Multiple sequence alignment - TraesCS3D01G363000

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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 TraesCS3D01G363000 chr3D 100.000 3154 0 0 1 3154 477410957 477407804 0.000000e+00 5825.0
1 TraesCS3D01G363000 chr3D 91.346 104 8 1 2375 2478 8307738 8307840 1.180000e-29 141.0
2 TraesCS3D01G363000 chr3D 89.189 111 10 2 2369 2478 517801273 517801382 1.530000e-28 137.0
3 TraesCS3D01G363000 chr3D 97.619 42 1 0 561 602 421287274 421287315 4.360000e-09 73.1
4 TraesCS3D01G363000 chr3D 100.000 29 0 0 669 697 513880593 513880621 2.000000e-03 54.7
5 TraesCS3D01G363000 chr3A 89.403 2076 106 47 349 2376 620990336 620988327 0.000000e+00 2510.0
6 TraesCS3D01G363000 chr3A 94.374 551 21 6 2613 3154 689387235 689386686 0.000000e+00 837.0
7 TraesCS3D01G363000 chr3A 87.037 324 38 3 1 323 620990775 620990455 2.310000e-96 363.0
8 TraesCS3D01G363000 chr3A 77.735 521 70 30 2635 3149 725331931 725332411 8.620000e-71 278.0
9 TraesCS3D01G363000 chr3A 85.882 85 10 1 722 804 529844789 529844705 4.330000e-14 89.8
10 TraesCS3D01G363000 chr3A 87.755 49 4 2 2358 2406 725331624 725331670 4.390000e-04 56.5
11 TraesCS3D01G363000 chr3B 93.469 1424 62 12 805 2215 636734684 636733279 0.000000e+00 2085.0
12 TraesCS3D01G363000 chr3B 93.804 581 23 10 2579 3154 17348440 17349012 0.000000e+00 861.0
13 TraesCS3D01G363000 chr3B 82.857 280 30 10 23 295 636735191 636734923 5.260000e-58 235.0
14 TraesCS3D01G363000 chr3B 88.050 159 15 3 342 496 636734921 636734763 5.370000e-43 185.0
15 TraesCS3D01G363000 chr7D 94.015 802 14 5 2380 3154 379567930 379567136 0.000000e+00 1184.0
16 TraesCS3D01G363000 chr7D 94.643 56 2 1 608 663 586489288 586489342 5.600000e-13 86.1
17 TraesCS3D01G363000 chr6A 95.172 580 23 5 2579 3154 521470301 521469723 0.000000e+00 911.0
18 TraesCS3D01G363000 chr6A 81.624 234 18 11 2374 2582 521470577 521470344 1.500000e-38 171.0
19 TraesCS3D01G363000 chr7A 93.000 600 33 8 2563 3154 670181455 670182053 0.000000e+00 867.0
20 TraesCS3D01G363000 chr7A 93.426 578 28 6 2580 3154 36305997 36305427 0.000000e+00 848.0
21 TraesCS3D01G363000 chr7A 80.519 231 19 9 2378 2582 36306271 36306041 1.510000e-33 154.0
22 TraesCS3D01G363000 chr7A 93.204 103 7 0 2480 2582 670181328 670181430 5.450000e-33 152.0
23 TraesCS3D01G363000 chr7A 93.069 101 6 1 2378 2478 681253118 681253019 2.530000e-31 147.0
24 TraesCS3D01G363000 chr4B 83.409 440 60 9 1701 2138 660703714 660704142 2.280000e-106 396.0
25 TraesCS3D01G363000 chr4B 81.609 435 69 7 1714 2147 660495209 660494785 1.800000e-92 350.0
26 TraesCS3D01G363000 chr4B 78.947 418 65 19 1098 1496 660703109 660703522 2.410000e-66 263.0
27 TraesCS3D01G363000 chr4B 85.043 234 35 0 1098 1331 660495898 660495665 4.070000e-59 239.0
28 TraesCS3D01G363000 chrUn 81.925 426 66 7 1714 2138 273156665 273157080 1.800000e-92 350.0
29 TraesCS3D01G363000 chrUn 84.937 239 33 3 1095 1331 110764521 110764758 4.070000e-59 239.0
30 TraesCS3D01G363000 chrUn 85.043 234 35 0 1098 1331 273155976 273156209 4.070000e-59 239.0
31 TraesCS3D01G363000 chr7B 89.565 115 9 2 2367 2480 4495095 4495207 3.280000e-30 143.0
32 TraesCS3D01G363000 chr7B 76.271 295 41 19 2693 2979 624187579 624187852 2.550000e-26 130.0
33 TraesCS3D01G363000 chr7B 94.000 50 2 1 608 656 573930392 573930441 1.210000e-09 75.0
34 TraesCS3D01G363000 chr7B 91.667 48 4 0 608 655 111367245 111367198 2.030000e-07 67.6
35 TraesCS3D01G363000 chr2B 92.157 102 7 1 2377 2478 784729291 784729191 3.280000e-30 143.0
36 TraesCS3D01G363000 chr5D 88.889 108 9 2 2374 2480 53896883 53896778 2.550000e-26 130.0
37 TraesCS3D01G363000 chr5D 93.182 44 3 0 608 651 150829045 150829002 7.300000e-07 65.8
38 TraesCS3D01G363000 chr1B 87.719 114 11 2 2367 2478 526368737 526368849 2.550000e-26 130.0
39 TraesCS3D01G363000 chr4A 83.133 83 13 1 722 804 650052201 650052120 1.210000e-09 75.0
40 TraesCS3D01G363000 chr4A 95.238 42 2 0 561 602 703329500 703329541 2.030000e-07 67.6
41 TraesCS3D01G363000 chr4A 95.238 42 2 0 561 602 703329982 703330023 2.030000e-07 67.6
42 TraesCS3D01G363000 chr2A 92.000 50 4 0 608 657 211486334 211486285 1.570000e-08 71.3
43 TraesCS3D01G363000 chr4D 90.196 51 5 0 561 611 43624320 43624370 2.030000e-07 67.6
44 TraesCS3D01G363000 chr5A 93.182 44 3 0 609 652 692767657 692767700 7.300000e-07 65.8
45 TraesCS3D01G363000 chr5A 91.111 45 4 0 608 652 3365308 3365352 9.450000e-06 62.1
46 TraesCS3D01G363000 chr6D 90.000 50 4 1 608 656 38894982 38894933 2.630000e-06 63.9
47 TraesCS3D01G363000 chr6D 96.970 33 1 0 667 699 422636693 422636661 4.390000e-04 56.5
48 TraesCS3D01G363000 chr6B 90.196 51 2 3 608 656 23449415 23449366 2.630000e-06 63.9
49 TraesCS3D01G363000 chr6B 97.222 36 1 0 566 601 12593081 12593046 9.450000e-06 62.1


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 TraesCS3D01G363000 chr3D 477407804 477410957 3153 True 5825.0 5825 100.000000 1 3154 1 chr3D.!!$R1 3153
1 TraesCS3D01G363000 chr3A 620988327 620990775 2448 True 1436.5 2510 88.220000 1 2376 2 chr3A.!!$R3 2375
2 TraesCS3D01G363000 chr3A 689386686 689387235 549 True 837.0 837 94.374000 2613 3154 1 chr3A.!!$R2 541
3 TraesCS3D01G363000 chr3B 17348440 17349012 572 False 861.0 861 93.804000 2579 3154 1 chr3B.!!$F1 575
4 TraesCS3D01G363000 chr3B 636733279 636735191 1912 True 835.0 2085 88.125333 23 2215 3 chr3B.!!$R1 2192
5 TraesCS3D01G363000 chr7D 379567136 379567930 794 True 1184.0 1184 94.015000 2380 3154 1 chr7D.!!$R1 774
6 TraesCS3D01G363000 chr6A 521469723 521470577 854 True 541.0 911 88.398000 2374 3154 2 chr6A.!!$R1 780
7 TraesCS3D01G363000 chr7A 670181328 670182053 725 False 509.5 867 93.102000 2480 3154 2 chr7A.!!$F1 674
8 TraesCS3D01G363000 chr7A 36305427 36306271 844 True 501.0 848 86.972500 2378 3154 2 chr7A.!!$R2 776
9 TraesCS3D01G363000 chr4B 660703109 660704142 1033 False 329.5 396 81.178000 1098 2138 2 chr4B.!!$F1 1040
10 TraesCS3D01G363000 chr4B 660494785 660495898 1113 True 294.5 350 83.326000 1098 2147 2 chr4B.!!$R1 1049
11 TraesCS3D01G363000 chrUn 273155976 273157080 1104 False 294.5 350 83.484000 1098 2138 2 chrUn.!!$F2 1040

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
786 933 0.037882 AGAGTGTCACGCATCTGGTG 60.038 55.0 9.5 0.0 36.74 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2409 2781 1.581954 CAGTCGACTGAGGCTTCGT 59.418 57.895 36.73 0.0 46.59 3.85 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
38 39 6.576662 TCCATGTCGACTCTAGATTAATCC 57.423 41.667 17.92 0.00 0.00 3.01
51 52 5.573380 AGATTAATCCTGCATCCTAGCAA 57.427 39.130 11.92 0.00 45.13 3.91
65 66 2.243407 CTAGCAACGTCGACTCAAGTC 58.757 52.381 14.70 0.00 41.47 3.01
92 93 1.134907 GCGGAGGAATACGAGTTGGAA 60.135 52.381 0.00 0.00 0.00 3.53
111 113 6.373005 TGGAATCTCAAACATGGTCTAAGA 57.627 37.500 0.00 0.00 0.00 2.10
117 119 5.544176 TCTCAAACATGGTCTAAGAGAACCT 59.456 40.000 0.00 0.00 28.56 3.50
204 206 5.139727 TCCATGTTGGACAAAGAATCAACT 58.860 37.500 0.00 0.00 42.67 3.16
215 217 6.294473 ACAAAGAATCAACTGAGTGTGATCT 58.706 36.000 9.55 7.05 0.00 2.75
216 218 7.445121 ACAAAGAATCAACTGAGTGTGATCTA 58.555 34.615 9.55 0.00 0.00 1.98
236 243 9.475620 TGATCTACAACTTAGAAATAGAGACCA 57.524 33.333 0.00 0.00 0.00 4.02
254 261 4.012374 GACCATCTCCTGAGCATTTTTGA 58.988 43.478 0.00 0.00 0.00 2.69
255 262 4.410099 ACCATCTCCTGAGCATTTTTGAA 58.590 39.130 0.00 0.00 0.00 2.69
256 263 4.834496 ACCATCTCCTGAGCATTTTTGAAA 59.166 37.500 0.00 0.00 0.00 2.69
295 303 5.221904 TGACCAAGACTTGAGGATTTCATGA 60.222 40.000 16.99 0.00 35.27 3.07
302 310 7.344134 AGACTTGAGGATTTCATGATTGATCA 58.656 34.615 0.00 0.00 41.70 2.92
310 318 8.414003 AGGATTTCATGATTGATCAATCTTGTG 58.586 33.333 37.63 31.84 45.51 3.33
313 321 4.951094 TCATGATTGATCAATCTTGTGGCA 59.049 37.500 37.63 26.78 45.51 4.92
319 327 5.114764 TGATCAATCTTGTGGCAGGATTA 57.885 39.130 6.23 0.00 37.94 1.75
323 331 6.455360 TCAATCTTGTGGCAGGATTAAATC 57.545 37.500 6.23 0.00 37.94 2.17
324 332 5.951148 TCAATCTTGTGGCAGGATTAAATCA 59.049 36.000 6.23 0.00 37.94 2.57
325 333 6.436847 TCAATCTTGTGGCAGGATTAAATCAA 59.563 34.615 6.23 0.00 37.94 2.57
326 334 5.902613 TCTTGTGGCAGGATTAAATCAAG 57.097 39.130 0.00 0.00 34.35 3.02
327 335 5.324409 TCTTGTGGCAGGATTAAATCAAGT 58.676 37.500 8.08 0.00 34.57 3.16
329 337 5.643379 TGTGGCAGGATTAAATCAAGTTC 57.357 39.130 0.00 0.00 0.00 3.01
330 338 4.155826 TGTGGCAGGATTAAATCAAGTTCG 59.844 41.667 0.00 0.00 0.00 3.95
331 339 4.394920 GTGGCAGGATTAAATCAAGTTCGA 59.605 41.667 0.00 0.00 0.00 3.71
333 341 5.652014 TGGCAGGATTAAATCAAGTTCGAAT 59.348 36.000 0.00 0.00 0.00 3.34
334 342 6.183360 TGGCAGGATTAAATCAAGTTCGAATC 60.183 38.462 0.00 0.00 0.00 2.52
335 343 6.202226 GCAGGATTAAATCAAGTTCGAATCC 58.798 40.000 0.00 0.00 39.88 3.01
336 344 6.038714 GCAGGATTAAATCAAGTTCGAATCCT 59.961 38.462 0.00 7.92 44.98 3.24
337 345 7.634522 CAGGATTAAATCAAGTTCGAATCCTC 58.365 38.462 10.32 0.00 43.70 3.71
338 346 6.768381 AGGATTAAATCAAGTTCGAATCCTCC 59.232 38.462 0.00 0.00 42.89 4.30
340 348 7.041712 GGATTAAATCAAGTTCGAATCCTCCTC 60.042 40.741 0.00 0.00 38.26 3.71
361 463 5.336150 TCATGTCATGTTTTGTTTGTGGT 57.664 34.783 12.54 0.00 0.00 4.16
379 482 0.442699 GTTTCCACGCCATCGACTTC 59.557 55.000 0.00 0.00 39.41 3.01
433 536 3.016736 CACTTAATCCCGTTTGCTCCAT 58.983 45.455 0.00 0.00 0.00 3.41
616 763 5.302360 TGGCAACTCTAAACGTTTAGTGAT 58.698 37.500 37.48 29.43 40.69 3.06
617 764 5.178623 TGGCAACTCTAAACGTTTAGTGATG 59.821 40.000 37.48 35.27 40.69 3.07
618 765 5.080068 GCAACTCTAAACGTTTAGTGATGC 58.920 41.667 39.03 39.03 45.95 3.91
640 787 4.618227 GCGAGGATGGCAACTTTAATTGTT 60.618 41.667 0.00 0.00 40.68 2.83
643 790 6.747280 CGAGGATGGCAACTTTAATTGTTAAG 59.253 38.462 0.00 0.00 37.61 1.85
703 850 9.663904 TTGAGTCATCTATTTTGAAACGAAAAG 57.336 29.630 0.00 0.00 0.00 2.27
704 851 8.836413 TGAGTCATCTATTTTGAAACGAAAAGT 58.164 29.630 0.00 0.00 0.00 2.66
741 888 1.364626 GCCATCCTTGCGTGACTGAG 61.365 60.000 0.00 0.00 0.00 3.35
750 897 0.654683 GCGTGACTGAGATTGCCATC 59.345 55.000 0.00 0.00 0.00 3.51
757 904 4.083324 TGACTGAGATTGCCATCGAAAAAC 60.083 41.667 0.00 0.00 34.17 2.43
758 905 3.120199 ACTGAGATTGCCATCGAAAAACG 60.120 43.478 0.00 0.00 44.09 3.60
764 911 1.265635 TGCCATCGAAAAACGTCAAGG 59.734 47.619 0.00 0.00 43.13 3.61
766 913 1.535462 CCATCGAAAAACGTCAAGGCT 59.465 47.619 0.00 0.00 43.13 4.58
773 920 3.470645 AAAACGTCAAGGCTAGAGTGT 57.529 42.857 0.00 0.00 0.00 3.55
786 933 0.037882 AGAGTGTCACGCATCTGGTG 60.038 55.000 9.50 0.00 36.74 4.17
804 951 6.009589 TCTGGTGTGACATTTATCATTTGGT 58.990 36.000 0.00 0.00 0.00 3.67
805 952 7.171653 TCTGGTGTGACATTTATCATTTGGTA 58.828 34.615 0.00 0.00 0.00 3.25
808 955 8.085296 TGGTGTGACATTTATCATTTGGTAAAC 58.915 33.333 0.00 0.00 0.00 2.01
823 971 5.733620 TGGTAAACTAATCCTTGACGAGT 57.266 39.130 0.00 0.00 0.00 4.18
859 1007 8.099364 TGAAGACTAGCAATTCCACTAAAAAG 57.901 34.615 0.00 0.00 0.00 2.27
861 1009 8.870075 AAGACTAGCAATTCCACTAAAAAGAT 57.130 30.769 0.00 0.00 0.00 2.40
886 1039 0.242825 TAGTCGAACGTGCTTCAGGG 59.757 55.000 0.00 0.00 0.00 4.45
903 1056 5.255397 TCAGGGGTATGTTCATCAAAACT 57.745 39.130 0.00 0.00 0.00 2.66
904 1057 6.381498 TCAGGGGTATGTTCATCAAAACTA 57.619 37.500 0.00 0.00 0.00 2.24
905 1058 6.414732 TCAGGGGTATGTTCATCAAAACTAG 58.585 40.000 0.00 0.00 0.00 2.57
906 1059 5.590259 CAGGGGTATGTTCATCAAAACTAGG 59.410 44.000 0.00 0.00 0.00 3.02
907 1060 5.491078 AGGGGTATGTTCATCAAAACTAGGA 59.509 40.000 0.00 0.00 0.00 2.94
908 1061 5.823045 GGGGTATGTTCATCAAAACTAGGAG 59.177 44.000 0.00 0.00 0.00 3.69
937 1090 1.331214 AACATGTGGCTTGACCCTTG 58.669 50.000 0.00 0.00 37.83 3.61
1054 1211 1.614824 CAGCTTCCCACCTCCTCCT 60.615 63.158 0.00 0.00 0.00 3.69
1055 1212 1.306568 AGCTTCCCACCTCCTCCTC 60.307 63.158 0.00 0.00 0.00 3.71
1056 1213 2.371259 GCTTCCCACCTCCTCCTCC 61.371 68.421 0.00 0.00 0.00 4.30
1415 1596 2.149578 CTGAGCTTGACTGTTCTTGGG 58.850 52.381 0.00 0.00 0.00 4.12
1447 1628 1.909302 GAGGTTGACTTCCTGATGGGA 59.091 52.381 0.00 0.00 43.41 4.37
1450 1631 2.040412 GGTTGACTTCCTGATGGGACTT 59.960 50.000 0.00 0.00 45.03 3.01
1489 1670 2.022129 CAGCGTCGCCGAGTTCTTT 61.022 57.895 14.86 0.00 35.63 2.52
1512 1705 4.624364 CACACGCCAGCCAGTCCA 62.624 66.667 0.00 0.00 0.00 4.02
1617 1824 3.531538 TGAATTAACGCACTGATCTCCC 58.468 45.455 0.00 0.00 0.00 4.30
1632 1839 1.486310 TCTCCCCAAATCCGAGTGATG 59.514 52.381 0.00 0.00 32.68 3.07
2189 2561 7.412853 AAGTTGGTGGTTTTAGAAGCTTTAA 57.587 32.000 0.00 0.00 34.41 1.52
2190 2562 7.597288 AGTTGGTGGTTTTAGAAGCTTTAAT 57.403 32.000 0.00 0.00 34.41 1.40
2191 2563 8.018537 AGTTGGTGGTTTTAGAAGCTTTAATT 57.981 30.769 0.00 0.00 34.41 1.40
2192 2564 9.138596 AGTTGGTGGTTTTAGAAGCTTTAATTA 57.861 29.630 0.00 0.00 34.41 1.40
2204 2576 5.824904 AGCTTTAATTAGTGCATGACTGG 57.175 39.130 0.00 0.00 35.96 4.00
2208 2580 6.868339 GCTTTAATTAGTGCATGACTGGTTTT 59.132 34.615 0.00 0.00 35.96 2.43
2209 2581 7.148755 GCTTTAATTAGTGCATGACTGGTTTTG 60.149 37.037 0.00 0.00 35.96 2.44
2211 2583 6.892658 AATTAGTGCATGACTGGTTTTGTA 57.107 33.333 0.00 0.00 35.96 2.41
2212 2584 5.940192 TTAGTGCATGACTGGTTTTGTAG 57.060 39.130 0.00 0.00 35.96 2.74
2214 2586 1.885887 TGCATGACTGGTTTTGTAGCC 59.114 47.619 0.00 0.00 0.00 3.93
2215 2587 1.885887 GCATGACTGGTTTTGTAGCCA 59.114 47.619 0.00 0.00 0.00 4.75
2216 2588 2.351738 GCATGACTGGTTTTGTAGCCAC 60.352 50.000 0.00 0.00 0.00 5.01
2217 2589 2.719531 TGACTGGTTTTGTAGCCACA 57.280 45.000 0.00 0.00 0.00 4.17
2218 2590 2.294074 TGACTGGTTTTGTAGCCACAC 58.706 47.619 0.00 0.00 33.30 3.82
2219 2591 2.092646 TGACTGGTTTTGTAGCCACACT 60.093 45.455 0.00 0.00 33.30 3.55
2220 2592 2.949644 GACTGGTTTTGTAGCCACACTT 59.050 45.455 0.00 0.00 33.30 3.16
2221 2593 2.687935 ACTGGTTTTGTAGCCACACTTG 59.312 45.455 0.00 0.00 33.30 3.16
2222 2594 2.948979 CTGGTTTTGTAGCCACACTTGA 59.051 45.455 0.00 0.00 33.30 3.02
2223 2595 3.561143 TGGTTTTGTAGCCACACTTGAT 58.439 40.909 0.00 0.00 33.30 2.57
2224 2596 3.568007 TGGTTTTGTAGCCACACTTGATC 59.432 43.478 0.00 0.00 33.30 2.92
2225 2597 3.821033 GGTTTTGTAGCCACACTTGATCT 59.179 43.478 0.00 0.00 33.30 2.75
2236 2608 5.294552 GCCACACTTGATCTTAGGTACATTC 59.705 44.000 0.00 0.00 0.00 2.67
2268 2640 4.904251 AGGGCATTTCTAGCAGATCTCTTA 59.096 41.667 0.00 0.00 0.00 2.10
2270 2642 6.728164 AGGGCATTTCTAGCAGATCTCTTATA 59.272 38.462 0.00 0.00 0.00 0.98
2271 2643 7.402650 AGGGCATTTCTAGCAGATCTCTTATAT 59.597 37.037 0.00 0.00 0.00 0.86
2272 2644 8.700051 GGGCATTTCTAGCAGATCTCTTATATA 58.300 37.037 0.00 0.00 0.00 0.86
2297 2669 4.376340 AAACTGTCAAAAGTGCTCCTTG 57.624 40.909 0.00 0.00 32.32 3.61
2303 2675 2.951642 TCAAAAGTGCTCCTTGTTCCAG 59.048 45.455 0.00 0.00 32.32 3.86
2310 2682 4.347000 AGTGCTCCTTGTTCCAGTTTACTA 59.653 41.667 0.00 0.00 0.00 1.82
2311 2683 5.013183 AGTGCTCCTTGTTCCAGTTTACTAT 59.987 40.000 0.00 0.00 0.00 2.12
2312 2684 5.705905 GTGCTCCTTGTTCCAGTTTACTATT 59.294 40.000 0.00 0.00 0.00 1.73
2415 2787 1.069159 TCGACTGAGACTTCACGAAGC 60.069 52.381 6.71 0.66 41.99 3.86
2801 3256 2.033372 GAGTAAGTGCTACCCCCTCTC 58.967 57.143 0.00 0.00 0.00 3.20
3083 3554 5.643379 TTTGTGAAATCAGTAGAATGGCC 57.357 39.130 0.00 0.00 0.00 5.36
3128 3599 1.629043 TAGAGTGGCTCGGTCTGTTT 58.371 50.000 0.00 0.00 35.36 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.272490 AGAGTCGACATGGAGCGAAAA 59.728 47.619 19.50 0.00 38.36 2.29
9 10 0.888619 AGAGTCGACATGGAGCGAAA 59.111 50.000 19.50 0.00 38.36 3.46
13 14 5.440234 TTAATCTAGAGTCGACATGGAGC 57.560 43.478 19.50 0.00 0.00 4.70
19 20 4.887655 TGCAGGATTAATCTAGAGTCGACA 59.112 41.667 19.50 0.00 0.00 4.35
38 39 0.179137 TCGACGTTGCTAGGATGCAG 60.179 55.000 0.00 0.00 44.27 4.41
65 66 0.317938 CGTATTCCTCCGCTCCTTCG 60.318 60.000 0.00 0.00 0.00 3.79
92 93 6.214412 AGGTTCTCTTAGACCATGTTTGAGAT 59.786 38.462 0.00 0.00 0.00 2.75
138 140 2.183478 AATCGTGTGTGGCTTGATGA 57.817 45.000 0.00 0.00 0.00 2.92
147 149 6.746104 TGCAAATTTTAGAAATCGTGTGTG 57.254 33.333 0.00 0.00 0.00 3.82
215 217 8.915036 GGAGATGGTCTCTATTTCTAAGTTGTA 58.085 37.037 6.89 0.00 42.95 2.41
216 218 7.621683 AGGAGATGGTCTCTATTTCTAAGTTGT 59.378 37.037 6.89 0.00 42.95 3.32
234 236 5.395682 TTTCAAAAATGCTCAGGAGATGG 57.604 39.130 0.00 0.00 0.00 3.51
262 270 7.461749 TCCTCAAGTCTTGGTCAATTAAGATT 58.538 34.615 12.66 0.00 35.58 2.40
263 271 7.020827 TCCTCAAGTCTTGGTCAATTAAGAT 57.979 36.000 12.66 0.00 35.58 2.40
267 275 7.230747 TGAAATCCTCAAGTCTTGGTCAATTA 58.769 34.615 12.66 0.00 0.00 1.40
271 279 4.705110 TGAAATCCTCAAGTCTTGGTCA 57.295 40.909 12.66 4.79 0.00 4.02
295 303 3.972133 TCCTGCCACAAGATTGATCAAT 58.028 40.909 20.85 20.85 0.00 2.57
302 310 6.438425 ACTTGATTTAATCCTGCCACAAGATT 59.562 34.615 0.00 0.00 37.49 2.40
310 318 5.560966 TTCGAACTTGATTTAATCCTGCC 57.439 39.130 2.22 0.00 0.00 4.85
313 321 6.768381 GGAGGATTCGAACTTGATTTAATCCT 59.232 38.462 12.88 12.88 46.31 3.24
319 327 5.165961 TGAGGAGGATTCGAACTTGATTT 57.834 39.130 0.00 0.00 0.00 2.17
323 331 3.866651 ACATGAGGAGGATTCGAACTTG 58.133 45.455 0.00 0.00 0.00 3.16
324 332 3.515502 TGACATGAGGAGGATTCGAACTT 59.484 43.478 0.00 0.00 0.00 2.66
325 333 3.099905 TGACATGAGGAGGATTCGAACT 58.900 45.455 0.00 0.00 0.00 3.01
326 334 3.526931 TGACATGAGGAGGATTCGAAC 57.473 47.619 0.00 0.00 0.00 3.95
327 335 3.452264 ACATGACATGAGGAGGATTCGAA 59.548 43.478 22.19 0.00 0.00 3.71
329 337 3.465742 ACATGACATGAGGAGGATTCG 57.534 47.619 22.19 0.00 0.00 3.34
330 338 5.416952 ACAAAACATGACATGAGGAGGATTC 59.583 40.000 22.19 0.00 0.00 2.52
331 339 5.327732 ACAAAACATGACATGAGGAGGATT 58.672 37.500 22.19 1.01 0.00 3.01
333 341 4.371624 ACAAAACATGACATGAGGAGGA 57.628 40.909 22.19 0.00 0.00 3.71
334 342 5.221303 ACAAACAAAACATGACATGAGGAGG 60.221 40.000 22.19 9.32 0.00 4.30
335 343 5.688621 CACAAACAAAACATGACATGAGGAG 59.311 40.000 22.19 10.90 0.00 3.69
336 344 5.451659 CCACAAACAAAACATGACATGAGGA 60.452 40.000 22.19 0.00 0.00 3.71
337 345 4.746115 CCACAAACAAAACATGACATGAGG 59.254 41.667 22.19 9.95 0.00 3.86
338 346 5.350633 ACCACAAACAAAACATGACATGAG 58.649 37.500 22.19 10.58 0.00 2.90
340 348 6.419980 AAACCACAAACAAAACATGACATG 57.580 33.333 14.02 14.02 0.00 3.21
361 463 1.011968 CGAAGTCGATGGCGTGGAAA 61.012 55.000 0.00 0.00 43.02 3.13
433 536 9.362151 ACAAACATTAAAATAGGGAGAAACAGA 57.638 29.630 0.00 0.00 0.00 3.41
522 628 0.948678 ACCATTGTGTTGTGCGTACC 59.051 50.000 0.00 0.00 0.00 3.34
526 632 1.851666 GTTGAACCATTGTGTTGTGCG 59.148 47.619 0.00 0.00 0.00 5.34
557 689 3.695060 CACGTCAGGTACTTATCAGGTCT 59.305 47.826 0.00 0.00 34.60 3.85
602 735 4.177165 TCCTCGCATCACTAAACGTTTA 57.823 40.909 19.12 19.12 0.00 2.01
603 736 3.034721 TCCTCGCATCACTAAACGTTT 57.965 42.857 18.90 18.90 0.00 3.60
616 763 2.192664 TTAAAGTTGCCATCCTCGCA 57.807 45.000 0.00 0.00 0.00 5.10
617 764 3.119495 ACAATTAAAGTTGCCATCCTCGC 60.119 43.478 0.00 0.00 32.32 5.03
618 765 4.701956 ACAATTAAAGTTGCCATCCTCG 57.298 40.909 0.00 0.00 32.32 4.63
677 824 9.663904 CTTTTCGTTTCAAAATAGATGACTCAA 57.336 29.630 0.00 0.00 0.00 3.02
678 825 8.836413 ACTTTTCGTTTCAAAATAGATGACTCA 58.164 29.630 0.00 0.00 0.00 3.41
705 852 9.404848 CAAGGATGGCAGAATATATTGACATAT 57.595 33.333 1.78 0.00 42.93 1.78
706 853 7.337689 GCAAGGATGGCAGAATATATTGACATA 59.662 37.037 1.78 0.00 42.93 2.29
707 854 6.152323 GCAAGGATGGCAGAATATATTGACAT 59.848 38.462 5.57 5.57 45.47 3.06
708 855 5.474532 GCAAGGATGGCAGAATATATTGACA 59.525 40.000 1.78 0.00 32.79 3.58
709 856 5.391310 CGCAAGGATGGCAGAATATATTGAC 60.391 44.000 1.78 0.00 30.95 3.18
710 857 4.696877 CGCAAGGATGGCAGAATATATTGA 59.303 41.667 1.78 0.00 30.95 2.57
711 858 4.456911 ACGCAAGGATGGCAGAATATATTG 59.543 41.667 1.78 0.00 46.39 1.90
712 859 4.456911 CACGCAAGGATGGCAGAATATATT 59.543 41.667 0.00 0.00 46.39 1.28
713 860 4.005650 CACGCAAGGATGGCAGAATATAT 58.994 43.478 0.00 0.00 46.39 0.86
714 861 3.070878 TCACGCAAGGATGGCAGAATATA 59.929 43.478 0.00 0.00 46.39 0.86
715 862 2.158769 TCACGCAAGGATGGCAGAATAT 60.159 45.455 0.00 0.00 46.39 1.28
716 863 1.209261 TCACGCAAGGATGGCAGAATA 59.791 47.619 0.00 0.00 46.39 1.75
724 871 2.306341 ATCTCAGTCACGCAAGGATG 57.694 50.000 0.00 0.00 46.39 3.51
741 888 3.196007 TGACGTTTTTCGATGGCAATC 57.804 42.857 0.00 0.00 42.86 2.67
750 897 3.057734 ACTCTAGCCTTGACGTTTTTCG 58.942 45.455 0.00 0.00 46.00 3.46
757 904 1.729472 CGTGACACTCTAGCCTTGACG 60.729 57.143 3.68 0.00 0.00 4.35
758 905 1.983972 CGTGACACTCTAGCCTTGAC 58.016 55.000 3.68 0.00 0.00 3.18
764 911 1.554392 CAGATGCGTGACACTCTAGC 58.446 55.000 3.68 0.01 0.00 3.42
766 913 1.202348 CACCAGATGCGTGACACTCTA 59.798 52.381 3.68 0.00 32.77 2.43
773 920 0.321346 ATGTCACACCAGATGCGTGA 59.679 50.000 7.99 4.46 37.33 4.35
804 951 7.705325 GCAAGATACTCGTCAAGGATTAGTTTA 59.295 37.037 0.00 0.00 0.00 2.01
805 952 6.535508 GCAAGATACTCGTCAAGGATTAGTTT 59.464 38.462 0.00 0.00 0.00 2.66
808 955 5.592054 TGCAAGATACTCGTCAAGGATTAG 58.408 41.667 0.00 0.00 0.00 1.73
819 967 6.292061 GCTAGTCTTCAATTGCAAGATACTCG 60.292 42.308 17.55 11.52 32.50 4.18
823 971 7.870509 ATTGCTAGTCTTCAATTGCAAGATA 57.129 32.000 17.55 12.15 42.38 1.98
859 1007 5.344128 TGAAGCACGTTCGACTAAGTAAATC 59.656 40.000 0.00 0.00 38.09 2.17
861 1009 4.609947 TGAAGCACGTTCGACTAAGTAAA 58.390 39.130 0.00 0.00 38.09 2.01
870 1018 1.180456 TACCCCTGAAGCACGTTCGA 61.180 55.000 0.00 0.00 38.09 3.71
886 1039 8.038944 TGTACTCCTAGTTTTGATGAACATACC 58.961 37.037 0.00 0.00 31.94 2.73
903 1056 5.472148 CCACATGTTTAACGTGTACTCCTA 58.528 41.667 20.64 0.00 45.79 2.94
904 1057 4.312443 CCACATGTTTAACGTGTACTCCT 58.688 43.478 20.64 0.00 45.79 3.69
905 1058 3.120442 GCCACATGTTTAACGTGTACTCC 60.120 47.826 20.64 7.57 45.79 3.85
906 1059 3.744426 AGCCACATGTTTAACGTGTACTC 59.256 43.478 20.64 13.01 45.79 2.59
907 1060 3.735591 AGCCACATGTTTAACGTGTACT 58.264 40.909 20.64 17.54 45.79 2.73
908 1061 4.024725 TCAAGCCACATGTTTAACGTGTAC 60.025 41.667 20.64 15.86 45.79 2.90
937 1090 2.951458 CCGTTGCTTCGAAACCCC 59.049 61.111 0.00 0.00 0.00 4.95
1415 1596 0.960364 TCAACCTCCGCCTGCAAATC 60.960 55.000 0.00 0.00 0.00 2.17
1447 1628 0.391263 GGATCACCCGCTCGAAAAGT 60.391 55.000 0.00 0.00 0.00 2.66
1450 1631 1.079405 GTGGATCACCCGCTCGAAA 60.079 57.895 0.00 0.00 42.19 3.46
1489 1670 1.884075 CTGGCTGGCGTGTGTACCTA 61.884 60.000 0.00 0.00 0.00 3.08
1512 1705 2.769663 TGTGAGGCCATTAATCTACGGT 59.230 45.455 5.01 0.00 0.00 4.83
1617 1824 3.073678 TGTGTTCATCACTCGGATTTGG 58.926 45.455 0.00 0.00 46.27 3.28
1632 1839 6.798959 GCTGTTCATCTGTAATCTTTGTGTTC 59.201 38.462 0.00 0.00 0.00 3.18
1650 1860 6.926826 TCTAACAGTAAAAATCGAGCTGTTCA 59.073 34.615 10.85 0.00 44.10 3.18
1674 1884 5.575957 CAGAACAGCAATCCACATGTTATC 58.424 41.667 0.00 0.00 36.08 1.75
2174 2546 9.840427 TCATGCACTAATTAAAGCTTCTAAAAC 57.160 29.630 0.00 0.00 0.00 2.43
2189 2561 5.106157 GCTACAAAACCAGTCATGCACTAAT 60.106 40.000 0.00 0.00 32.21 1.73
2190 2562 4.215399 GCTACAAAACCAGTCATGCACTAA 59.785 41.667 0.00 0.00 32.21 2.24
2191 2563 3.751175 GCTACAAAACCAGTCATGCACTA 59.249 43.478 0.00 0.00 32.21 2.74
2192 2564 2.554032 GCTACAAAACCAGTCATGCACT 59.446 45.455 0.00 0.00 34.67 4.40
2204 2576 5.438761 AAGATCAAGTGTGGCTACAAAAC 57.561 39.130 3.74 0.00 38.82 2.43
2208 2580 3.838317 ACCTAAGATCAAGTGTGGCTACA 59.162 43.478 0.00 0.00 0.00 2.74
2209 2581 4.473477 ACCTAAGATCAAGTGTGGCTAC 57.527 45.455 0.00 0.00 0.00 3.58
2211 2583 3.838317 TGTACCTAAGATCAAGTGTGGCT 59.162 43.478 0.00 0.00 0.00 4.75
2212 2584 4.202245 TGTACCTAAGATCAAGTGTGGC 57.798 45.455 0.00 0.00 0.00 5.01
2214 2586 5.520288 CCGAATGTACCTAAGATCAAGTGTG 59.480 44.000 0.00 0.00 0.00 3.82
2215 2587 5.661458 CCGAATGTACCTAAGATCAAGTGT 58.339 41.667 0.00 0.00 0.00 3.55
2216 2588 4.508124 GCCGAATGTACCTAAGATCAAGTG 59.492 45.833 0.00 0.00 0.00 3.16
2217 2589 4.161565 TGCCGAATGTACCTAAGATCAAGT 59.838 41.667 0.00 0.00 0.00 3.16
2218 2590 4.693283 TGCCGAATGTACCTAAGATCAAG 58.307 43.478 0.00 0.00 0.00 3.02
2219 2591 4.404394 TCTGCCGAATGTACCTAAGATCAA 59.596 41.667 0.00 0.00 0.00 2.57
2220 2592 3.958147 TCTGCCGAATGTACCTAAGATCA 59.042 43.478 0.00 0.00 0.00 2.92
2221 2593 4.585955 TCTGCCGAATGTACCTAAGATC 57.414 45.455 0.00 0.00 0.00 2.75
2222 2594 6.295349 CCTTATCTGCCGAATGTACCTAAGAT 60.295 42.308 0.00 0.00 0.00 2.40
2223 2595 5.010719 CCTTATCTGCCGAATGTACCTAAGA 59.989 44.000 0.00 0.00 0.00 2.10
2224 2596 5.230942 CCTTATCTGCCGAATGTACCTAAG 58.769 45.833 0.00 0.00 0.00 2.18
2225 2597 4.039973 CCCTTATCTGCCGAATGTACCTAA 59.960 45.833 0.00 0.00 0.00 2.69
2236 2608 1.972872 AGAAATGCCCTTATCTGCCG 58.027 50.000 0.00 0.00 0.00 5.69
2268 2640 7.553044 GGAGCACTTTTGACAGTTTACCTATAT 59.447 37.037 0.00 0.00 0.00 0.86
2270 2642 5.705905 GGAGCACTTTTGACAGTTTACCTAT 59.294 40.000 0.00 0.00 0.00 2.57
2271 2643 5.061179 GGAGCACTTTTGACAGTTTACCTA 58.939 41.667 0.00 0.00 0.00 3.08
2272 2644 3.883489 GGAGCACTTTTGACAGTTTACCT 59.117 43.478 0.00 0.00 0.00 3.08
2371 2743 5.195001 TGATTTTTAGCAGCTCCGTTTTT 57.805 34.783 0.00 0.00 0.00 1.94
2409 2781 1.581954 CAGTCGACTGAGGCTTCGT 59.418 57.895 36.73 0.00 46.59 3.85
2415 2787 2.716017 GCTCCCCAGTCGACTGAGG 61.716 68.421 40.21 36.95 46.59 3.86
2859 3314 6.061022 ACAAGAAAATGGAACCCAAAACTT 57.939 33.333 0.00 0.00 36.95 2.66


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

AutoCloner maintained by Alex Coulton.