Multiple sequence alignment - TraesCS2B01G387500

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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 TraesCS2B01G387500 chr2B 100.000 3990 0 0 1 3990 550721730 550717741 0.000000e+00 7369
1 TraesCS2B01G387500 chr2B 79.209 1467 120 75 672 2016 550859510 550858107 0.000000e+00 848
2 TraesCS2B01G387500 chr2B 84.346 856 90 20 2155 3000 550857634 550856813 0.000000e+00 798
3 TraesCS2B01G387500 chr2B 87.740 677 70 3 2324 3000 550996536 550995873 0.000000e+00 778
4 TraesCS2B01G387500 chr2B 81.056 966 94 44 713 1618 550998213 550997277 0.000000e+00 688
5 TraesCS2B01G387500 chr2B 82.746 794 71 20 403 1158 550513170 550512405 0.000000e+00 647
6 TraesCS2B01G387500 chr2B 88.248 451 31 6 1162 1593 550512372 550511925 1.640000e-143 520
7 TraesCS2B01G387500 chr2B 85.950 484 40 15 1867 2331 550997047 550996573 3.580000e-135 492
8 TraesCS2B01G387500 chr2B 82.382 403 56 13 253 647 550861470 550861075 1.780000e-88 337
9 TraesCS2B01G387500 chr2B 85.659 258 31 5 1868 2121 550511629 550511374 2.360000e-67 267
10 TraesCS2B01G387500 chr2B 90.291 103 5 4 2232 2331 550511160 550511060 3.240000e-26 130
11 TraesCS2B01G387500 chr2D 88.574 1339 97 19 434 1741 471451909 471450596 0.000000e+00 1574
12 TraesCS2B01G387500 chr2D 83.276 1154 123 27 42 1160 471374587 471373469 0.000000e+00 998
13 TraesCS2B01G387500 chr2D 93.103 667 40 1 2353 3019 471448849 471448189 0.000000e+00 972
14 TraesCS2B01G387500 chr2D 86.657 682 72 9 2325 3000 471896206 471895538 0.000000e+00 737
15 TraesCS2B01G387500 chr2D 85.331 634 65 13 2364 2993 471372093 471371484 7.280000e-177 630
16 TraesCS2B01G387500 chr2D 89.462 465 37 9 1162 1619 471373438 471372979 9.620000e-161 577
17 TraesCS2B01G387500 chr2D 92.697 356 12 6 1859 2205 471450574 471450224 5.950000e-138 501
18 TraesCS2B01G387500 chr2D 84.390 410 29 11 1247 1626 471896886 471896482 1.750000e-98 370
19 TraesCS2B01G387500 chr2D 79.588 485 66 27 1871 2331 471372741 471372266 2.310000e-82 316
20 TraesCS2B01G387500 chr2D 93.210 162 11 0 999 1160 471897076 471896915 5.150000e-59 239
21 TraesCS2B01G387500 chr2D 96.528 144 3 2 2203 2345 471450076 471449934 1.850000e-58 237
22 TraesCS2B01G387500 chr2D 85.870 184 24 2 255 436 471454487 471454304 1.130000e-45 195
23 TraesCS2B01G387500 chr2D 85.821 134 10 2 2200 2331 471896370 471896244 2.500000e-27 134
24 TraesCS2B01G387500 chr2A 87.997 1308 91 27 740 2029 613176037 613174778 0.000000e+00 1485
25 TraesCS2B01G387500 chr2A 91.593 1023 55 13 2025 3019 613174590 613173571 0.000000e+00 1384
26 TraesCS2B01G387500 chr2A 83.779 1048 111 38 1975 2993 613037805 613036788 0.000000e+00 939
27 TraesCS2B01G387500 chr2A 83.591 969 77 35 694 1621 613275398 613274471 0.000000e+00 833
28 TraesCS2B01G387500 chr2A 85.736 666 75 12 2324 2988 613273668 613273022 0.000000e+00 686
29 TraesCS2B01G387500 chr2A 85.224 670 58 16 511 1160 613039283 613038635 0.000000e+00 651
30 TraesCS2B01G387500 chr2A 85.472 530 47 19 1227 1736 613038557 613038038 3.530000e-145 525
31 TraesCS2B01G387500 chr2A 83.173 416 45 13 333 738 613176541 613176141 1.360000e-94 357
32 TraesCS2B01G387500 chr2A 82.090 402 41 14 511 892 613043457 613043847 8.320000e-82 315
33 TraesCS2B01G387500 chr2A 87.500 272 15 5 1868 2136 613274229 613273974 3.010000e-76 296
34 TraesCS2B01G387500 chr2A 84.444 135 12 2 2199 2331 613273833 613273706 1.510000e-24 124
35 TraesCS2B01G387500 chr5D 93.667 979 57 5 3016 3990 232838410 232839387 0.000000e+00 1459
36 TraesCS2B01G387500 chr5D 92.821 975 63 7 3021 3990 335881590 335882562 0.000000e+00 1406
37 TraesCS2B01G387500 chr3B 93.492 968 59 4 3022 3985 191156995 191157962 0.000000e+00 1435
38 TraesCS2B01G387500 chr3B 92.997 971 63 4 3023 3990 29577010 29577978 0.000000e+00 1411
39 TraesCS2B01G387500 chr3B 85.983 692 92 3 2324 3013 739693792 739694480 0.000000e+00 736
40 TraesCS2B01G387500 chr1B 93.299 970 53 7 3022 3981 17633548 17634515 0.000000e+00 1421
41 TraesCS2B01G387500 chr3D 92.543 979 68 5 3015 3990 565791842 565792818 0.000000e+00 1399
42 TraesCS2B01G387500 chr4B 92.638 978 61 9 3023 3990 131434442 131433466 0.000000e+00 1397
43 TraesCS2B01G387500 chr4B 92.316 976 71 4 3019 3990 510875848 510874873 0.000000e+00 1384
44 TraesCS2B01G387500 chr1D 92.410 975 69 4 3020 3990 107214860 107213887 0.000000e+00 1386


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 TraesCS2B01G387500 chr2B 550717741 550721730 3989 True 7369.000000 7369 100.000000 1 3990 1 chr2B.!!$R1 3989
1 TraesCS2B01G387500 chr2B 550856813 550861470 4657 True 661.000000 848 81.979000 253 3000 3 chr2B.!!$R3 2747
2 TraesCS2B01G387500 chr2B 550995873 550998213 2340 True 652.666667 778 84.915333 713 3000 3 chr2B.!!$R4 2287
3 TraesCS2B01G387500 chr2B 550511060 550513170 2110 True 391.000000 647 86.736000 403 2331 4 chr2B.!!$R2 1928
4 TraesCS2B01G387500 chr2D 471448189 471454487 6298 True 695.800000 1574 91.354400 255 3019 5 chr2D.!!$R2 2764
5 TraesCS2B01G387500 chr2D 471371484 471374587 3103 True 630.250000 998 84.414250 42 2993 4 chr2D.!!$R1 2951
6 TraesCS2B01G387500 chr2D 471895538 471897076 1538 True 370.000000 737 87.519500 999 3000 4 chr2D.!!$R3 2001
7 TraesCS2B01G387500 chr2A 613173571 613176541 2970 True 1075.333333 1485 87.587667 333 3019 3 chr2A.!!$R2 2686
8 TraesCS2B01G387500 chr2A 613036788 613039283 2495 True 705.000000 939 84.825000 511 2993 3 chr2A.!!$R1 2482
9 TraesCS2B01G387500 chr2A 613273022 613275398 2376 True 484.750000 833 85.317750 694 2988 4 chr2A.!!$R3 2294
10 TraesCS2B01G387500 chr5D 232838410 232839387 977 False 1459.000000 1459 93.667000 3016 3990 1 chr5D.!!$F1 974
11 TraesCS2B01G387500 chr5D 335881590 335882562 972 False 1406.000000 1406 92.821000 3021 3990 1 chr5D.!!$F2 969
12 TraesCS2B01G387500 chr3B 191156995 191157962 967 False 1435.000000 1435 93.492000 3022 3985 1 chr3B.!!$F2 963
13 TraesCS2B01G387500 chr3B 29577010 29577978 968 False 1411.000000 1411 92.997000 3023 3990 1 chr3B.!!$F1 967
14 TraesCS2B01G387500 chr3B 739693792 739694480 688 False 736.000000 736 85.983000 2324 3013 1 chr3B.!!$F3 689
15 TraesCS2B01G387500 chr1B 17633548 17634515 967 False 1421.000000 1421 93.299000 3022 3981 1 chr1B.!!$F1 959
16 TraesCS2B01G387500 chr3D 565791842 565792818 976 False 1399.000000 1399 92.543000 3015 3990 1 chr3D.!!$F1 975
17 TraesCS2B01G387500 chr4B 131433466 131434442 976 True 1397.000000 1397 92.638000 3023 3990 1 chr4B.!!$R1 967
18 TraesCS2B01G387500 chr4B 510874873 510875848 975 True 1384.000000 1384 92.316000 3019 3990 1 chr4B.!!$R2 971
19 TraesCS2B01G387500 chr1D 107213887 107214860 973 True 1386.000000 1386 92.410000 3020 3990 1 chr1D.!!$R1 970

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
20 21 0.106015 AGTGGTGCCAAGCCTTTCTT 60.106 50.0 0.0 0.0 34.78 2.52 F
560 2979 0.320771 CAAGGTTCACAGAGGACGGG 60.321 60.0 0.0 0.0 0.00 5.28 F
1873 6256 0.670162 GCTGGCAAGCTGAGTTTTGA 59.330 50.0 5.6 0.0 46.60 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1609 5871 0.671781 CGAGGTGGCAAAGGTGAGAG 60.672 60.000 0.00 0.0 0.00 3.20 R
1928 6316 1.632409 AGGTGTCAGCATCAACTCCAT 59.368 47.619 4.59 0.0 32.68 3.41 R
3258 9732 0.249120 TGGAAGATGGTAGCGTGGTG 59.751 55.000 0.00 0.0 0.00 4.17 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
18 19 3.339547 TAGTGGTGCCAAGCCTTTC 57.660 52.632 0.00 0.00 0.00 2.62
19 20 0.771127 TAGTGGTGCCAAGCCTTTCT 59.229 50.000 0.00 0.00 0.00 2.52
20 21 0.106015 AGTGGTGCCAAGCCTTTCTT 60.106 50.000 0.00 0.00 34.78 2.52
21 22 0.752658 GTGGTGCCAAGCCTTTCTTT 59.247 50.000 0.00 0.00 31.27 2.52
22 23 1.960689 GTGGTGCCAAGCCTTTCTTTA 59.039 47.619 0.00 0.00 31.27 1.85
23 24 2.364002 GTGGTGCCAAGCCTTTCTTTAA 59.636 45.455 0.00 0.00 31.27 1.52
24 25 3.034635 TGGTGCCAAGCCTTTCTTTAAA 58.965 40.909 0.00 0.00 31.27 1.52
25 26 3.645687 TGGTGCCAAGCCTTTCTTTAAAT 59.354 39.130 0.00 0.00 31.27 1.40
26 27 3.996363 GGTGCCAAGCCTTTCTTTAAATG 59.004 43.478 0.00 0.00 31.27 2.32
27 28 3.996363 GTGCCAAGCCTTTCTTTAAATGG 59.004 43.478 0.00 0.00 31.27 3.16
28 29 3.007831 TGCCAAGCCTTTCTTTAAATGGG 59.992 43.478 3.16 0.00 31.27 4.00
29 30 3.599343 CCAAGCCTTTCTTTAAATGGGC 58.401 45.455 10.76 10.76 36.59 5.36
30 31 3.261643 CCAAGCCTTTCTTTAAATGGGCT 59.738 43.478 13.80 13.80 44.15 5.19
31 32 4.498241 CAAGCCTTTCTTTAAATGGGCTC 58.502 43.478 17.50 0.00 42.45 4.70
32 33 3.099905 AGCCTTTCTTTAAATGGGCTCC 58.900 45.455 13.80 0.00 40.46 4.70
33 34 2.831526 GCCTTTCTTTAAATGGGCTCCA 59.168 45.455 11.20 0.00 34.58 3.86
34 35 8.260029 CAAGCCTTTCTTTAAATGGGCTCCAT 62.260 42.308 17.50 1.21 42.45 3.41
35 36 9.633962 CAAGCCTTTCTTTAAATGGGCTCCATT 62.634 40.741 17.50 12.21 42.45 3.16
75 76 7.835181 TGCATTATGATCATTATATTCCTGGCA 59.165 33.333 14.65 10.86 0.00 4.92
76 77 8.350722 GCATTATGATCATTATATTCCTGGCAG 58.649 37.037 14.65 7.75 0.00 4.85
77 78 7.870509 TTATGATCATTATATTCCTGGCAGC 57.129 36.000 14.65 0.00 0.00 5.25
84 85 6.376299 TCATTATATTCCTGGCAGCATTCATC 59.624 38.462 9.56 0.00 0.00 2.92
87 88 2.048444 TCCTGGCAGCATTCATCTTC 57.952 50.000 9.56 0.00 0.00 2.87
93 95 3.192001 TGGCAGCATTCATCTTCAAGAAC 59.808 43.478 0.00 0.00 0.00 3.01
126 128 8.236084 TCTTTGTGACTAAGTATAAAAGTCGC 57.764 34.615 6.67 13.24 46.19 5.19
140 142 9.221775 GTATAAAAGTCGCAACCTAAATGAATG 57.778 33.333 0.00 0.00 0.00 2.67
154 156 8.352942 ACCTAAATGAATGTGAGTTTGAAGTTC 58.647 33.333 0.00 0.00 0.00 3.01
165 167 5.885352 TGAGTTTGAAGTTCAGATTCCACAA 59.115 36.000 14.01 0.00 0.00 3.33
166 168 6.547141 TGAGTTTGAAGTTCAGATTCCACAAT 59.453 34.615 14.01 0.00 0.00 2.71
169 171 8.912988 AGTTTGAAGTTCAGATTCCACAATTTA 58.087 29.630 5.56 0.00 0.00 1.40
170 172 9.696917 GTTTGAAGTTCAGATTCCACAATTTAT 57.303 29.630 5.56 0.00 0.00 1.40
171 173 9.912634 TTTGAAGTTCAGATTCCACAATTTATC 57.087 29.630 5.56 0.00 0.00 1.75
172 174 8.634335 TGAAGTTCAGATTCCACAATTTATCA 57.366 30.769 0.08 0.00 0.00 2.15
173 175 9.076781 TGAAGTTCAGATTCCACAATTTATCAA 57.923 29.630 0.08 0.00 0.00 2.57
174 176 9.565213 GAAGTTCAGATTCCACAATTTATCAAG 57.435 33.333 0.00 0.00 0.00 3.02
180 183 7.977293 CAGATTCCACAATTTATCAAGCATCAA 59.023 33.333 0.00 0.00 0.00 2.57
196 199 9.066892 TCAAGCATCAACTTTCTAACAAATAGT 57.933 29.630 0.00 0.00 33.08 2.12
234 237 9.657419 AATATTTAGAAGCCTTCAAAATTGGTG 57.343 29.630 7.29 0.00 0.00 4.17
238 241 4.405358 AGAAGCCTTCAAAATTGGTGTTCA 59.595 37.500 7.29 0.00 0.00 3.18
241 244 3.555547 GCCTTCAAAATTGGTGTTCACAC 59.444 43.478 1.10 1.10 45.72 3.82
268 271 8.504815 GGAGTTCTTCTTATTGTAACTTGGTTC 58.495 37.037 0.00 0.00 30.83 3.62
269 272 8.974060 AGTTCTTCTTATTGTAACTTGGTTCA 57.026 30.769 0.00 0.00 0.00 3.18
315 319 6.094464 TGAGTTGCCATCAGACATTTTCTATG 59.906 38.462 0.00 0.00 31.12 2.23
323 329 9.293404 CCATCAGACATTTTCTATGGATTATGT 57.707 33.333 6.36 6.36 37.51 2.29
336 342 3.643320 TGGATTATGTGAGCAGTAGGGAG 59.357 47.826 0.00 0.00 0.00 4.30
346 352 1.137282 GCAGTAGGGAGGCTCTACAAC 59.863 57.143 15.23 7.94 39.48 3.32
469 2876 9.723601 AAGATTCAAATTTAAAATGCTAGGCAA 57.276 25.926 0.00 0.00 43.62 4.52
483 2890 2.332654 GGCAAGCAACTACACGGGG 61.333 63.158 0.00 0.00 0.00 5.73
486 2893 1.149627 AAGCAACTACACGGGGCAA 59.850 52.632 0.00 0.00 0.00 4.52
491 2906 1.274167 CAACTACACGGGGCAACTAGA 59.726 52.381 0.00 0.00 0.00 2.43
495 2910 1.861982 ACACGGGGCAACTAGATAGT 58.138 50.000 0.00 0.00 38.39 2.12
520 2935 5.702670 TGCCTCTCAAACAAAGATCAACTAG 59.297 40.000 0.00 0.00 0.00 2.57
532 2947 7.884877 ACAAAGATCAACTAGAATTGTCCATGA 59.115 33.333 0.00 0.00 30.55 3.07
542 2958 8.328758 ACTAGAATTGTCCATGATTTACCTTCA 58.671 33.333 0.00 0.00 0.00 3.02
560 2979 0.320771 CAAGGTTCACAGAGGACGGG 60.321 60.000 0.00 0.00 0.00 5.28
569 2988 3.134081 TCACAGAGGACGGGGAATTATTC 59.866 47.826 0.00 0.00 0.00 1.75
572 2991 4.018779 ACAGAGGACGGGGAATTATTCAAA 60.019 41.667 7.29 0.00 0.00 2.69
573 2992 4.947388 CAGAGGACGGGGAATTATTCAAAA 59.053 41.667 7.29 0.00 0.00 2.44
574 2993 5.417580 CAGAGGACGGGGAATTATTCAAAAA 59.582 40.000 7.29 0.00 0.00 1.94
651 3071 3.426615 ACAATTCCACGCCTTTTGGATA 58.573 40.909 0.00 0.00 42.88 2.59
663 4634 8.511321 CACGCCTTTTGGATAATTATATGCTAA 58.489 33.333 0.00 0.00 44.07 3.09
664 4635 9.243105 ACGCCTTTTGGATAATTATATGCTAAT 57.757 29.630 0.00 0.00 44.07 1.73
730 4708 7.599171 CATTGCAGAAATCAATGGATATGCTA 58.401 34.615 13.23 8.22 44.14 3.49
758 4853 9.443283 CTCAAAGAGTTTGTGATCACTAAAAAG 57.557 33.333 25.55 11.83 41.36 2.27
785 4880 7.419711 TCGGTGACTAATCTTTCTTTATCCT 57.580 36.000 0.00 0.00 0.00 3.24
787 4882 7.342284 TCGGTGACTAATCTTTCTTTATCCTCT 59.658 37.037 0.00 0.00 0.00 3.69
805 4900 3.121030 CGAGAAGGCGCCCAACAG 61.121 66.667 26.15 8.81 0.00 3.16
815 4912 0.813184 CGCCCAACAGCTCATCATTT 59.187 50.000 0.00 0.00 0.00 2.32
818 4915 2.953466 CCAACAGCTCATCATTTGGG 57.047 50.000 0.00 0.00 34.26 4.12
934 5072 2.256117 AACCTCCTTCGTTGTTCCTG 57.744 50.000 0.00 0.00 0.00 3.86
1204 5429 6.483307 TGGACAGATTTTCTTCTTGTGTACTG 59.517 38.462 0.00 0.00 0.00 2.74
1205 5430 6.483640 GGACAGATTTTCTTCTTGTGTACTGT 59.516 38.462 0.00 0.00 37.53 3.55
1257 5483 1.643310 TCCCAATTTCCCCTGCTTTG 58.357 50.000 0.00 0.00 0.00 2.77
1330 5560 4.640647 GGGAATTAAAATCGCCAGAGAACT 59.359 41.667 0.00 0.00 0.00 3.01
1609 5871 1.317613 TCCCAAGCACACATCACAAC 58.682 50.000 0.00 0.00 0.00 3.32
1620 5882 3.879295 ACACATCACAACTCTCACCTTTG 59.121 43.478 0.00 0.00 0.00 2.77
1637 5902 4.459089 GCCACCTCGCCTCCAGAC 62.459 72.222 0.00 0.00 0.00 3.51
1658 5929 2.271800 CAAGTAGATTGGTGACGAGCC 58.728 52.381 0.00 0.00 35.08 4.70
1670 5941 1.145377 ACGAGCCAAACGTCACCTT 59.855 52.632 0.00 0.00 39.87 3.50
1671 5942 1.157870 ACGAGCCAAACGTCACCTTG 61.158 55.000 0.00 0.00 39.87 3.61
1672 5943 0.878523 CGAGCCAAACGTCACCTTGA 60.879 55.000 0.00 0.00 0.00 3.02
1673 5944 1.523758 GAGCCAAACGTCACCTTGAT 58.476 50.000 0.00 0.00 0.00 2.57
1674 5945 1.880027 GAGCCAAACGTCACCTTGATT 59.120 47.619 0.00 0.00 0.00 2.57
1804 6103 8.287503 TCTTAGCGGTTCAATAAGAAGAAAAAC 58.712 33.333 0.00 0.00 36.78 2.43
1805 6104 6.635030 AGCGGTTCAATAAGAAGAAAAACT 57.365 33.333 0.00 0.00 36.78 2.66
1810 6109 8.443937 CGGTTCAATAAGAAGAAAAACTCTAGG 58.556 37.037 0.00 0.00 36.78 3.02
1811 6110 9.503399 GGTTCAATAAGAAGAAAAACTCTAGGA 57.497 33.333 0.00 0.00 36.78 2.94
1873 6256 0.670162 GCTGGCAAGCTGAGTTTTGA 59.330 50.000 5.60 0.00 46.60 2.69
1925 6313 1.830145 CCATGTAGGCCGCCTTACT 59.170 57.895 19.35 0.00 34.61 2.24
1928 6316 1.134521 CATGTAGGCCGCCTTACTTGA 60.135 52.381 19.35 0.00 34.61 3.02
2022 6592 0.164647 CGAACAAGAGCCTCGCTTTG 59.835 55.000 0.00 0.00 39.88 2.77
2287 7500 4.215908 AGGACTAGTCAACTGTTGAGACA 58.784 43.478 22.61 10.26 41.01 3.41
2293 7506 5.998454 AGTCAACTGTTGAGACAAATGAG 57.002 39.130 22.61 0.00 41.01 2.90
2294 7507 4.274459 AGTCAACTGTTGAGACAAATGAGC 59.726 41.667 22.61 7.74 41.01 4.26
2295 7508 4.035558 GTCAACTGTTGAGACAAATGAGCA 59.964 41.667 22.61 0.00 41.01 4.26
2296 7509 4.639755 TCAACTGTTGAGACAAATGAGCAA 59.360 37.500 18.69 0.00 34.85 3.91
2297 7510 5.300034 TCAACTGTTGAGACAAATGAGCAAT 59.700 36.000 18.69 0.00 34.85 3.56
2298 7511 5.117355 ACTGTTGAGACAAATGAGCAATG 57.883 39.130 0.00 0.00 34.85 2.82
2299 7512 4.823442 ACTGTTGAGACAAATGAGCAATGA 59.177 37.500 0.00 0.00 34.85 2.57
2584 9026 2.777969 ACGCAACACCGTTAACCAA 58.222 47.368 0.00 0.00 38.47 3.67
3013 9470 4.688021 CGACCCCTCTGAAAAATAGAGAG 58.312 47.826 3.71 0.00 43.41 3.20
3079 9539 2.076100 ACGATGCATACGGCCATATTG 58.924 47.619 18.34 0.00 43.89 1.90
3120 9580 8.506168 TCAACAAGTTCTTACAGTCTTGAAAT 57.494 30.769 10.09 0.00 39.39 2.17
3121 9581 9.607988 TCAACAAGTTCTTACAGTCTTGAAATA 57.392 29.630 10.09 0.00 39.39 1.40
3155 9616 1.871080 CTCACAAAGAGCCTCAACGT 58.129 50.000 0.00 0.00 37.59 3.99
3183 9656 2.827921 CAAAAAGCCCTAGAGCCACAAT 59.172 45.455 0.00 0.00 0.00 2.71
3204 9677 2.887783 TCGGCTGGCAAAACAAAGATAA 59.112 40.909 1.08 0.00 0.00 1.75
3248 9722 1.673993 ATGACCGCATGCAAACCGA 60.674 52.632 19.57 0.00 32.31 4.69
3258 9732 4.037690 GCATGCAAACCGATTGAAGATAC 58.962 43.478 14.21 0.00 41.85 2.24
3259 9733 4.438608 GCATGCAAACCGATTGAAGATACA 60.439 41.667 14.21 0.00 41.85 2.29
3274 9748 3.031736 AGATACACCACGCTACCATCTT 58.968 45.455 0.00 0.00 0.00 2.40
3305 9779 2.301870 AGATCCAGTAACCAAACGCTCA 59.698 45.455 0.00 0.00 0.00 4.26
3354 9828 1.269102 ACATACGGATCAGCGCTGTAC 60.269 52.381 34.70 27.06 30.52 2.90
3526 10000 4.703899 ATAACGTATTGACCGAATTCGC 57.296 40.909 22.36 10.26 38.13 4.70
3653 10127 7.914427 ACACCTAGTAGATCATGTCCAATTA 57.086 36.000 0.00 0.00 0.00 1.40
3819 10293 6.816640 CGAGTTAACCATAAATTCTCCAGACA 59.183 38.462 0.88 0.00 0.00 3.41
3843 10317 3.942748 AGTAAGTTTCCAACGCAACTGAA 59.057 39.130 0.00 0.00 33.38 3.02
3846 10320 1.088306 TTTCCAACGCAACTGAACGT 58.912 45.000 0.00 0.00 46.07 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.752658 AAAGAAAGGCTTGGCACCAC 59.247 50.000 0.00 0.00 36.80 4.16
4 5 3.744238 TTTAAAGAAAGGCTTGGCACC 57.256 42.857 0.00 0.00 36.80 5.01
5 6 3.996363 CCATTTAAAGAAAGGCTTGGCAC 59.004 43.478 0.00 0.00 36.80 5.01
6 7 3.007831 CCCATTTAAAGAAAGGCTTGGCA 59.992 43.478 0.00 0.00 36.80 4.92
7 8 3.599343 CCCATTTAAAGAAAGGCTTGGC 58.401 45.455 0.00 0.00 36.80 4.52
8 9 3.261643 AGCCCATTTAAAGAAAGGCTTGG 59.738 43.478 14.15 5.54 41.24 3.61
9 10 4.498241 GAGCCCATTTAAAGAAAGGCTTG 58.502 43.478 18.60 0.71 43.04 4.01
10 11 3.515502 GGAGCCCATTTAAAGAAAGGCTT 59.484 43.478 18.60 0.00 43.04 4.35
11 12 3.099905 GGAGCCCATTTAAAGAAAGGCT 58.900 45.455 17.96 17.96 44.70 4.58
12 13 2.831526 TGGAGCCCATTTAAAGAAAGGC 59.168 45.455 10.88 10.88 36.55 4.35
25 26 2.734755 CTACAATCCAATGGAGCCCA 57.265 50.000 8.40 0.00 38.19 5.36
29 30 4.082081 TGCAAAAGCTACAATCCAATGGAG 60.082 41.667 8.40 0.00 34.05 3.86
30 31 3.831333 TGCAAAAGCTACAATCCAATGGA 59.169 39.130 3.67 3.67 35.55 3.41
31 32 4.191033 TGCAAAAGCTACAATCCAATGG 57.809 40.909 0.00 0.00 0.00 3.16
32 33 7.707464 TCATAATGCAAAAGCTACAATCCAATG 59.293 33.333 0.00 0.00 0.00 2.82
33 34 7.784037 TCATAATGCAAAAGCTACAATCCAAT 58.216 30.769 0.00 0.00 0.00 3.16
34 35 7.167924 TCATAATGCAAAAGCTACAATCCAA 57.832 32.000 0.00 0.00 0.00 3.53
35 36 6.772360 TCATAATGCAAAAGCTACAATCCA 57.228 33.333 0.00 0.00 0.00 3.41
36 37 7.428020 TGATCATAATGCAAAAGCTACAATCC 58.572 34.615 0.00 0.00 0.00 3.01
37 38 9.472361 AATGATCATAATGCAAAAGCTACAATC 57.528 29.630 9.04 0.00 0.00 2.67
66 67 2.750141 AGATGAATGCTGCCAGGAAT 57.250 45.000 0.00 0.00 0.00 3.01
72 73 3.442977 AGTTCTTGAAGATGAATGCTGCC 59.557 43.478 0.00 0.00 0.00 4.85
75 76 6.889301 TTTCAGTTCTTGAAGATGAATGCT 57.111 33.333 10.90 0.00 46.01 3.79
76 77 9.448294 GATATTTCAGTTCTTGAAGATGAATGC 57.552 33.333 10.90 0.80 46.01 3.56
84 85 9.604626 GTCACAAAGATATTTCAGTTCTTGAAG 57.395 33.333 0.00 0.00 46.01 3.02
103 105 7.949903 TGCGACTTTTATACTTAGTCACAAA 57.050 32.000 0.00 0.00 38.52 2.83
104 106 7.095523 GGTTGCGACTTTTATACTTAGTCACAA 60.096 37.037 3.59 0.00 38.13 3.33
107 109 6.694447 AGGTTGCGACTTTTATACTTAGTCA 58.306 36.000 3.59 0.00 38.52 3.41
114 116 9.221775 CATTCATTTAGGTTGCGACTTTTATAC 57.778 33.333 3.59 0.00 0.00 1.47
124 126 4.685169 ACTCACATTCATTTAGGTTGCG 57.315 40.909 0.00 0.00 0.00 4.85
126 128 8.137437 ACTTCAAACTCACATTCATTTAGGTTG 58.863 33.333 0.00 0.00 36.44 3.77
127 129 8.237811 ACTTCAAACTCACATTCATTTAGGTT 57.762 30.769 0.00 0.00 0.00 3.50
128 130 7.823745 ACTTCAAACTCACATTCATTTAGGT 57.176 32.000 0.00 0.00 0.00 3.08
129 131 8.352201 TGAACTTCAAACTCACATTCATTTAGG 58.648 33.333 0.00 0.00 0.00 2.69
140 142 5.296780 TGTGGAATCTGAACTTCAAACTCAC 59.703 40.000 0.00 0.00 0.00 3.51
154 156 7.485810 TGATGCTTGATAAATTGTGGAATCTG 58.514 34.615 0.00 0.00 0.00 2.90
170 172 9.066892 ACTATTTGTTAGAAAGTTGATGCTTGA 57.933 29.630 0.00 0.00 0.00 3.02
216 219 4.507756 GTGAACACCAATTTTGAAGGCTTC 59.492 41.667 20.27 20.27 0.00 3.86
221 224 3.796178 CCGTGTGAACACCAATTTTGAAG 59.204 43.478 7.96 0.00 43.66 3.02
224 227 3.181491 ACTCCGTGTGAACACCAATTTTG 60.181 43.478 7.96 0.00 43.66 2.44
228 231 2.158813 AGAACTCCGTGTGAACACCAAT 60.159 45.455 7.96 0.00 43.66 3.16
234 237 5.465724 ACAATAAGAAGAACTCCGTGTGAAC 59.534 40.000 0.00 0.00 0.00 3.18
238 241 6.756221 AGTTACAATAAGAAGAACTCCGTGT 58.244 36.000 0.00 0.00 0.00 4.49
241 244 6.649557 ACCAAGTTACAATAAGAAGAACTCCG 59.350 38.462 0.00 0.00 30.20 4.63
242 245 7.981102 ACCAAGTTACAATAAGAAGAACTCC 57.019 36.000 0.00 0.00 30.20 3.85
245 248 9.827411 GATGAACCAAGTTACAATAAGAAGAAC 57.173 33.333 0.00 0.00 0.00 3.01
251 254 6.978343 TCCGATGAACCAAGTTACAATAAG 57.022 37.500 0.00 0.00 0.00 1.73
307 311 7.933577 CCTACTGCTCACATAATCCATAGAAAA 59.066 37.037 0.00 0.00 0.00 2.29
315 319 3.007398 CCTCCCTACTGCTCACATAATCC 59.993 52.174 0.00 0.00 0.00 3.01
336 342 7.764443 TCATTTACAATACTCAGTTGTAGAGCC 59.236 37.037 0.00 0.00 41.50 4.70
420 428 8.522830 TCTTGGAATCTAATGTGTTCATTTTCC 58.477 33.333 12.27 12.27 42.64 3.13
469 2876 1.599797 GTTGCCCCGTGTAGTTGCT 60.600 57.895 0.00 0.00 0.00 3.91
474 2881 2.957006 ACTATCTAGTTGCCCCGTGTAG 59.043 50.000 0.00 0.00 31.13 2.74
495 2910 4.889409 AGTTGATCTTTGTTTGAGAGGCAA 59.111 37.500 0.00 0.00 33.88 4.52
498 2913 7.969536 TTCTAGTTGATCTTTGTTTGAGAGG 57.030 36.000 0.00 0.00 0.00 3.69
503 2918 8.352201 TGGACAATTCTAGTTGATCTTTGTTTG 58.648 33.333 0.40 0.00 33.37 2.93
520 2935 7.260603 CCTTGAAGGTAAATCATGGACAATTC 58.739 38.462 2.25 0.00 42.01 2.17
542 2958 1.481056 CCCCGTCCTCTGTGAACCTT 61.481 60.000 0.00 0.00 0.00 3.50
546 2965 1.358152 AATTCCCCGTCCTCTGTGAA 58.642 50.000 0.00 0.00 0.00 3.18
572 2991 9.539825 TCATAAGTTGTGCAAATTGTGTATTTT 57.460 25.926 16.78 0.00 38.21 1.82
573 2992 9.709495 ATCATAAGTTGTGCAAATTGTGTATTT 57.291 25.926 16.78 4.04 38.21 1.40
574 2993 9.709495 AATCATAAGTTGTGCAAATTGTGTATT 57.291 25.926 16.78 13.17 38.21 1.89
575 2994 9.142515 CAATCATAAGTTGTGCAAATTGTGTAT 57.857 29.630 16.78 9.58 38.21 2.29
589 3008 4.588899 TGGAGACACCCAATCATAAGTTG 58.411 43.478 0.00 0.00 38.00 3.16
597 3016 2.239654 TCCATCTTGGAGACACCCAATC 59.760 50.000 0.00 0.00 42.67 2.67
686 4657 7.997482 TGCAATGCCCGTTTATTTATTTAGTA 58.003 30.769 1.53 0.00 0.00 1.82
687 4658 6.868622 TGCAATGCCCGTTTATTTATTTAGT 58.131 32.000 1.53 0.00 0.00 2.24
688 4659 7.199766 TCTGCAATGCCCGTTTATTTATTTAG 58.800 34.615 1.53 0.00 0.00 1.85
689 4660 7.101652 TCTGCAATGCCCGTTTATTTATTTA 57.898 32.000 1.53 0.00 0.00 1.40
690 4661 5.971763 TCTGCAATGCCCGTTTATTTATTT 58.028 33.333 1.53 0.00 0.00 1.40
691 4662 5.590530 TCTGCAATGCCCGTTTATTTATT 57.409 34.783 1.53 0.00 0.00 1.40
692 4663 5.590530 TTCTGCAATGCCCGTTTATTTAT 57.409 34.783 1.53 0.00 0.00 1.40
703 4678 3.530265 TCCATTGATTTCTGCAATGCC 57.470 42.857 1.53 0.00 46.94 4.40
758 4853 8.766151 GGATAAAGAAAGATTAGTCACCGATTC 58.234 37.037 0.00 0.00 0.00 2.52
785 4880 2.994995 TTGGGCGCCTTCTCGAGA 60.995 61.111 28.56 12.08 0.00 4.04
787 4882 3.589654 CTGTTGGGCGCCTTCTCGA 62.590 63.158 28.56 6.29 0.00 4.04
805 4900 2.941720 GTGAGACTCCCAAATGATGAGC 59.058 50.000 0.00 0.00 0.00 4.26
815 4912 1.679305 GCTCTCGGTGAGACTCCCA 60.679 63.158 11.04 0.00 45.39 4.37
934 5072 2.743636 TGCTGTGTAGTACTCCAAGC 57.256 50.000 0.00 7.12 0.00 4.01
1071 5234 1.000955 ACGATGAAGTCACGGAGCTTT 59.999 47.619 0.00 0.00 0.00 3.51
1204 5429 2.967615 GCAGGCTCGCGGGAATAC 60.968 66.667 12.03 0.00 0.00 1.89
1205 5430 4.235762 GGCAGGCTCGCGGGAATA 62.236 66.667 12.03 0.00 0.00 1.75
1257 5483 1.449246 ATTGCAGAGCCTCGACAGC 60.449 57.895 0.00 0.00 0.00 4.40
1330 5560 6.920817 TGAATTCTAAAGAGCTTCGTCTACA 58.079 36.000 7.05 0.00 0.00 2.74
1609 5871 0.671781 CGAGGTGGCAAAGGTGAGAG 60.672 60.000 0.00 0.00 0.00 3.20
1620 5882 4.459089 GTCTGGAGGCGAGGTGGC 62.459 72.222 0.00 0.00 45.27 5.01
1658 5929 6.176975 TGCTAATAATCAAGGTGACGTTTG 57.823 37.500 0.00 0.00 0.00 2.93
1670 5941 4.702831 TCAATCACGCCTGCTAATAATCA 58.297 39.130 0.00 0.00 0.00 2.57
1671 5942 5.673337 TTCAATCACGCCTGCTAATAATC 57.327 39.130 0.00 0.00 0.00 1.75
1672 5943 5.764686 TGATTCAATCACGCCTGCTAATAAT 59.235 36.000 0.00 0.00 33.59 1.28
1673 5944 5.122519 TGATTCAATCACGCCTGCTAATAA 58.877 37.500 0.00 0.00 33.59 1.40
1674 5945 4.702831 TGATTCAATCACGCCTGCTAATA 58.297 39.130 0.00 0.00 33.59 0.98
1765 6060 3.896272 ACCGCTAAGAAATACCCCTAGAG 59.104 47.826 0.00 0.00 0.00 2.43
1804 6103 7.118680 GCAAGCATACTAGTAGTACTCCTAGAG 59.881 44.444 24.69 15.75 32.84 2.43
1805 6104 6.935771 GCAAGCATACTAGTAGTACTCCTAGA 59.064 42.308 24.69 11.64 32.84 2.43
1873 6256 2.611225 TTTCCTTTTGTTTGCGCCAT 57.389 40.000 4.18 0.00 0.00 4.40
1925 6313 3.076621 GTGTCAGCATCAACTCCATCAA 58.923 45.455 0.00 0.00 0.00 2.57
1928 6316 1.632409 AGGTGTCAGCATCAACTCCAT 59.368 47.619 4.59 0.00 32.68 3.41
2022 6592 5.678955 ACTTTCCATCCAGTAGGTTAGTC 57.321 43.478 0.00 0.00 35.89 2.59
2085 6925 7.817962 AGTTTAGCGATTCTTAGCTGTTCTTTA 59.182 33.333 0.00 0.00 44.32 1.85
2287 7500 8.618677 CATCTGTTACACTATCATTGCTCATTT 58.381 33.333 0.00 0.00 0.00 2.32
2293 7506 5.998454 AGCATCTGTTACACTATCATTGC 57.002 39.130 0.00 0.00 0.00 3.56
2294 7507 7.907045 GTCAAAGCATCTGTTACACTATCATTG 59.093 37.037 0.00 0.00 0.00 2.82
2295 7508 7.607607 TGTCAAAGCATCTGTTACACTATCATT 59.392 33.333 0.00 0.00 0.00 2.57
2296 7509 7.105588 TGTCAAAGCATCTGTTACACTATCAT 58.894 34.615 0.00 0.00 0.00 2.45
2297 7510 6.463360 TGTCAAAGCATCTGTTACACTATCA 58.537 36.000 0.00 0.00 0.00 2.15
2298 7511 6.968131 TGTCAAAGCATCTGTTACACTATC 57.032 37.500 0.00 0.00 0.00 2.08
2299 7512 7.607607 TCAATGTCAAAGCATCTGTTACACTAT 59.392 33.333 0.00 0.00 0.00 2.12
2345 7603 8.848474 AAGCAAACTATTGTACAGTCAGTAAT 57.152 30.769 0.00 0.00 38.85 1.89
2346 7604 8.148351 AGAAGCAAACTATTGTACAGTCAGTAA 58.852 33.333 0.00 0.00 38.85 2.24
2347 8682 7.667557 AGAAGCAAACTATTGTACAGTCAGTA 58.332 34.615 0.00 0.00 38.85 2.74
2349 8684 6.870965 AGAGAAGCAAACTATTGTACAGTCAG 59.129 38.462 0.00 0.00 38.85 3.51
2496 8932 3.537206 GACTTGGCTGGTGACCGCT 62.537 63.158 15.71 0.00 0.00 5.52
2571 9013 0.532640 GGACGGTTGGTTAACGGTGT 60.533 55.000 7.88 0.00 46.36 4.16
2624 9066 3.030308 CGAATCGTCGGCCATCGG 61.030 66.667 14.93 0.00 43.81 4.18
2638 9080 0.033504 GGACTGTGAGGTTGCTCGAA 59.966 55.000 0.00 0.00 0.00 3.71
2864 9315 1.526575 CCGAGCCCATGCAACAAGTT 61.527 55.000 0.00 0.00 41.13 2.66
2868 9319 4.657408 TGCCGAGCCCATGCAACA 62.657 61.111 0.00 0.00 41.13 3.33
2892 9343 1.336887 CGTCGAACTCCCAACAGATGT 60.337 52.381 0.00 0.00 0.00 3.06
3120 9580 7.620880 TCTTTGTGAGCTAGCCTATCTTTTTA 58.379 34.615 12.13 0.00 0.00 1.52
3121 9581 6.476378 TCTTTGTGAGCTAGCCTATCTTTTT 58.524 36.000 12.13 0.00 0.00 1.94
3155 9616 4.202212 GGCTCTAGGGCTTTTTGTTTTTGA 60.202 41.667 15.73 0.00 37.53 2.69
3183 9656 1.327303 ATCTTTGTTTTGCCAGCCGA 58.673 45.000 0.00 0.00 0.00 5.54
3240 9714 3.438781 TGGTGTATCTTCAATCGGTTTGC 59.561 43.478 0.00 0.00 35.16 3.68
3248 9722 3.196901 TGGTAGCGTGGTGTATCTTCAAT 59.803 43.478 0.00 0.00 0.00 2.57
3258 9732 0.249120 TGGAAGATGGTAGCGTGGTG 59.751 55.000 0.00 0.00 0.00 4.17
3259 9733 0.249398 GTGGAAGATGGTAGCGTGGT 59.751 55.000 0.00 0.00 0.00 4.16
3526 10000 6.311200 GCAAATTGCCTTTAACATTACTCCTG 59.689 38.462 6.72 0.00 37.42 3.86
3653 10127 2.632987 AGGACAACTTGGTTAAGCGT 57.367 45.000 0.00 0.00 37.43 5.07
3797 10271 9.614792 ACTATGTCTGGAGAATTTATGGTTAAC 57.385 33.333 0.00 0.00 0.00 2.01
3819 10293 5.302360 TCAGTTGCGTTGGAAACTTACTAT 58.698 37.500 0.00 0.00 46.99 2.12


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

AutoCloner maintained by Alex Coulton.