2820 3.839490 TGTACTCCCTCCGTTCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
2372 2821 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2373 2822 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2374 2823 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2375 2824 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2376 2825 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2377 2826 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2378 2827 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
2379 2828 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
2380 2829 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
2381 2830 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
2382 2831 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
2383 2832 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
2384 2833 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
2385 2834 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
2386 2835 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
2387 2836 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
2388 2837 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
2389 2838 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
2390 2839 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
2391 2840 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
2392 2841 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
2393 2842 9.802039 AAATAGATGACCCAACTTTGTACTAAA 57.198 29.630 0.00 0.00 0.00 1.85
2394 2843 9.449719 AATAGATGACCCAACTTTGTACTAAAG 57.550 33.333 13.08 13.08 0.00 1.85
2395 2844 6.838382 AGATGACCCAACTTTGTACTAAAGT 58.162 36.000 14.04 14.04 41.82 2.66
2397 2846 8.434392 AGATGACCCAACTTTGTACTAAAGTTA 58.566 33.333 23.56 14.79 45.57 2.24
2398 2847 8.617290 ATGACCCAACTTTGTACTAAAGTTAG 57.383 34.615 23.56 20.79 45.57 2.34
2399 2848 7.567458 TGACCCAACTTTGTACTAAAGTTAGT 58.433 34.615 23.56 22.58 45.57 2.24
2400 2849 8.703743 TGACCCAACTTTGTACTAAAGTTAGTA 58.296 33.333 23.56 6.81 45.57 1.82
2401 2850 9.716531 GACCCAACTTTGTACTAAAGTTAGTAT 57.283 33.333 23.56 15.20 45.57 2.12
2428 2877 9.918630 AAAATTGAGTCATCTATTTTGGAACAG 57.081 29.630 11.47 0.00 44.08 3.16
2429 2878 8.868522 AATTGAGTCATCTATTTTGGAACAGA 57.131 30.769 0.00 0.00 42.39 3.41
2430 2879 7.912056 TTGAGTCATCTATTTTGGAACAGAG 57.088 36.000 0.00 0.00 42.39 3.35
2431 2880 6.409704 TGAGTCATCTATTTTGGAACAGAGG 58.590 40.000 0.00 0.00 42.39 3.69
2432 2881 5.749462 AGTCATCTATTTTGGAACAGAGGG 58.251 41.667 0.00 0.00 42.39 4.30
2433 2882 5.488919 AGTCATCTATTTTGGAACAGAGGGA 59.511 40.000 0.00 0.00 42.39 4.20
2434 2883 5.819901 GTCATCTATTTTGGAACAGAGGGAG 59.180 44.000 0.00 0.00 42.39 4.30
2492 2941 6.319658 GTCAGTATTGTGAATCATGGACCAAT 59.680 38.462 0.00 2.42 0.00 3.16
2531 2980 7.527084 TTGTGGTTTTGCACTAAAATGTAAC 57.473 32.000 0.00 0.00 40.17 2.50
2560 3009 4.218200 TCTGTTGGATGGTGCATTTAACAG 59.782 41.667 16.32 16.32 42.46 3.16
2689 3138 1.133823 TGGGGTATCAGCATTGCGAAT 60.134 47.619 2.38 3.69 0.00 3.34
2769 3218 4.037222 TCCATGTAGTCCAGGCAATTCTA 58.963 43.478 0.00 0.00 0.00 2.10
2786 3235 5.552870 ATTCTACACTTGTGTTCCAGACT 57.447 39.130 11.80 1.25 0.00 3.24
2914 3364 3.869065 CATGGTCATTACACCGGTAAGT 58.131 45.455 6.87 4.41 42.42 2.24
2980 3434 4.966168 TGCACTAAGGAGGTGTGGATTATA 59.034 41.667 0.00 0.00 37.07 0.98
2982 3436 6.101150 TGCACTAAGGAGGTGTGGATTATATT 59.899 38.462 0.00 0.00 37.07 1.28
3062 3516 9.440773 GTTGCATGGATCTTCTGATATTATACA 57.559 33.333 0.00 0.00 32.19 2.29
3089 3543 5.722172 TTAACTACTCCCTAGACTGGCTA 57.278 43.478 0.00 0.00 0.00 3.93
3210 3664 9.965824 AACAATCACTTTCCTTGTTATTAACTG 57.034 29.630 7.99 1.70 40.34 3.16
3258 3719 0.610232 GTTCCTGAGCAGCAATGGGT 60.610 55.000 0.00 0.00 0.00 4.51
3274 3736 2.411583 TGGGTGGCATAGAGACATGAT 58.588 47.619 0.00 0.00 37.77 2.45
3351 3851 4.096532 TGTGTTCTCCATTTTAACGTTGCA 59.903 37.500 11.99 0.00 0.00 4.08
3447 3947 3.341823 CACAGGCTTGTATCAGCTTTCT 58.658 45.455 0.00 0.00 39.97 2.52
3479 3979 4.196193 AGGTTTGTCACGAAGTTGATTCA 58.804 39.130 0.00 0.00 41.61 2.57
3608 4109 4.023980 TCACTGGAAGGATAGTGACGAAT 58.976 43.478 3.18 0.00 45.97 3.34
3669 4170 4.902308 CGCAGGGATGTGTCGTTA 57.098 55.556 0.00 0.00 0.00 3.18
3670 4171 3.362581 CGCAGGGATGTGTCGTTAT 57.637 52.632 0.00 0.00 0.00 1.89
3732 4235 0.742635 TTGTGTCGCTCAGTTGCACA 60.743 50.000 0.00 0.00 38.15 4.57
3734 4237 2.237066 TGTCGCTCAGTTGCACACG 61.237 57.895 0.00 0.00 0.00 4.49
3739 4242 0.041839 GCTCAGTTGCACACGTGAAG 60.042 55.000 25.01 15.23 0.00 3.02
3835 4352 1.541379 ACCGGTCCCTTGTATTTTGC 58.459 50.000 0.00 0.00 0.00 3.68
3889 4619 0.899717 AGTTGGCATCCGCAATGGTT 60.900 50.000 0.00 0.00 41.24 3.67
3918 4648 0.521735 CTTTTGCACGAGTAAGGGCC 59.478 55.000 0.00 0.00 40.47 5.80
3952 4682 1.507141 CGTGCACGAAGCCTCCTTTT 61.507 55.000 34.93 0.00 44.83 2.27
3953 4683 0.668535 GTGCACGAAGCCTCCTTTTT 59.331 50.000 0.00 0.00 44.83 1.94
3954 4684 0.951558 TGCACGAAGCCTCCTTTTTC 59.048 50.000 0.00 0.00 44.83 2.29
4011 4741 1.388065 CGAAGCCTCCTGAGTCGGAT 61.388 60.000 0.00 0.00 31.43 4.18
4014 4744 1.626686 AGCCTCCTGAGTCGGATATG 58.373 55.000 0.00 0.00 31.43 1.78
4015 4745 0.605589 GCCTCCTGAGTCGGATATGG 59.394 60.000 0.00 2.51 31.43 2.74
4103 4866 0.528470 GACTACAGTCCTTCAGCGCT 59.472 55.000 2.64 2.64 39.07 5.92
4140 4903 6.826893 TTTCTTTTCCTCTTTTTGCATTCG 57.173 33.333 0.00 0.00 0.00 3.34
4245 5008 7.931578 ATCATGCATTTGAAAATTGTTGGAT 57.068 28.000 0.00 0.00 30.30 3.41
4315 5078 9.247126 TGTGTGAAAAATAGACATCAAAACATG 57.753 29.630 0.00 0.00 0.00 3.21
4382 5258 4.084223 ACGTGTATACAAAAAGCGTTCCTG 60.084 41.667 7.25 0.00 0.00 3.86
4406 5282 8.464770 TGAAGTATGCAGAAAATGTAAAATGC 57.535 30.769 0.00 0.00 0.00 3.56
4417 5293 7.443879 AGAAAATGTAAAATGCGTTTGGGAAAT 59.556 29.630 4.29 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 21 3.417101 ACATCCAAGTCGCCAAACATAA 58.583 40.909 0.00 0.00 0.00 1.90
32 34 7.604164 ACAATAGTGAACAGAACTACATCCAAG 59.396 37.037 0.00 0.00 33.11 3.61
108 110 7.513371 TTGAACTAACATACCAATCCGTTTT 57.487 32.000 0.00 0.00 0.00 2.43
174 176 7.974243 TGAAATATGCTTTGAATGTCATTCG 57.026 32.000 18.46 7.60 42.15 3.34
217 219 3.428532 AGCCAAATTGAAGAGCATGTCT 58.571 40.909 0.00 0.00 36.94 3.41
313 316 9.136323 ACAACTTTCAATGGAAGAGAATAACTT 57.864 29.630 8.51 0.00 33.82 2.66
368 371 9.896645 ATAAAATATGTGGCATCCTAGTCATAG 57.103 33.333 0.00 0.00 0.00 2.23
495 508 8.518430 AGTTTGCCAAGTTGGATTTTAAATTT 57.482 26.923 26.52 0.00 40.96 1.82
505 518 3.626930 ACTGTTAGTTTGCCAAGTTGGA 58.373 40.909 26.52 7.98 40.96 3.53
568 581 1.690985 GGCCCTGCTCCTACTCCTT 60.691 63.158 0.00 0.00 0.00 3.36
570 583 1.562672 TTTGGCCCTGCTCCTACTCC 61.563 60.000 0.00 0.00 0.00 3.85
701 804 9.331282 GCCAATAAACTCTCTACATACATTCTT 57.669 33.333 0.00 0.00 0.00 2.52
702 805 8.709308 AGCCAATAAACTCTCTACATACATTCT 58.291 33.333 0.00 0.00 0.00 2.40
895 1007 9.916397 CAAACATAAAATCGTATCTGTAAGTCC 57.084 33.333 0.00 0.00 33.76 3.85
898 1017 9.988350 AAGCAAACATAAAATCGTATCTGTAAG 57.012 29.630 0.00 0.00 0.00 2.34
979 1098 1.868498 TGAAACTAACACGGGCTTTCG 59.132 47.619 0.00 0.00 0.00 3.46
981 1100 3.005367 CCATTGAAACTAACACGGGCTTT 59.995 43.478 0.00 0.00 0.00 3.51
1080 1200 7.668469 AGAAATAACAACTACAAACTTAGGGGG 59.332 37.037 0.00 0.00 0.00 5.40
1081 1201 8.631480 AGAAATAACAACTACAAACTTAGGGG 57.369 34.615 0.00 0.00 0.00 4.79
1092 1212 9.750882 GACAACCGAAATAGAAATAACAACTAC 57.249 33.333 0.00 0.00 0.00 2.73
1107 1227 3.511146 AGATGGCAATTGACAACCGAAAT 59.489 39.130 19.96 0.00 36.16 2.17
1111 1231 3.302365 AAAGATGGCAATTGACAACCG 57.698 42.857 19.96 0.00 36.16 4.44
1152 1272 7.148507 CCATGAAAGTCATTACAGAGTGTCTTC 60.149 40.741 0.00 0.00 34.28 2.87
1170 1290 6.669278 CATGCTATCTTGATGTCCATGAAAG 58.331 40.000 0.00 0.00 33.42 2.62
1227 1347 5.240891 GGCTATCACATCTAAGCAATGCTA 58.759 41.667 8.68 0.00 38.25 3.49
1240 1360 1.417517 TCTGGCAATCGGCTATCACAT 59.582 47.619 0.00 0.00 44.01 3.21
1241 1361 0.829990 TCTGGCAATCGGCTATCACA 59.170 50.000 0.00 0.00 44.01 3.58
1267 1387 4.314740 AGCATCACTCTCGTCCTAAATC 57.685 45.455 0.00 0.00 0.00 2.17
1276 1396 2.890311 AGAATCCCTAGCATCACTCTCG 59.110 50.000 0.00 0.00 0.00 4.04
1289 1409 6.154363 TGTTTTGAACTGAACAAAGAATCCCT 59.846 34.615 0.00 0.00 38.25 4.20
1336 1457 0.036875 GACAAAGCTGGCTACCTGGT 59.963 55.000 4.05 4.05 34.79 4.00
1337 1458 1.021390 CGACAAAGCTGGCTACCTGG 61.021 60.000 0.00 0.00 0.00 4.45
1338 1459 0.037326 TCGACAAAGCTGGCTACCTG 60.037 55.000 0.00 0.00 0.00 4.00
1339 1460 0.037232 GTCGACAAAGCTGGCTACCT 60.037 55.000 11.55 0.00 0.00 3.08
1363 1484 1.364269 TGGTCGTTCCATAAGGGGTT 58.636 50.000 0.00 0.00 41.93 4.11
1371 1492 2.879103 ATTCAGGTTGGTCGTTCCAT 57.121 45.000 3.33 0.00 46.60 3.41
1377 1498 5.531122 TCTCCTAATATTCAGGTTGGTCG 57.469 43.478 0.00 0.00 34.56 4.79
1385 1506 7.281100 GGACAACTGGTTTCTCCTAATATTCAG 59.719 40.741 0.00 0.00 37.07 3.02
1387 1508 7.339482 AGGACAACTGGTTTCTCCTAATATTC 58.661 38.462 7.37 0.00 37.07 1.75
1402 1523 2.806244 CAACCGTTCTTAGGACAACTGG 59.194 50.000 0.00 0.00 0.00 4.00
1507 1628 7.071196 AGGGAAAAAGCTAAAAGGACAAAGAAT 59.929 33.333 0.00 0.00 0.00 2.40
1514 1635 5.289595 CACAAGGGAAAAAGCTAAAAGGAC 58.710 41.667 0.00 0.00 0.00 3.85
1549 1670 0.980231 AAACCTGGCAAGCCCAACAA 60.980 50.000 8.89 0.00 44.81 2.83
1577 1698 7.096884 ACGTATAGTACTTCTGCATTCAAGA 57.903 36.000 0.00 0.00 0.00 3.02
1599 1720 5.737290 CCATTTAATGAAAAGCGGAGTAACG 59.263 40.000 6.50 0.00 0.00 3.18
1607 1728 3.434637 CGGTCCCATTTAATGAAAAGCG 58.565 45.455 6.50 8.54 0.00 4.68
1680 1897 8.680903 CAATCTGGCTGTTATTTTGTATTCTCT 58.319 33.333 0.00 0.00 0.00 3.10
1692 1909 5.530171 GTGATGTCATCAATCTGGCTGTTAT 59.470 40.000 17.11 0.00 41.69 1.89
1694 1911 3.693085 GTGATGTCATCAATCTGGCTGTT 59.307 43.478 17.11 0.00 41.69 3.16
1696 1913 3.275999 TGTGATGTCATCAATCTGGCTG 58.724 45.455 17.11 0.00 41.69 4.85
1733 1950 2.237643 TGCCGCCTCTAGGTTCATTTTA 59.762 45.455 0.00 0.00 37.57 1.52
1922 2146 6.207614 GGAATATGAGGAATAAGTTCTTGGCC 59.792 42.308 0.00 0.00 34.68 5.36
1942 2166 4.900684 TGGAATCAGAACACAACGGAATA 58.099 39.130 0.00 0.00 0.00 1.75
1967 2228 4.023707 GCGAGGGACATATTCAAATCAAGG 60.024 45.833 0.00 0.00 0.00 3.61
1989 2250 2.009774 ACACTCCATATTGCACTTCGC 58.990 47.619 0.00 0.00 42.89 4.70
1991 2252 3.609853 TCCACACTCCATATTGCACTTC 58.390 45.455 0.00 0.00 0.00 3.01
2134 2438 4.562767 ACAAGTTTACCAGGGGGAAATTT 58.437 39.130 0.00 0.00 38.05 1.82
2228 2652 3.772025 TCTTTGGGGCTTGAGAAAACAAA 59.228 39.130 0.00 0.00 0.00 2.83
2229 2653 3.370104 TCTTTGGGGCTTGAGAAAACAA 58.630 40.909 0.00 0.00 0.00 2.83
2332 2781 6.480320 GGGAGTACATTGCTAAGTTCAGTATG 59.520 42.308 0.00 0.00 37.54 2.39
2348 2797 1.946984 TTGGAACGGAGGGAGTACAT 58.053 50.000 0.00 0.00 0.00 2.29
2350 2799 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
2351 2800 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
2352 2801 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2353 2802 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2354 2803 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2355 2804 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2356 2805 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
2357 2806 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
2358 2807 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
2359 2808 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
2360 2809 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
2361 2810 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
2362 2811 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
2363 2812 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
2364 2813 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
2365 2814 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
2366 2815 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
2367 2816 9.802039 TTTAGTACAAAGTTGGGTCATCTATTT 57.198 29.630 0.00 0.00 0.00 1.40
2368 2817 9.449719 CTTTAGTACAAAGTTGGGTCATCTATT 57.550 33.333 0.00 0.00 0.00 1.73
2369 2818 8.603304 ACTTTAGTACAAAGTTGGGTCATCTAT 58.397 33.333 14.04 0.00 37.18 1.98
2370 2819 7.970102 ACTTTAGTACAAAGTTGGGTCATCTA 58.030 34.615 14.04 0.00 37.18 1.98
2371 2820 6.838382 ACTTTAGTACAAAGTTGGGTCATCT 58.162 36.000 14.04 0.00 37.18 2.90
2372 2821 7.506328 AACTTTAGTACAAAGTTGGGTCATC 57.494 36.000 23.48 0.00 45.58 2.92
2373 2822 8.215736 ACTAACTTTAGTACAAAGTTGGGTCAT 58.784 33.333 28.62 17.19 46.38 3.06
2374 2823 7.567458 ACTAACTTTAGTACAAAGTTGGGTCA 58.433 34.615 28.62 17.50 46.38 4.02
2375 2824 9.716531 ATACTAACTTTAGTACAAAGTTGGGTC 57.283 33.333 28.62 0.00 46.38 4.46
2402 2851 9.918630 CTGTTCCAAAATAGATGACTCAATTTT 57.081 29.630 0.00 0.00 33.07 1.82
2403 2852 9.300681 TCTGTTCCAAAATAGATGACTCAATTT 57.699 29.630 0.00 0.00 28.72 1.82
2404 2853 8.868522 TCTGTTCCAAAATAGATGACTCAATT 57.131 30.769 0.00 0.00 28.72 2.32
2405 2854 7.555554 CCTCTGTTCCAAAATAGATGACTCAAT 59.444 37.037 0.00 0.00 32.88 2.57
2406 2855 6.881065 CCTCTGTTCCAAAATAGATGACTCAA 59.119 38.462 0.00 0.00 32.88 3.02
2407 2856 6.409704 CCTCTGTTCCAAAATAGATGACTCA 58.590 40.000 0.00 0.00 32.88 3.41
2408 2857 5.819901 CCCTCTGTTCCAAAATAGATGACTC 59.180 44.000 0.00 0.00 32.88 3.36
2409 2858 5.488919 TCCCTCTGTTCCAAAATAGATGACT 59.511 40.000 0.00 0.00 32.88 3.41
2410 2859 5.745227 TCCCTCTGTTCCAAAATAGATGAC 58.255 41.667 0.00 0.00 32.88 3.06
2411 2860 5.488919 ACTCCCTCTGTTCCAAAATAGATGA 59.511 40.000 0.00 0.00 32.88 2.92
2412 2861 5.749462 ACTCCCTCTGTTCCAAAATAGATG 58.251 41.667 0.00 0.00 32.88 2.90
2413 2862 6.674419 AGTACTCCCTCTGTTCCAAAATAGAT 59.326 38.462 0.00 0.00 32.88 1.98
2414 2863 6.023603 AGTACTCCCTCTGTTCCAAAATAGA 58.976 40.000 0.00 0.00 32.42 1.98
2415 2864 6.301169 AGTACTCCCTCTGTTCCAAAATAG 57.699 41.667 0.00 0.00 0.00 1.73
2416 2865 6.958192 ACTAGTACTCCCTCTGTTCCAAAATA 59.042 38.462 0.00 0.00 0.00 1.40
2417 2866 5.785940 ACTAGTACTCCCTCTGTTCCAAAAT 59.214 40.000 0.00 0.00 0.00 1.82
2418 2867 5.152934 ACTAGTACTCCCTCTGTTCCAAAA 58.847 41.667 0.00 0.00 0.00 2.44
2419 2868 4.748701 ACTAGTACTCCCTCTGTTCCAAA 58.251 43.478 0.00 0.00 0.00 3.28
2420 2869 4.399483 ACTAGTACTCCCTCTGTTCCAA 57.601 45.455 0.00 0.00 0.00 3.53
2421 2870 4.399483 AACTAGTACTCCCTCTGTTCCA 57.601 45.455 0.00 0.00 0.00 3.53
2422 2871 4.527427 ACAAACTAGTACTCCCTCTGTTCC 59.473 45.833 0.00 0.00 0.00 3.62
2423 2872 5.725325 ACAAACTAGTACTCCCTCTGTTC 57.275 43.478 0.00 0.00 0.00 3.18
2424 2873 7.234988 ACAATACAAACTAGTACTCCCTCTGTT 59.765 37.037 0.00 0.00 0.00 3.16
2425 2874 6.724905 ACAATACAAACTAGTACTCCCTCTGT 59.275 38.462 0.00 0.78 0.00 3.41
2426 2875 7.036220 CACAATACAAACTAGTACTCCCTCTG 58.964 42.308 0.00 0.00 0.00 3.35
2427 2876 6.154706 CCACAATACAAACTAGTACTCCCTCT 59.845 42.308 0.00 0.00 0.00 3.69
2428 2877 6.070938 ACCACAATACAAACTAGTACTCCCTC 60.071 42.308 0.00 0.00 0.00 4.30
2429 2878 5.783875 ACCACAATACAAACTAGTACTCCCT 59.216 40.000 0.00 0.00 0.00 4.20
2430 2879 6.046290 ACCACAATACAAACTAGTACTCCC 57.954 41.667 0.00 0.00 0.00 4.30
2431 2880 9.662947 ATTTACCACAATACAAACTAGTACTCC 57.337 33.333 0.00 0.00 0.00 3.85
2492 2941 4.213564 ACCACAAAGTTTGGCATTTGAA 57.786 36.364 19.45 0.00 38.42 2.69
2531 2980 1.133025 GCACCATCCAACAGATTTCCG 59.867 52.381 0.00 0.00 30.59 4.30
2620 3069 7.609918 TGAACTGCAATGTAGGTATATTGTGTT 59.390 33.333 2.97 13.81 37.20 3.32
2786 3235 4.897140 ACGTAGTAAACAAGTGGGCATTA 58.103 39.130 0.00 0.00 41.94 1.90
2914 3364 7.031372 GGTACGTACTGAACAAGTATCAATGA 58.969 38.462 24.07 0.00 43.30 2.57
2950 3404 2.939103 CACCTCCTTAGTGCATAACAGC 59.061 50.000 0.00 0.00 0.00 4.40
3015 3469 6.644592 GCAACAACCAATATCTTTTTAGCACA 59.355 34.615 0.00 0.00 0.00 4.57
3110 3564 6.826741 GGCTCCGGAATATTAGGCATTTATTA 59.173 38.462 5.23 0.00 34.84 0.98
3151 3605 1.279271 CTGGGGTTCAAGGGTACTCAG 59.721 57.143 0.00 0.00 0.00 3.35
3293 3755 1.341209 GGTGCTCCAACAGAAAAAGGG 59.659 52.381 0.00 0.00 0.00 3.95
3447 3947 6.479660 ACTTCGTGACAAACCTTATTTTACGA 59.520 34.615 0.00 0.00 36.42 3.43
3479 3979 4.339872 TGAAGCAGCAAATGGAAAACAT 57.660 36.364 0.00 0.00 43.07 2.71
3608 4109 3.541632 GGGCTTTCAGTCGATTAATCCA 58.458 45.455 9.87 0.00 0.00 3.41
3669 4170 7.580910 AGAAACAATGGATTCCTGTCAGATAT 58.419 34.615 0.00 0.00 0.00 1.63
3670 4171 6.962182 AGAAACAATGGATTCCTGTCAGATA 58.038 36.000 0.00 0.00 0.00 1.98
3732 4235 1.151668 GCACATTGCTCTCTTCACGT 58.848 50.000 0.00 0.00 40.96 4.49
3734 4237 3.631145 TTTGCACATTGCTCTCTTCAC 57.369 42.857 0.00 0.00 45.31 3.18
3739 4242 6.144577 GTGTAAATTTTGCACATTGCTCTC 57.855 37.500 20.94 0.00 45.31 3.20
3801 4318 3.192633 GGACCGGTTGATGTATTTGCTTT 59.807 43.478 9.42 0.00 0.00 3.51
3803 4320 2.365582 GGACCGGTTGATGTATTTGCT 58.634 47.619 9.42 0.00 0.00 3.91
3820 4337 1.204704 GCAGGGCAAAATACAAGGGAC 59.795 52.381 0.00 0.00 0.00 4.46
4011 4741 3.194542 GCCCATAAAACAAGCACACCATA 59.805 43.478 0.00 0.00 0.00 2.74
4014 4744 1.668628 CGCCCATAAAACAAGCACACC 60.669 52.381 0.00 0.00 0.00 4.16
4015 4745 1.000717 ACGCCCATAAAACAAGCACAC 60.001 47.619 0.00 0.00 0.00 3.82
4075 4838 3.984200 GACTGTAGTCCACGCCGGC 62.984 68.421 19.07 19.07 39.07 6.13
4112 4875 7.775397 TGCAAAAAGAGGAAAAGAAAATGAG 57.225 32.000 0.00 0.00 0.00 2.90
4382 5258 7.273381 ACGCATTTTACATTTTCTGCATACTTC 59.727 33.333 0.00 0.00 0.00 3.01
4406 5282 2.752354 TGGCATCTACATTTCCCAAACG 59.248 45.455 0.00 0.00 0.00 3.60


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

AutoCloner maintained by Alex Coulton.