Multiple sequence alignment - TraesCS3B01G171800

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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 TraesCS3B01G171800 chr3B 100.000 2588 0 0 1 2588 172767854 172770441 0.000000e+00 4780.0
1 TraesCS3B01G171800 chr3B 88.406 621 68 3 301 918 99735102 99735721 0.000000e+00 745.0
2 TraesCS3B01G171800 chr3B 85.366 82 8 4 2441 2518 99752443 99752524 5.940000e-12 82.4
3 TraesCS3B01G171800 chr1B 87.095 2162 227 25 2 2132 17721723 17719583 0.000000e+00 2399.0
4 TraesCS3B01G171800 chr1B 87.634 186 22 1 2159 2343 44546172 44545987 5.610000e-52 215.0
5 TraesCS3B01G171800 chr1B 81.000 200 35 1 2154 2353 17719361 17719165 3.450000e-34 156.0
6 TraesCS3B01G171800 chr1B 85.057 87 9 4 2 87 44546751 44546668 4.590000e-13 86.1
7 TraesCS3B01G171800 chr5D 87.943 1974 200 25 306 2265 491607739 491609688 0.000000e+00 2292.0
8 TraesCS3B01G171800 chr6A 87.581 1393 157 14 552 1934 589184324 589185710 0.000000e+00 1600.0
9 TraesCS3B01G171800 chr6A 87.604 960 111 6 552 1505 589180254 589179297 0.000000e+00 1107.0
10 TraesCS3B01G171800 chr6A 84.591 318 41 8 1845 2157 589185671 589185985 2.500000e-80 309.0
11 TraesCS3B01G171800 chr6A 91.304 46 1 3 2543 2588 91787356 91787314 2.780000e-05 60.2
12 TraesCS3B01G171800 chr6D 86.452 1395 150 24 552 1934 441402940 441401573 0.000000e+00 1493.0
13 TraesCS3B01G171800 chr6D 86.107 1238 138 21 705 1934 441329506 441328295 0.000000e+00 1303.0
14 TraesCS3B01G171800 chr6D 79.733 1125 188 20 511 1615 85211255 85212359 0.000000e+00 778.0
15 TraesCS3B01G171800 chr6D 80.556 972 164 17 517 1470 84690468 84689504 0.000000e+00 725.0
16 TraesCS3B01G171800 chr6D 83.699 319 35 12 1844 2156 441328334 441328027 4.220000e-73 285.0
17 TraesCS3B01G171800 chr6D 83.019 318 37 13 1844 2156 441401612 441401307 3.280000e-69 272.0
18 TraesCS3B01G171800 chr6D 96.512 86 3 0 551 636 441329591 441329506 2.680000e-30 143.0
19 TraesCS3B01G171800 chr2D 87.879 693 80 3 924 1613 54100594 54101285 0.000000e+00 811.0
20 TraesCS3B01G171800 chr2D 91.534 189 14 2 626 813 20776423 20776610 2.550000e-65 259.0
21 TraesCS3B01G171800 chr2D 77.580 281 34 13 2 258 151439844 151440119 2.680000e-30 143.0
22 TraesCS3B01G171800 chr2D 79.562 137 20 6 1987 2119 635991513 635991645 9.860000e-15 91.6
23 TraesCS3B01G171800 chr4A 85.822 529 63 10 1834 2355 715947402 715946879 3.760000e-153 551.0
24 TraesCS3B01G171800 chr4A 84.201 557 76 9 1806 2355 715556889 715557440 4.900000e-147 531.0
25 TraesCS3B01G171800 chr4A 84.211 57 8 1 2532 2588 152488269 152488214 1.000000e-03 54.7
26 TraesCS3B01G171800 chr7D 88.268 179 21 0 2165 2343 30421091 30421269 5.610000e-52 215.0
27 TraesCS3B01G171800 chr7D 90.769 65 5 1 11 75 30420308 30420371 4.590000e-13 86.1
28 TraesCS3B01G171800 chr7D 89.796 49 4 1 2537 2585 179162535 179162488 7.730000e-06 62.1
29 TraesCS3B01G171800 chr2B 77.818 275 36 12 2 253 210017041 210017313 2.080000e-31 147.0
30 TraesCS3B01G171800 chr2B 81.752 137 18 6 1987 2119 794055642 794055775 9.790000e-20 108.0
31 TraesCS3B01G171800 chr2A 89.130 92 7 3 2 93 149636771 149636683 7.570000e-21 111.0
32 TraesCS3B01G171800 chr2A 81.890 127 16 6 1987 2109 761241495 761241372 1.640000e-17 100.0
33 TraesCS3B01G171800 chr3D 88.095 84 8 2 16 99 41018047 41017966 5.890000e-17 99.0
34 TraesCS3B01G171800 chr3D 93.182 44 2 1 2545 2588 331681686 331681644 2.150000e-06 63.9
35 TraesCS3B01G171800 chr3D 87.037 54 5 2 2536 2588 471995780 471995832 2.780000e-05 60.2
36 TraesCS3B01G171800 chr7A 90.196 51 4 1 2539 2588 335552849 335552899 5.980000e-07 65.8
37 TraesCS3B01G171800 chr6B 97.436 39 0 1 2551 2588 410131791 410131829 5.980000e-07 65.8
38 TraesCS3B01G171800 chr1A 80.488 82 12 3 2511 2588 117758756 117758675 2.780000e-05 60.2
39 TraesCS3B01G171800 chr4B 84.746 59 5 4 2533 2588 431249218 431249275 3.600000e-04 56.5


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 TraesCS3B01G171800 chr3B 172767854 172770441 2587 False 4780.0 4780 100.000000 1 2588 1 chr3B.!!$F3 2587
1 TraesCS3B01G171800 chr3B 99735102 99735721 619 False 745.0 745 88.406000 301 918 1 chr3B.!!$F1 617
2 TraesCS3B01G171800 chr1B 17719165 17721723 2558 True 1277.5 2399 84.047500 2 2353 2 chr1B.!!$R1 2351
3 TraesCS3B01G171800 chr5D 491607739 491609688 1949 False 2292.0 2292 87.943000 306 2265 1 chr5D.!!$F1 1959
4 TraesCS3B01G171800 chr6A 589179297 589180254 957 True 1107.0 1107 87.604000 552 1505 1 chr6A.!!$R2 953
5 TraesCS3B01G171800 chr6A 589184324 589185985 1661 False 954.5 1600 86.086000 552 2157 2 chr6A.!!$F1 1605
6 TraesCS3B01G171800 chr6D 441401307 441402940 1633 True 882.5 1493 84.735500 552 2156 2 chr6D.!!$R3 1604
7 TraesCS3B01G171800 chr6D 85211255 85212359 1104 False 778.0 778 79.733000 511 1615 1 chr6D.!!$F1 1104
8 TraesCS3B01G171800 chr6D 84689504 84690468 964 True 725.0 725 80.556000 517 1470 1 chr6D.!!$R1 953
9 TraesCS3B01G171800 chr6D 441328027 441329591 1564 True 577.0 1303 88.772667 551 2156 3 chr6D.!!$R2 1605
10 TraesCS3B01G171800 chr2D 54100594 54101285 691 False 811.0 811 87.879000 924 1613 1 chr2D.!!$F2 689
11 TraesCS3B01G171800 chr4A 715946879 715947402 523 True 551.0 551 85.822000 1834 2355 1 chr4A.!!$R2 521
12 TraesCS3B01G171800 chr4A 715556889 715557440 551 False 531.0 531 84.201000 1806 2355 1 chr4A.!!$F1 549

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
247 266 0.749454 AGGGGCATGCTTCGTTCATC 60.749 55.0 18.92 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2236 2604 0.099613 CGCTCGAGCAGTGTGTAGAT 59.9 55.0 34.69 0.0 42.21 1.98 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
31 32 1.270094 GGACCACACACATGAACTCGA 60.270 52.381 0.00 0.00 0.00 4.04
120 125 6.158598 GGCACAACATTATGAAATGACAAGT 58.841 36.000 0.00 0.00 44.50 3.16
121 126 6.308766 GGCACAACATTATGAAATGACAAGTC 59.691 38.462 0.00 0.00 44.50 3.01
151 170 5.459762 ACAAAATGAATGCTTCACAAAGTCG 59.540 36.000 1.44 0.00 43.48 4.18
153 172 4.836125 ATGAATGCTTCACAAAGTCGTT 57.164 36.364 1.44 0.00 43.48 3.85
154 173 3.951306 TGAATGCTTCACAAAGTCGTTG 58.049 40.909 0.00 0.00 43.43 4.10
189 208 5.581874 CACAAATTTCTTTGCAAGTGACCTT 59.418 36.000 0.00 0.00 44.63 3.50
214 233 3.347216 CTTGTAACATGCACCTAGCCTT 58.653 45.455 0.00 0.00 44.83 4.35
215 234 3.433306 TGTAACATGCACCTAGCCTTT 57.567 42.857 0.00 0.00 44.83 3.11
216 235 3.761897 TGTAACATGCACCTAGCCTTTT 58.238 40.909 0.00 0.00 44.83 2.27
219 238 2.162681 ACATGCACCTAGCCTTTTGTC 58.837 47.619 0.00 0.00 44.83 3.18
220 239 2.161855 CATGCACCTAGCCTTTTGTCA 58.838 47.619 0.00 0.00 44.83 3.58
247 266 0.749454 AGGGGCATGCTTCGTTCATC 60.749 55.000 18.92 0.00 0.00 2.92
249 268 1.369091 GGGCATGCTTCGTTCATCGT 61.369 55.000 18.92 0.00 40.80 3.73
253 272 2.034507 GCATGCTTCGTTCATCGTCTAC 60.035 50.000 11.37 0.00 40.80 2.59
327 349 7.690952 TGTGTTAAACCACAAACTTCTTAGT 57.309 32.000 0.00 0.00 42.13 2.24
376 401 8.947055 AAGAACTAACAATTGCAAACATTCTT 57.053 26.923 1.71 10.47 0.00 2.52
396 424 7.595130 CATTCTTACTATGAATAGCACGTAGCA 59.405 37.037 11.58 0.40 37.61 3.49
438 466 0.883153 TGCATGCTTCGTTCATTGCT 59.117 45.000 20.33 0.00 0.00 3.91
537 567 8.899771 GCCTAACTATAAATAGAGGCAACAAAA 58.100 33.333 18.24 0.00 44.05 2.44
547 577 4.559153 AGAGGCAACAAAATTGTGCATAC 58.441 39.130 16.66 10.23 41.31 2.39
686 718 9.868277 TTTGATGTGTTCTAACAAAGTTGAATT 57.132 25.926 0.00 0.00 41.21 2.17
733 765 1.999735 CGTCTGCGACATTTGTGGTAT 59.000 47.619 8.91 0.00 41.33 2.73
774 810 7.050377 CACCTTAGATCATGAACAAGTACCAT 58.950 38.462 0.00 0.00 0.00 3.55
830 878 4.852134 TGGGATTGTGAGTCAACATTTG 57.148 40.909 0.00 0.00 38.97 2.32
971 1020 5.412594 ACATCGAGCAACAATATTTCACAGT 59.587 36.000 0.00 0.00 0.00 3.55
972 1021 5.281693 TCGAGCAACAATATTTCACAGTG 57.718 39.130 0.00 0.00 0.00 3.66
973 1022 4.994217 TCGAGCAACAATATTTCACAGTGA 59.006 37.500 0.00 0.00 0.00 3.41
991 1040 3.192422 AGTGAAGACTTCTCACGGATCTG 59.808 47.826 16.02 0.00 39.18 2.90
1014 1063 3.342395 CAGGATGTGTGCGAGAGAG 57.658 57.895 0.00 0.00 0.00 3.20
1031 1080 6.928492 GCGAGAGAGAATGGAGATAGAATTTT 59.072 38.462 0.00 0.00 0.00 1.82
1061 1110 3.134442 GGCATTGGATGGGATTGCTTTTA 59.866 43.478 0.00 0.00 33.86 1.52
1277 1331 3.520290 AGCCGATGTATTTGACGAAGA 57.480 42.857 0.00 0.00 0.00 2.87
1297 1351 3.997021 AGAAGAAAGACCTGTTGCATACG 59.003 43.478 0.00 0.00 0.00 3.06
1304 1358 2.083774 ACCTGTTGCATACGACAATGG 58.916 47.619 0.00 0.00 39.75 3.16
1316 1370 7.500892 TGCATACGACAATGGGTTTAATCTAAT 59.499 33.333 0.00 0.00 0.00 1.73
1341 1405 3.549997 GCAAGTCAACAACATGCGT 57.450 47.368 0.00 0.00 42.12 5.24
1348 1412 5.591643 AGTCAACAACATGCGTACTTTAG 57.408 39.130 0.00 0.00 0.00 1.85
1414 1481 7.896383 ACAACTGCCAACATATATGGTAATT 57.104 32.000 16.96 0.00 40.23 1.40
1544 1643 5.185056 GCCTTGGTCTACAACAATATGGTTT 59.815 40.000 0.00 0.00 34.76 3.27
1585 1685 2.545532 CGGCAAACACACCAATCAACAT 60.546 45.455 0.00 0.00 0.00 2.71
1683 1783 6.573434 ACATGAGATATATGTTGACGTGTGT 58.427 36.000 0.00 0.00 35.32 3.72
1719 1819 7.156876 TGTTATTCCTGAAAACAATAGGCAG 57.843 36.000 0.00 0.00 30.54 4.85
1741 1841 4.511826 AGGAAGTGACGTTGAGATTCAAAC 59.488 41.667 0.00 0.00 38.22 2.93
1765 1865 2.738587 TACACCAGTTGGAAGGCAAA 57.261 45.000 4.92 0.00 38.94 3.68
1776 1876 7.035612 CAGTTGGAAGGCAAATATTAAGTTCC 58.964 38.462 10.03 10.03 33.89 3.62
1795 1895 6.409704 AGTTCCGATGAAGATTCTGATTCAA 58.590 36.000 2.77 0.00 38.80 2.69
1961 2121 7.910162 AGTGTGCGTTACAATGATTCATATTTC 59.090 33.333 0.00 0.00 41.89 2.17
2092 2257 8.582433 ACGAAACGGAAATTAATCAATGTTTT 57.418 26.923 0.00 0.00 0.00 2.43
2114 2279 9.827411 GTTTTGTGATATTTTAGACACTCCTTC 57.173 33.333 0.00 0.00 34.81 3.46
2121 2286 1.919240 TAGACACTCCTTCGAAGGCA 58.081 50.000 34.93 23.19 46.06 4.75
2274 2642 2.764128 GAGGCGGACAGGGGATCA 60.764 66.667 0.00 0.00 0.00 2.92
2278 2646 2.660064 GCGGACAGGGGATCAGTGT 61.660 63.158 0.00 0.00 0.00 3.55
2282 2650 1.280457 GACAGGGGATCAGTGTCCTT 58.720 55.000 9.20 0.00 38.38 3.36
2283 2651 2.467880 GACAGGGGATCAGTGTCCTTA 58.532 52.381 9.20 0.00 38.38 2.69
2284 2652 2.432510 GACAGGGGATCAGTGTCCTTAG 59.567 54.545 9.20 4.88 38.38 2.18
2291 2659 1.561643 TCAGTGTCCTTAGCTGAGGG 58.438 55.000 23.40 7.95 37.41 4.30
2300 2668 0.178873 TTAGCTGAGGGGGAGTTGGT 60.179 55.000 0.00 0.00 0.00 3.67
2305 2673 2.780924 AGGGGGAGTTGGTTGCCA 60.781 61.111 0.00 0.00 0.00 4.92
2355 2723 1.151450 GGCCATCACATTCGGGGAT 59.849 57.895 0.00 0.00 0.00 3.85
2356 2724 1.174712 GGCCATCACATTCGGGGATG 61.175 60.000 0.00 0.00 38.47 3.51
2357 2725 0.179020 GCCATCACATTCGGGGATGA 60.179 55.000 8.08 0.00 40.61 2.92
2358 2726 1.888215 CCATCACATTCGGGGATGAG 58.112 55.000 8.08 0.00 40.61 2.90
2359 2727 1.544093 CCATCACATTCGGGGATGAGG 60.544 57.143 8.08 0.00 40.61 3.86
2360 2728 1.417517 CATCACATTCGGGGATGAGGA 59.582 52.381 0.27 0.00 40.61 3.71
2361 2729 0.830648 TCACATTCGGGGATGAGGAC 59.169 55.000 0.00 0.00 0.00 3.85
2362 2730 0.530650 CACATTCGGGGATGAGGACG 60.531 60.000 0.00 0.00 0.00 4.79
2363 2731 1.069765 CATTCGGGGATGAGGACGG 59.930 63.158 0.00 0.00 0.00 4.79
2364 2732 2.808206 ATTCGGGGATGAGGACGGC 61.808 63.158 0.00 0.00 0.00 5.68
2374 2742 3.459063 AGGACGGCCTCGGCTAAC 61.459 66.667 2.12 0.00 42.19 2.34
2375 2743 4.867599 GGACGGCCTCGGCTAACG 62.868 72.222 0.00 5.76 45.36 3.18
2385 2753 4.068302 GGCTAACGAAGACGACCG 57.932 61.111 0.00 0.00 42.66 4.79
2386 2754 2.157073 GGCTAACGAAGACGACCGC 61.157 63.158 0.00 0.00 42.66 5.68
2387 2755 2.494591 GCTAACGAAGACGACCGCG 61.495 63.158 0.00 0.00 42.66 6.46
2388 2756 1.866496 CTAACGAAGACGACCGCGG 60.866 63.158 26.86 26.86 43.17 6.46
2406 2774 3.546543 CAAGGGGGCCGCGATAGA 61.547 66.667 15.57 0.00 39.76 1.98
2407 2775 3.234730 AAGGGGGCCGCGATAGAG 61.235 66.667 15.57 0.00 39.76 2.43
2415 2783 4.159266 CGCGATAGAGGACAGGGA 57.841 61.111 0.00 0.00 39.76 4.20
2416 2784 2.415825 CGCGATAGAGGACAGGGAA 58.584 57.895 0.00 0.00 39.76 3.97
2417 2785 0.030908 CGCGATAGAGGACAGGGAAC 59.969 60.000 0.00 0.00 39.76 3.62
2434 2802 2.359975 CCCAAGGACGAGGGTTGC 60.360 66.667 0.00 0.00 40.34 4.17
2435 2803 2.359975 CCAAGGACGAGGGTTGCC 60.360 66.667 0.00 0.00 0.00 4.52
2436 2804 2.742372 CAAGGACGAGGGTTGCCG 60.742 66.667 0.00 0.00 0.00 5.69
2437 2805 3.239253 AAGGACGAGGGTTGCCGT 61.239 61.111 0.00 0.00 42.17 5.68
2438 2806 3.530910 AAGGACGAGGGTTGCCGTG 62.531 63.158 0.00 0.00 39.30 4.94
2470 2838 3.519930 GCGACGGAGGAGGAGGAC 61.520 72.222 0.00 0.00 0.00 3.85
2471 2839 2.829458 CGACGGAGGAGGAGGACC 60.829 72.222 0.00 0.00 0.00 4.46
2472 2840 2.442458 GACGGAGGAGGAGGACCC 60.442 72.222 0.00 0.00 36.73 4.46
2473 2841 4.077180 ACGGAGGAGGAGGACCCC 62.077 72.222 0.00 0.00 36.73 4.95
2475 2843 4.862823 GGAGGAGGAGGACCCCGG 62.863 77.778 0.00 0.00 36.73 5.73
2476 2844 4.077180 GAGGAGGAGGACCCCGGT 62.077 72.222 0.00 0.00 36.73 5.28
2477 2845 4.400251 AGGAGGAGGACCCCGGTG 62.400 72.222 0.00 0.00 36.73 4.94
2479 2847 4.393778 GAGGAGGACCCCGGTGGA 62.394 72.222 15.08 0.00 38.00 4.02
2480 2848 4.716977 AGGAGGACCCCGGTGGAC 62.717 72.222 15.08 9.07 38.00 4.02
2498 2866 4.767255 GAGGGCTGCCACGGTGAG 62.767 72.222 22.05 0.72 0.00 3.51
2521 2889 4.135153 CACGACGGAGGAGGGCAG 62.135 72.222 0.00 0.00 0.00 4.85
2536 2904 3.197790 CAGGCGCGGTGAAGGATG 61.198 66.667 8.83 0.00 0.00 3.51
2537 2905 4.473520 AGGCGCGGTGAAGGATGG 62.474 66.667 8.83 0.00 0.00 3.51
2539 2907 4.467084 GCGCGGTGAAGGATGGGA 62.467 66.667 8.83 0.00 0.00 4.37
2540 2908 2.202932 CGCGGTGAAGGATGGGAG 60.203 66.667 0.00 0.00 0.00 4.30
2541 2909 2.514824 GCGGTGAAGGATGGGAGC 60.515 66.667 0.00 0.00 0.00 4.70
2542 2910 2.202932 CGGTGAAGGATGGGAGCG 60.203 66.667 0.00 0.00 0.00 5.03
2543 2911 2.190578 GGTGAAGGATGGGAGCGG 59.809 66.667 0.00 0.00 0.00 5.52
2544 2912 2.514824 GTGAAGGATGGGAGCGGC 60.515 66.667 0.00 0.00 0.00 6.53
2545 2913 3.008517 TGAAGGATGGGAGCGGCA 61.009 61.111 1.45 0.00 0.00 5.69
2546 2914 2.272146 GAAGGATGGGAGCGGCAA 59.728 61.111 1.45 0.00 0.00 4.52
2547 2915 2.044946 AAGGATGGGAGCGGCAAC 60.045 61.111 1.45 0.00 0.00 4.17
2565 2933 3.838271 GAGGGGAGCGCGTGATGA 61.838 66.667 8.43 0.00 0.00 2.92
2566 2934 4.148825 AGGGGAGCGCGTGATGAC 62.149 66.667 8.43 0.00 0.00 3.06
2569 2937 4.451150 GGAGCGCGTGATGACCCA 62.451 66.667 8.43 0.00 0.00 4.51
2570 2938 3.188786 GAGCGCGTGATGACCCAC 61.189 66.667 8.43 0.00 0.00 4.61
2571 2939 3.932580 GAGCGCGTGATGACCCACA 62.933 63.158 8.43 0.00 36.89 4.17
2572 2940 3.047280 GCGCGTGATGACCCACAA 61.047 61.111 8.43 0.00 36.89 3.33
2573 2941 3.027170 GCGCGTGATGACCCACAAG 62.027 63.158 8.43 0.00 36.89 3.16
2574 2942 1.667830 CGCGTGATGACCCACAAGT 60.668 57.895 0.00 0.00 36.89 3.16
2575 2943 0.389296 CGCGTGATGACCCACAAGTA 60.389 55.000 0.00 0.00 36.89 2.24
2576 2944 1.739035 CGCGTGATGACCCACAAGTAT 60.739 52.381 0.00 0.00 36.89 2.12
2577 2945 2.480587 CGCGTGATGACCCACAAGTATA 60.481 50.000 0.00 0.00 36.89 1.47
2578 2946 3.123804 GCGTGATGACCCACAAGTATAG 58.876 50.000 0.00 0.00 36.89 1.31
2579 2947 3.717707 CGTGATGACCCACAAGTATAGG 58.282 50.000 0.00 0.00 36.89 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.827507 GTGTGGTCCACTTGCCCATT 60.828 55.000 22.56 0.00 41.11 3.16
10 11 1.540146 CGAGTTCATGTGTGTGGTCCA 60.540 52.381 0.00 0.00 0.00 4.02
24 25 0.321387 GTTGGGGAAGGGTCGAGTTC 60.321 60.000 0.00 0.00 0.00 3.01
51 52 3.680642 TCTTTTTATCATGCTCAGCGC 57.319 42.857 0.00 0.00 39.77 5.92
144 163 5.462068 TGTGTAGATCTTCACAACGACTTTG 59.538 40.000 27.07 0.00 40.81 2.77
153 172 7.862372 GCAAAGAAATTTGTGTAGATCTTCACA 59.138 33.333 25.93 25.93 41.81 3.58
154 173 7.862372 TGCAAAGAAATTTGTGTAGATCTTCAC 59.138 33.333 21.82 21.82 34.56 3.18
189 208 4.258543 GCTAGGTGCATGTTACAAGGTTA 58.741 43.478 0.00 0.00 42.31 2.85
214 233 1.228793 CCCCTGGTGTGGTGACAAA 59.771 57.895 0.00 0.00 46.06 2.83
215 234 2.923035 CCCCTGGTGTGGTGACAA 59.077 61.111 0.00 0.00 46.06 3.18
216 235 3.884774 GCCCCTGGTGTGGTGACA 61.885 66.667 0.00 0.00 38.70 3.58
219 238 2.677524 CATGCCCCTGGTGTGGTG 60.678 66.667 0.00 0.00 0.00 4.17
220 239 4.684134 GCATGCCCCTGGTGTGGT 62.684 66.667 6.36 0.00 0.00 4.16
304 326 6.471198 GCACTAAGAAGTTTGTGGTTTAACAC 59.529 38.462 0.00 0.00 39.12 3.32
352 377 9.463443 GTAAGAATGTTTGCAATTGTTAGTTCT 57.537 29.630 7.40 7.11 0.00 3.01
362 387 9.956720 GCTATTCATAGTAAGAATGTTTGCAAT 57.043 29.630 10.22 0.00 36.45 3.56
376 401 7.174426 ACAGTATGCTACGTGCTATTCATAGTA 59.826 37.037 0.00 0.00 42.53 1.82
382 410 3.664486 CGACAGTATGCTACGTGCTATTC 59.336 47.826 0.00 0.00 42.53 1.75
396 424 1.596934 CCTGGTGTGGCGACAGTAT 59.403 57.895 0.12 0.00 44.46 2.12
469 497 7.339721 TGGTTCTAACAAAAATAGGTTGTGTGA 59.660 33.333 0.00 0.00 39.14 3.58
537 567 5.939764 TCTTACCTCTCAGTATGCACAAT 57.060 39.130 0.00 0.00 34.76 2.71
538 568 5.939764 ATCTTACCTCTCAGTATGCACAA 57.060 39.130 0.00 0.00 34.76 3.33
541 571 5.939764 ACAATCTTACCTCTCAGTATGCA 57.060 39.130 0.00 0.00 34.76 3.96
547 577 6.867550 TGTGTGATACAATCTTACCTCTCAG 58.132 40.000 0.00 0.00 36.06 3.35
686 718 7.775053 AGCCATTTGAACCTGAAATAGTTAA 57.225 32.000 0.00 0.00 0.00 2.01
797 835 5.760253 ACTCACAATCCCATAACGATGATTC 59.240 40.000 0.00 0.00 34.73 2.52
830 878 9.554724 CAGTTACATATCACATTACAAACCAAC 57.445 33.333 0.00 0.00 0.00 3.77
928 977 7.959175 TCGATGTAGTACCTAAATGGCTAAAT 58.041 34.615 0.00 0.00 40.22 1.40
931 980 5.048224 GCTCGATGTAGTACCTAAATGGCTA 60.048 44.000 0.00 0.00 40.22 3.93
935 984 6.040247 TGTTGCTCGATGTAGTACCTAAATG 58.960 40.000 0.00 0.00 0.00 2.32
971 1020 2.493675 CCAGATCCGTGAGAAGTCTTCA 59.506 50.000 14.97 0.00 0.00 3.02
972 1021 2.737039 GCCAGATCCGTGAGAAGTCTTC 60.737 54.545 4.26 4.26 0.00 2.87
973 1022 1.205893 GCCAGATCCGTGAGAAGTCTT 59.794 52.381 0.00 0.00 0.00 3.01
991 1040 0.807667 CTCGCACACATCCTGTAGCC 60.808 60.000 0.00 0.00 0.00 3.93
1031 1080 3.608067 TCCCATCCAATGCCCTCTATAA 58.392 45.455 0.00 0.00 0.00 0.98
1061 1110 9.661563 CTCCTCTTCTTATATCATAGTCGTAGT 57.338 37.037 0.00 0.00 0.00 2.73
1260 1314 7.167481 GTCTTTCTTCTTCGTCAAATACATCG 58.833 38.462 0.00 0.00 0.00 3.84
1263 1317 6.423905 CAGGTCTTTCTTCTTCGTCAAATACA 59.576 38.462 0.00 0.00 0.00 2.29
1277 1331 3.746492 GTCGTATGCAACAGGTCTTTCTT 59.254 43.478 0.00 0.00 0.00 2.52
1304 1358 8.736244 TGACTTGCCTTTGTATTAGATTAAACC 58.264 33.333 0.00 0.00 0.00 3.27
1316 1370 4.930963 CATGTTGTTGACTTGCCTTTGTA 58.069 39.130 0.00 0.00 0.00 2.41
1348 1412 6.294286 GCAGGATAGTCCTCATAAGTCTGTAC 60.294 46.154 0.00 0.00 45.66 2.90
1356 1420 2.297315 CTGCGCAGGATAGTCCTCATAA 59.703 50.000 29.88 0.00 45.66 1.90
1444 1511 4.611310 AATGTGAAGTGATGAGATTGCG 57.389 40.909 0.00 0.00 0.00 4.85
1487 1564 9.507329 CTATTGGTCTATGTATTACCTGCATTT 57.493 33.333 0.00 0.00 34.23 2.32
1544 1643 4.258543 CCGGCTCATTTCCAGTAAAAGTA 58.741 43.478 0.00 0.00 0.00 2.24
1555 1655 0.313672 TGTGTTTGCCGGCTCATTTC 59.686 50.000 29.70 13.85 0.00 2.17
1615 1715 5.492895 TGCAGGACCGTTAATTTTGAGATA 58.507 37.500 0.00 0.00 0.00 1.98
1616 1716 4.331968 TGCAGGACCGTTAATTTTGAGAT 58.668 39.130 0.00 0.00 0.00 2.75
1677 1777 8.589629 GGAATAACAAGTATTACTACACACACG 58.410 37.037 0.00 0.00 32.26 4.49
1719 1819 4.319549 GGTTTGAATCTCAACGTCACTTCC 60.320 45.833 0.00 0.00 35.89 3.46
1741 1841 3.279434 GCCTTCCAACTGGTGTAATAGG 58.721 50.000 0.00 0.00 36.34 2.57
1776 1876 8.610035 TCATCTTTTGAATCAGAATCTTCATCG 58.390 33.333 0.00 0.00 31.83 3.84
1795 1895 6.380079 ACAATGGTCCTAGTCTTCATCTTT 57.620 37.500 0.00 0.00 0.00 2.52
2051 2216 5.050227 CCGTTTCGTAACATTTTGGACACTA 60.050 40.000 5.74 0.00 33.75 2.74
2092 2257 7.165460 TCGAAGGAGTGTCTAAAATATCACA 57.835 36.000 0.00 0.00 33.84 3.58
2114 2279 6.732154 AGATGAATTGATTAACATGCCTTCG 58.268 36.000 0.00 0.00 0.00 3.79
2234 2602 2.223272 CGCTCGAGCAGTGTGTAGATAA 60.223 50.000 34.69 0.00 42.21 1.75
2235 2603 1.330829 CGCTCGAGCAGTGTGTAGATA 59.669 52.381 34.69 0.00 42.21 1.98
2236 2604 0.099613 CGCTCGAGCAGTGTGTAGAT 59.900 55.000 34.69 0.00 42.21 1.98
2267 2635 1.139853 CAGCTAAGGACACTGATCCCC 59.860 57.143 0.00 0.00 39.91 4.81
2274 2642 0.618968 CCCCCTCAGCTAAGGACACT 60.619 60.000 3.71 0.00 38.87 3.55
2278 2646 0.417841 AACTCCCCCTCAGCTAAGGA 59.582 55.000 3.71 0.00 38.87 3.36
2282 2650 0.178873 AACCAACTCCCCCTCAGCTA 60.179 55.000 0.00 0.00 0.00 3.32
2283 2651 1.464198 AACCAACTCCCCCTCAGCT 60.464 57.895 0.00 0.00 0.00 4.24
2284 2652 1.303643 CAACCAACTCCCCCTCAGC 60.304 63.158 0.00 0.00 0.00 4.26
2291 2659 3.365265 CGCTGGCAACCAACTCCC 61.365 66.667 0.00 0.00 30.80 4.30
2346 2714 2.808206 GCCGTCCTCATCCCCGAAT 61.808 63.158 0.00 0.00 0.00 3.34
2358 2726 4.867599 CGTTAGCCGAGGCCGTCC 62.868 72.222 10.95 0.00 43.17 4.79
2359 2727 3.818787 TCGTTAGCCGAGGCCGTC 61.819 66.667 10.95 0.53 41.60 4.79
2366 2734 1.503542 GGTCGTCTTCGTTAGCCGA 59.496 57.895 0.00 0.00 45.66 5.54
2367 2735 1.866496 CGGTCGTCTTCGTTAGCCG 60.866 63.158 0.00 0.00 38.33 5.52
2368 2736 2.157073 GCGGTCGTCTTCGTTAGCC 61.157 63.158 0.00 0.00 38.33 3.93
2369 2737 2.494591 CGCGGTCGTCTTCGTTAGC 61.495 63.158 0.00 0.00 38.33 3.09
2370 2738 1.866496 CCGCGGTCGTCTTCGTTAG 60.866 63.158 19.50 0.00 38.33 2.34
2371 2739 2.176546 CCGCGGTCGTCTTCGTTA 59.823 61.111 19.50 0.00 38.33 3.18
2375 2743 3.479269 CTTGCCGCGGTCGTCTTC 61.479 66.667 28.70 8.52 0.00 2.87
2389 2757 3.521529 CTCTATCGCGGCCCCCTTG 62.522 68.421 6.13 0.00 0.00 3.61
2390 2758 3.234730 CTCTATCGCGGCCCCCTT 61.235 66.667 6.13 0.00 0.00 3.95
2393 2761 3.992317 GTCCTCTATCGCGGCCCC 61.992 72.222 6.13 0.00 0.00 5.80
2394 2762 3.214250 CTGTCCTCTATCGCGGCCC 62.214 68.421 6.13 0.00 0.00 5.80
2395 2763 2.336809 CTGTCCTCTATCGCGGCC 59.663 66.667 6.13 0.00 0.00 6.13
2396 2764 2.336809 CCTGTCCTCTATCGCGGC 59.663 66.667 6.13 0.00 0.00 6.53
2397 2765 1.107538 TTCCCTGTCCTCTATCGCGG 61.108 60.000 6.13 0.00 0.00 6.46
2398 2766 0.030908 GTTCCCTGTCCTCTATCGCG 59.969 60.000 0.00 0.00 0.00 5.87
2399 2767 0.389757 GGTTCCCTGTCCTCTATCGC 59.610 60.000 0.00 0.00 0.00 4.58
2400 2768 1.041437 GGGTTCCCTGTCCTCTATCG 58.959 60.000 0.00 0.00 0.00 2.92
2401 2769 2.176247 TGGGTTCCCTGTCCTCTATC 57.824 55.000 9.43 0.00 0.00 2.08
2402 2770 2.482494 CTTGGGTTCCCTGTCCTCTAT 58.518 52.381 9.43 0.00 0.00 1.98
2403 2771 1.554822 CCTTGGGTTCCCTGTCCTCTA 60.555 57.143 9.43 0.00 0.00 2.43
2404 2772 0.842467 CCTTGGGTTCCCTGTCCTCT 60.842 60.000 9.43 0.00 0.00 3.69
2405 2773 0.840722 TCCTTGGGTTCCCTGTCCTC 60.841 60.000 9.43 0.00 0.00 3.71
2406 2774 1.134438 GTCCTTGGGTTCCCTGTCCT 61.134 60.000 9.43 0.00 0.00 3.85
2407 2775 1.379146 GTCCTTGGGTTCCCTGTCC 59.621 63.158 9.43 0.00 0.00 4.02
2408 2776 1.003718 CGTCCTTGGGTTCCCTGTC 60.004 63.158 9.43 0.00 0.00 3.51
2409 2777 1.460689 TCGTCCTTGGGTTCCCTGT 60.461 57.895 9.43 0.00 0.00 4.00
2410 2778 1.296715 CTCGTCCTTGGGTTCCCTG 59.703 63.158 9.43 2.48 0.00 4.45
2411 2779 1.918800 CCTCGTCCTTGGGTTCCCT 60.919 63.158 9.43 0.00 0.00 4.20
2412 2780 2.669240 CCTCGTCCTTGGGTTCCC 59.331 66.667 0.12 0.12 0.00 3.97
2413 2781 2.669240 CCCTCGTCCTTGGGTTCC 59.331 66.667 0.00 0.00 38.65 3.62
2418 2786 2.359975 GGCAACCCTCGTCCTTGG 60.360 66.667 0.00 0.00 0.00 3.61
2419 2787 2.742372 CGGCAACCCTCGTCCTTG 60.742 66.667 0.00 0.00 0.00 3.61
2420 2788 3.239253 ACGGCAACCCTCGTCCTT 61.239 61.111 0.00 0.00 34.20 3.36
2421 2789 4.003788 CACGGCAACCCTCGTCCT 62.004 66.667 0.00 0.00 37.53 3.85
2453 2821 3.519930 GTCCTCCTCCTCCGTCGC 61.520 72.222 0.00 0.00 0.00 5.19
2454 2822 2.829458 GGTCCTCCTCCTCCGTCG 60.829 72.222 0.00 0.00 0.00 5.12
2455 2823 2.442458 GGGTCCTCCTCCTCCGTC 60.442 72.222 0.00 0.00 0.00 4.79
2456 2824 4.077180 GGGGTCCTCCTCCTCCGT 62.077 72.222 0.00 0.00 35.33 4.69
2458 2826 4.862823 CCGGGGTCCTCCTCCTCC 62.863 77.778 0.00 0.00 35.33 4.30
2459 2827 4.077180 ACCGGGGTCCTCCTCCTC 62.077 72.222 6.32 0.00 35.33 3.71
2460 2828 4.400251 CACCGGGGTCCTCCTCCT 62.400 72.222 6.32 0.00 35.33 3.69
2462 2830 4.393778 TCCACCGGGGTCCTCCTC 62.394 72.222 6.32 0.00 38.11 3.71
2463 2831 4.716977 GTCCACCGGGGTCCTCCT 62.717 72.222 6.32 0.00 38.11 3.69
2481 2849 4.767255 CTCACCGTGGCAGCCCTC 62.767 72.222 9.64 0.84 0.00 4.30
2504 2872 4.135153 CTGCCCTCCTCCGTCGTG 62.135 72.222 0.00 0.00 0.00 4.35
2519 2887 3.197790 CATCCTTCACCGCGCCTG 61.198 66.667 0.00 0.00 0.00 4.85
2520 2888 4.473520 CCATCCTTCACCGCGCCT 62.474 66.667 0.00 0.00 0.00 5.52
2522 2890 4.467084 TCCCATCCTTCACCGCGC 62.467 66.667 0.00 0.00 0.00 6.86
2523 2891 2.202932 CTCCCATCCTTCACCGCG 60.203 66.667 0.00 0.00 0.00 6.46
2524 2892 2.514824 GCTCCCATCCTTCACCGC 60.515 66.667 0.00 0.00 0.00 5.68
2525 2893 2.202932 CGCTCCCATCCTTCACCG 60.203 66.667 0.00 0.00 0.00 4.94
2526 2894 2.190578 CCGCTCCCATCCTTCACC 59.809 66.667 0.00 0.00 0.00 4.02
2527 2895 2.514824 GCCGCTCCCATCCTTCAC 60.515 66.667 0.00 0.00 0.00 3.18
2528 2896 2.601702 TTGCCGCTCCCATCCTTCA 61.602 57.895 0.00 0.00 0.00 3.02
2529 2897 2.115291 GTTGCCGCTCCCATCCTTC 61.115 63.158 0.00 0.00 0.00 3.46
2530 2898 2.044946 GTTGCCGCTCCCATCCTT 60.045 61.111 0.00 0.00 0.00 3.36
2531 2899 4.473520 CGTTGCCGCTCCCATCCT 62.474 66.667 0.00 0.00 0.00 3.24
2532 2900 4.467084 TCGTTGCCGCTCCCATCC 62.467 66.667 0.00 0.00 0.00 3.51
2533 2901 2.892425 CTCGTTGCCGCTCCCATC 60.892 66.667 0.00 0.00 0.00 3.51
2534 2902 4.473520 CCTCGTTGCCGCTCCCAT 62.474 66.667 0.00 0.00 0.00 4.00
2538 2906 4.821589 CTCCCCTCGTTGCCGCTC 62.822 72.222 0.00 0.00 0.00 5.03
2548 2916 3.838271 TCATCACGCGCTCCCCTC 61.838 66.667 5.73 0.00 0.00 4.30
2549 2917 4.148825 GTCATCACGCGCTCCCCT 62.149 66.667 5.73 0.00 0.00 4.79
2552 2920 4.451150 TGGGTCATCACGCGCTCC 62.451 66.667 5.73 0.00 38.32 4.70
2553 2921 3.188786 GTGGGTCATCACGCGCTC 61.189 66.667 5.73 0.00 41.58 5.03
2554 2922 3.529341 TTGTGGGTCATCACGCGCT 62.529 57.895 5.73 0.00 44.35 5.92
2555 2923 3.027170 CTTGTGGGTCATCACGCGC 62.027 63.158 5.73 0.00 44.31 6.86
2556 2924 0.389296 TACTTGTGGGTCATCACGCG 60.389 55.000 3.53 3.53 40.31 6.01
2557 2925 2.024176 ATACTTGTGGGTCATCACGC 57.976 50.000 0.00 0.00 40.31 5.34
2558 2926 3.492656 CCCTATACTTGTGGGTCATCACG 60.493 52.174 0.00 0.00 40.31 4.35
2559 2927 3.181454 CCCCTATACTTGTGGGTCATCAC 60.181 52.174 0.00 0.00 39.31 3.06
2560 2928 3.045634 CCCCTATACTTGTGGGTCATCA 58.954 50.000 0.00 0.00 39.31 3.07
2561 2929 3.314693 TCCCCTATACTTGTGGGTCATC 58.685 50.000 0.00 0.00 39.31 2.92
2562 2930 3.431411 TCCCCTATACTTGTGGGTCAT 57.569 47.619 0.00 0.00 39.31 3.06
2563 2931 2.953093 TCCCCTATACTTGTGGGTCA 57.047 50.000 0.00 0.00 39.31 4.02
2564 2932 3.314693 TGATCCCCTATACTTGTGGGTC 58.685 50.000 0.00 0.00 39.31 4.46
2565 2933 3.431411 TGATCCCCTATACTTGTGGGT 57.569 47.619 0.00 0.00 39.31 4.51


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

AutoCloner maintained by Alex Coulton.