Multiple sequence alignment - TraesCS5D01G217300

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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 TraesCS5D01G217300 chr5D 100.000 3781 0 0 1 3781 326381773 326385553 0.000000e+00 6983.0
1 TraesCS5D01G217300 chr5D 95.266 1035 39 7 1869 2902 326403763 326402738 0.000000e+00 1631.0
2 TraesCS5D01G217300 chr5D 88.927 1156 86 22 436 1567 326404984 326403847 0.000000e+00 1387.0
3 TraesCS5D01G217300 chr5D 88.550 524 28 7 3258 3781 6388672 6389163 1.160000e-169 606.0
4 TraesCS5D01G217300 chr5D 89.683 252 22 3 1578 1825 534789065 534789316 6.090000e-83 318.0
5 TraesCS5D01G217300 chr5B 95.354 1399 49 8 1867 3256 378852350 378853741 0.000000e+00 2209.0
6 TraesCS5D01G217300 chr5B 95.777 1042 35 8 1866 2902 378904305 378903268 0.000000e+00 1672.0
7 TraesCS5D01G217300 chr5B 86.840 1269 124 33 304 1544 378851041 378852294 0.000000e+00 1378.0
8 TraesCS5D01G217300 chr5B 92.043 842 61 5 436 1276 378905531 378904695 0.000000e+00 1179.0
9 TraesCS5D01G217300 chr5B 85.310 919 122 10 1868 2778 375224032 375224945 0.000000e+00 937.0
10 TraesCS5D01G217300 chr5B 89.931 288 16 2 1272 1547 378904651 378904365 3.590000e-95 359.0
11 TraesCS5D01G217300 chr5A 94.826 1179 34 8 1866 3026 430042523 430041354 0.000000e+00 1814.0
12 TraesCS5D01G217300 chr5A 91.321 1279 78 20 304 1567 430043818 430042558 0.000000e+00 1716.0
13 TraesCS5D01G217300 chr5A 94.943 1048 31 9 1867 2902 429997244 429998281 0.000000e+00 1622.0
14 TraesCS5D01G217300 chr5A 93.445 839 52 3 436 1273 429995994 429996830 0.000000e+00 1242.0
15 TraesCS5D01G217300 chr5A 85.044 916 122 12 1868 2774 419829959 419830868 0.000000e+00 918.0
16 TraesCS5D01G217300 chr5A 85.401 411 52 4 3371 3781 615915882 615916284 1.620000e-113 420.0
17 TraesCS5D01G217300 chr5A 92.282 298 17 5 1272 1567 429996877 429997170 5.840000e-113 418.0
18 TraesCS5D01G217300 chr5A 84.871 271 21 11 42 301 430046038 430045777 4.850000e-64 255.0
19 TraesCS5D01G217300 chr5A 91.803 61 5 0 465 525 429995935 429995995 6.730000e-13 86.1
20 TraesCS5D01G217300 chr5A 93.333 45 3 0 1823 1867 429997172 429997216 2.440000e-07 67.6
21 TraesCS5D01G217300 chr2D 83.919 939 136 12 1867 2802 538598418 538597492 0.000000e+00 883.0
22 TraesCS5D01G217300 chr2D 91.129 248 18 4 1580 1823 14087561 14087314 2.180000e-87 333.0
23 TraesCS5D01G217300 chr2D 90.763 249 19 4 1578 1822 644999379 644999131 2.820000e-86 329.0
24 TraesCS5D01G217300 chr2D 96.899 129 3 1 3654 3781 83155629 83155501 8.230000e-52 215.0
25 TraesCS5D01G217300 chr2B 83.067 939 144 12 1867 2802 641194304 641193378 0.000000e+00 839.0
26 TraesCS5D01G217300 chr2B 90.323 248 20 4 1578 1821 75899596 75899349 4.710000e-84 322.0
27 TraesCS5D01G217300 chr2B 93.182 44 3 0 782 825 745765305 745765348 8.770000e-07 65.8
28 TraesCS5D01G217300 chr2A 83.067 939 144 12 1867 2802 680549048 680548122 0.000000e+00 839.0
29 TraesCS5D01G217300 chr1B 83.294 838 122 12 1871 2708 52294472 52293653 0.000000e+00 756.0
30 TraesCS5D01G217300 chr1B 85.413 521 65 6 3260 3779 20099398 20099908 7.190000e-147 531.0
31 TraesCS5D01G217300 chr1B 90.726 248 20 2 1578 1822 603277358 603277605 1.010000e-85 327.0
32 TraesCS5D01G217300 chr3B 87.782 532 55 4 3251 3781 381975993 381975471 6.940000e-172 614.0
33 TraesCS5D01G217300 chr6B 86.857 525 60 4 3257 3781 125419551 125420066 2.530000e-161 579.0
34 TraesCS5D01G217300 chr6B 86.450 524 58 8 3258 3779 691345040 691344528 2.550000e-156 562.0
35 TraesCS5D01G217300 chr6B 90.079 252 20 5 1578 1824 571453883 571454134 4.710000e-84 322.0
36 TraesCS5D01G217300 chr6B 89.105 257 24 3 1569 1821 679451773 679452029 2.190000e-82 316.0
37 TraesCS5D01G217300 chr4A 85.417 528 65 7 3253 3779 647443887 647443371 4.300000e-149 538.0
38 TraesCS5D01G217300 chr7B 84.916 537 59 9 3256 3781 307715545 307716070 1.200000e-144 523.0
39 TraesCS5D01G217300 chr7A 86.635 419 48 7 3251 3669 521449211 521449621 1.240000e-124 457.0
40 TraesCS5D01G217300 chr7A 96.875 128 4 0 3654 3781 521449634 521449761 8.230000e-52 215.0
41 TraesCS5D01G217300 chr3D 90.763 249 18 4 1578 1822 306028975 306029222 1.010000e-85 327.0
42 TraesCS5D01G217300 chr6D 88.889 261 23 6 1578 1832 25852767 25853027 2.190000e-82 316.0


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 TraesCS5D01G217300 chr5D 326381773 326385553 3780 False 6983.000000 6983 100.000000 1 3781 1 chr5D.!!$F2 3780
1 TraesCS5D01G217300 chr5D 326402738 326404984 2246 True 1509.000000 1631 92.096500 436 2902 2 chr5D.!!$R1 2466
2 TraesCS5D01G217300 chr5B 378851041 378853741 2700 False 1793.500000 2209 91.097000 304 3256 2 chr5B.!!$F2 2952
3 TraesCS5D01G217300 chr5B 378903268 378905531 2263 True 1070.000000 1672 92.583667 436 2902 3 chr5B.!!$R1 2466
4 TraesCS5D01G217300 chr5B 375224032 375224945 913 False 937.000000 937 85.310000 1868 2778 1 chr5B.!!$F1 910
5 TraesCS5D01G217300 chr5A 430041354 430046038 4684 True 1261.666667 1814 90.339333 42 3026 3 chr5A.!!$R1 2984
6 TraesCS5D01G217300 chr5A 419829959 419830868 909 False 918.000000 918 85.044000 1868 2774 1 chr5A.!!$F1 906
7 TraesCS5D01G217300 chr5A 429995935 429998281 2346 False 687.140000 1622 93.161200 436 2902 5 chr5A.!!$F3 2466
8 TraesCS5D01G217300 chr2D 538597492 538598418 926 True 883.000000 883 83.919000 1867 2802 1 chr2D.!!$R3 935
9 TraesCS5D01G217300 chr2B 641193378 641194304 926 True 839.000000 839 83.067000 1867 2802 1 chr2B.!!$R2 935
10 TraesCS5D01G217300 chr2A 680548122 680549048 926 True 839.000000 839 83.067000 1867 2802 1 chr2A.!!$R1 935
11 TraesCS5D01G217300 chr1B 52293653 52294472 819 True 756.000000 756 83.294000 1871 2708 1 chr1B.!!$R1 837
12 TraesCS5D01G217300 chr1B 20099398 20099908 510 False 531.000000 531 85.413000 3260 3779 1 chr1B.!!$F1 519
13 TraesCS5D01G217300 chr3B 381975471 381975993 522 True 614.000000 614 87.782000 3251 3781 1 chr3B.!!$R1 530
14 TraesCS5D01G217300 chr6B 125419551 125420066 515 False 579.000000 579 86.857000 3257 3781 1 chr6B.!!$F1 524
15 TraesCS5D01G217300 chr6B 691344528 691345040 512 True 562.000000 562 86.450000 3258 3779 1 chr6B.!!$R1 521
16 TraesCS5D01G217300 chr4A 647443371 647443887 516 True 538.000000 538 85.417000 3253 3779 1 chr4A.!!$R1 526
17 TraesCS5D01G217300 chr7B 307715545 307716070 525 False 523.000000 523 84.916000 3256 3781 1 chr7B.!!$F1 525
18 TraesCS5D01G217300 chr7A 521449211 521449761 550 False 336.000000 457 91.755000 3251 3781 2 chr7A.!!$F1 530

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
210 220 0.323629 TCATCGTGGTGGGGAACTTC 59.676 55.0 0.0 0.0 0.0 3.01 F
211 221 0.324943 CATCGTGGTGGGGAACTTCT 59.675 55.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1829 3880 0.038166 CCCCTGCTTGCTCCTACAAA 59.962 55.000 0.0 0.0 0.00 2.83 R
2884 5011 3.234630 TAGGCAGCACCACCACGAC 62.235 63.158 0.0 0.0 43.14 4.34 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.813346 AACGGTTGCGGGAGATTT 57.187 50.000 0.00 0.00 0.00 2.17
18 19 3.940229 AACGGTTGCGGGAGATTTA 57.060 47.368 0.00 0.00 0.00 1.40
19 20 1.445871 AACGGTTGCGGGAGATTTAC 58.554 50.000 0.00 0.00 0.00 2.01
21 22 1.006832 CGGTTGCGGGAGATTTACAG 58.993 55.000 0.00 0.00 0.00 2.74
22 23 1.379527 GGTTGCGGGAGATTTACAGG 58.620 55.000 0.00 0.00 0.00 4.00
23 24 1.339727 GGTTGCGGGAGATTTACAGGT 60.340 52.381 0.00 0.00 0.00 4.00
24 25 2.007608 GTTGCGGGAGATTTACAGGTC 58.992 52.381 0.00 0.00 0.00 3.85
25 26 0.539986 TGCGGGAGATTTACAGGTCC 59.460 55.000 0.00 0.00 0.00 4.46
26 27 0.539986 GCGGGAGATTTACAGGTCCA 59.460 55.000 0.00 0.00 0.00 4.02
27 28 1.742750 GCGGGAGATTTACAGGTCCAC 60.743 57.143 0.00 0.00 0.00 4.02
30 31 2.576648 GGGAGATTTACAGGTCCACCTT 59.423 50.000 0.00 0.00 46.09 3.50
33 34 5.280830 GGGAGATTTACAGGTCCACCTTAAA 60.281 44.000 0.00 5.74 46.09 1.52
34 35 5.880887 GGAGATTTACAGGTCCACCTTAAAG 59.119 44.000 0.00 0.00 46.09 1.85
35 36 6.296259 GGAGATTTACAGGTCCACCTTAAAGA 60.296 42.308 0.00 0.00 46.09 2.52
36 37 7.272144 AGATTTACAGGTCCACCTTAAAGAT 57.728 36.000 0.00 0.00 46.09 2.40
37 38 7.112779 AGATTTACAGGTCCACCTTAAAGATG 58.887 38.462 0.00 0.00 46.09 2.90
39 40 2.290960 ACAGGTCCACCTTAAAGATGGC 60.291 50.000 0.00 0.00 46.09 4.40
40 41 1.285078 AGGTCCACCTTAAAGATGGCC 59.715 52.381 0.00 0.00 46.09 5.36
48 49 2.033424 CCTTAAAGATGGCCTAAAGCGC 59.967 50.000 3.32 0.00 45.17 5.92
56 57 0.467474 GGCCTAAAGCGCCCCTTATT 60.467 55.000 2.29 0.00 45.17 1.40
100 101 2.819595 CGGCCCTCACGAATGTGG 60.820 66.667 0.00 0.00 46.42 4.17
104 105 1.303236 CCCTCACGAATGTGGCCAA 60.303 57.895 7.24 0.00 46.42 4.52
148 149 2.050477 GAACGTGCTTTGTTCCCATG 57.950 50.000 0.00 0.00 39.80 3.66
149 150 0.673437 AACGTGCTTTGTTCCCATGG 59.327 50.000 4.14 4.14 0.00 3.66
150 151 1.080569 CGTGCTTTGTTCCCATGGC 60.081 57.895 6.09 0.00 0.00 4.40
152 153 1.152376 TGCTTTGTTCCCATGGCCA 60.152 52.632 8.56 8.56 0.00 5.36
153 154 1.186917 TGCTTTGTTCCCATGGCCAG 61.187 55.000 13.05 3.10 0.00 4.85
154 155 1.187567 GCTTTGTTCCCATGGCCAGT 61.188 55.000 13.05 0.00 0.00 4.00
155 156 1.890573 GCTTTGTTCCCATGGCCAGTA 60.891 52.381 13.05 0.00 0.00 2.74
156 157 2.524306 CTTTGTTCCCATGGCCAGTAA 58.476 47.619 13.05 0.00 0.00 2.24
173 176 4.285292 CAGTAAGTGCTGCTGTTTGAAAG 58.715 43.478 0.00 0.00 0.00 2.62
174 177 3.947834 AGTAAGTGCTGCTGTTTGAAAGT 59.052 39.130 0.00 0.00 0.00 2.66
175 178 3.874392 AAGTGCTGCTGTTTGAAAGTT 57.126 38.095 0.00 0.00 0.00 2.66
176 179 3.155093 AGTGCTGCTGTTTGAAAGTTG 57.845 42.857 0.00 0.00 0.00 3.16
177 180 2.754552 AGTGCTGCTGTTTGAAAGTTGA 59.245 40.909 0.00 0.00 0.00 3.18
210 220 0.323629 TCATCGTGGTGGGGAACTTC 59.676 55.000 0.00 0.00 0.00 3.01
211 221 0.324943 CATCGTGGTGGGGAACTTCT 59.675 55.000 0.00 0.00 0.00 2.85
212 222 1.064825 ATCGTGGTGGGGAACTTCTT 58.935 50.000 0.00 0.00 0.00 2.52
213 223 0.395312 TCGTGGTGGGGAACTTCTTC 59.605 55.000 0.00 0.00 0.00 2.87
214 224 0.396811 CGTGGTGGGGAACTTCTTCT 59.603 55.000 0.00 0.00 0.00 2.85
215 225 1.878102 CGTGGTGGGGAACTTCTTCTG 60.878 57.143 0.00 0.00 0.00 3.02
222 232 1.066143 GGGAACTTCTTCTGATCGCCA 60.066 52.381 0.00 0.00 0.00 5.69
234 244 0.743345 GATCGCCAGGGTTTAACGCT 60.743 55.000 8.90 8.90 42.51 5.07
238 248 1.918868 GCCAGGGTTTAACGCTTCCG 61.919 60.000 12.01 4.45 39.54 4.30
272 282 1.143305 CAAGGAGCGCCATTAGATCG 58.857 55.000 9.88 0.00 36.29 3.69
276 286 2.280797 GCGCCATTAGATCGCCCA 60.281 61.111 0.00 0.00 42.71 5.36
289 301 3.897122 GCCCACCCACCAACTGGA 61.897 66.667 1.86 0.00 43.95 3.86
290 302 2.436109 CCCACCCACCAACTGGAG 59.564 66.667 1.86 0.00 43.95 3.86
291 303 2.460853 CCCACCCACCAACTGGAGT 61.461 63.158 1.86 0.00 43.95 3.85
292 304 1.073199 CCACCCACCAACTGGAGTC 59.927 63.158 1.86 0.00 43.95 3.36
293 305 1.301716 CACCCACCAACTGGAGTCG 60.302 63.158 1.86 0.00 43.95 4.18
294 306 2.358737 CCCACCAACTGGAGTCGC 60.359 66.667 1.86 0.00 43.95 5.19
295 307 2.738521 CCACCAACTGGAGTCGCG 60.739 66.667 0.00 0.00 43.95 5.87
296 308 3.414700 CACCAACTGGAGTCGCGC 61.415 66.667 0.00 0.00 38.94 6.86
337 2304 9.224267 CTTTGATAAAGACATCTTCAAAGAGGA 57.776 33.333 20.35 0.00 42.12 3.71
338 2305 9.573166 TTTGATAAAGACATCTTCAAAGAGGAA 57.427 29.630 11.05 0.00 39.04 3.36
339 2306 9.573166 TTGATAAAGACATCTTCAAAGAGGAAA 57.427 29.630 11.05 0.00 39.04 3.13
431 2399 3.676172 CGATCACTTTAGTTACACCGCAA 59.324 43.478 0.00 0.00 0.00 4.85
434 2402 3.560896 TCACTTTAGTTACACCGCAAACC 59.439 43.478 0.00 0.00 0.00 3.27
534 2502 7.557358 ACACATGTATCAAATATTCAAGCCTCA 59.443 33.333 0.00 0.00 0.00 3.86
535 2503 8.407832 CACATGTATCAAATATTCAAGCCTCAA 58.592 33.333 0.00 0.00 0.00 3.02
798 2766 4.821589 CTGCCGAGGAACCGCTCC 62.822 72.222 0.00 0.00 45.81 4.70
1176 3144 0.858583 GCACGTTTCAAAATGGTGCC 59.141 50.000 17.03 6.13 41.36 5.01
1200 3168 6.090898 CCGATTAGTGTGAGAACTCGAAATTT 59.909 38.462 0.00 0.00 0.00 1.82
1212 3180 7.023575 AGAACTCGAAATTTATTGTGATGTGC 58.976 34.615 0.00 0.00 0.00 4.57
1257 3230 5.161358 CAGTTACAGAATCAGTTGCGAGTA 58.839 41.667 0.00 0.00 0.00 2.59
1338 3359 8.561738 TGGAATGTAAAGTTCATTTCTCTACC 57.438 34.615 0.00 0.00 35.94 3.18
1420 3455 4.570926 TCCCCAGAGTTCAGATAATGGAT 58.429 43.478 0.00 0.00 0.00 3.41
1496 3544 2.806244 TGGCTTTTCTGCTTAGAACGAC 59.194 45.455 0.00 0.00 0.00 4.34
1532 3580 0.682532 TTCAGTGCAGGCAACCAACA 60.683 50.000 0.00 0.00 37.17 3.33
1535 3584 1.588667 GTGCAGGCAACCAACAACG 60.589 57.895 0.00 0.00 37.17 4.10
1567 3618 5.168569 CGAAACCTAGTCTCAAAGCACATA 58.831 41.667 0.00 0.00 0.00 2.29
1568 3619 5.062308 CGAAACCTAGTCTCAAAGCACATAC 59.938 44.000 0.00 0.00 0.00 2.39
1569 3620 5.746990 AACCTAGTCTCAAAGCACATACT 57.253 39.130 0.00 0.00 0.00 2.12
1570 3621 5.331876 ACCTAGTCTCAAAGCACATACTC 57.668 43.478 0.00 0.00 0.00 2.59
1571 3622 5.020132 ACCTAGTCTCAAAGCACATACTCT 58.980 41.667 0.00 0.00 0.00 3.24
1572 3623 5.126384 ACCTAGTCTCAAAGCACATACTCTC 59.874 44.000 0.00 0.00 0.00 3.20
1573 3624 5.126222 CCTAGTCTCAAAGCACATACTCTCA 59.874 44.000 0.00 0.00 0.00 3.27
1574 3625 5.674052 AGTCTCAAAGCACATACTCTCAT 57.326 39.130 0.00 0.00 0.00 2.90
1575 3626 5.659463 AGTCTCAAAGCACATACTCTCATC 58.341 41.667 0.00 0.00 0.00 2.92
1576 3627 5.186603 AGTCTCAAAGCACATACTCTCATCA 59.813 40.000 0.00 0.00 0.00 3.07
1577 3628 6.047870 GTCTCAAAGCACATACTCTCATCAT 58.952 40.000 0.00 0.00 0.00 2.45
1578 3629 6.538021 GTCTCAAAGCACATACTCTCATCATT 59.462 38.462 0.00 0.00 0.00 2.57
1579 3630 7.065563 GTCTCAAAGCACATACTCTCATCATTT 59.934 37.037 0.00 0.00 0.00 2.32
1580 3631 7.609146 TCTCAAAGCACATACTCTCATCATTTT 59.391 33.333 0.00 0.00 0.00 1.82
1581 3632 8.114331 TCAAAGCACATACTCTCATCATTTTT 57.886 30.769 0.00 0.00 0.00 1.94
1582 3633 9.230122 TCAAAGCACATACTCTCATCATTTTTA 57.770 29.630 0.00 0.00 0.00 1.52
1583 3634 9.499585 CAAAGCACATACTCTCATCATTTTTAG 57.500 33.333 0.00 0.00 0.00 1.85
1584 3635 8.798859 AAGCACATACTCTCATCATTTTTAGT 57.201 30.769 0.00 0.00 0.00 2.24
1585 3636 8.798859 AGCACATACTCTCATCATTTTTAGTT 57.201 30.769 0.00 0.00 0.00 2.24
1586 3637 9.236006 AGCACATACTCTCATCATTTTTAGTTT 57.764 29.630 0.00 0.00 0.00 2.66
1587 3638 9.282247 GCACATACTCTCATCATTTTTAGTTTG 57.718 33.333 0.00 0.00 0.00 2.93
1588 3639 9.282247 CACATACTCTCATCATTTTTAGTTTGC 57.718 33.333 0.00 0.00 0.00 3.68
1589 3640 9.013229 ACATACTCTCATCATTTTTAGTTTGCA 57.987 29.630 0.00 0.00 0.00 4.08
1608 3659 9.777297 AGTTTGCATATAAAATTTGGTCAAAGT 57.223 25.926 0.00 0.00 33.32 2.66
1610 3661 9.770097 TTTGCATATAAAATTTGGTCAAAGTCA 57.230 25.926 0.00 0.00 33.32 3.41
1611 3662 9.770097 TTGCATATAAAATTTGGTCAAAGTCAA 57.230 25.926 0.00 0.00 33.32 3.18
1612 3663 9.421806 TGCATATAAAATTTGGTCAAAGTCAAG 57.578 29.630 0.00 0.00 33.32 3.02
1613 3664 9.423061 GCATATAAAATTTGGTCAAAGTCAAGT 57.577 29.630 0.00 0.00 33.32 3.16
1795 3846 9.455847 GGTTGACTTTGATCAAATCTTATATGC 57.544 33.333 20.76 6.12 40.22 3.14
1798 3849 9.617523 TGACTTTGATCAAATCTTATATGCAGA 57.382 29.630 20.76 0.00 0.00 4.26
1799 3850 9.875675 GACTTTGATCAAATCTTATATGCAGAC 57.124 33.333 20.76 2.27 0.00 3.51
1800 3851 9.624373 ACTTTGATCAAATCTTATATGCAGACT 57.376 29.630 20.76 0.00 0.00 3.24
1829 3880 8.721133 AAAATGGAGGGAGTACTAAATTGTTT 57.279 30.769 0.00 0.00 0.00 2.83
1984 4075 2.756283 CGAAGCTCTCCCCCTCGT 60.756 66.667 0.00 0.00 0.00 4.18
2806 4927 1.943340 GAAGCTCCATTGGGATCGAAC 59.057 52.381 2.09 0.00 43.91 3.95
2884 5011 1.239968 GCTTGAGCTGGGTGTTGAGG 61.240 60.000 0.00 0.00 38.21 3.86
2939 5072 3.016474 GAACTGGAAGAGCGCGTGC 62.016 63.158 14.39 14.39 38.55 5.34
3014 5147 4.509616 TGGAAAACTTGACTGACGAAGAA 58.490 39.130 0.00 0.00 0.00 2.52
3037 5170 2.776312 TTCGTGTGAGACACTCAGAC 57.224 50.000 15.72 15.72 46.46 3.51
3092 5225 6.931838 TCGGAAGAAATGTAAGTATGTCACT 58.068 36.000 0.00 0.00 36.49 3.41
3093 5226 8.058667 TCGGAAGAAATGTAAGTATGTCACTA 57.941 34.615 0.00 0.00 34.36 2.74
3094 5227 8.525316 TCGGAAGAAATGTAAGTATGTCACTAA 58.475 33.333 0.00 0.00 34.36 2.24
3150 5283 7.655328 AGATAATGACTAGTGTGATTTAGCTGC 59.345 37.037 0.00 0.00 32.52 5.25
3155 5288 6.590292 TGACTAGTGTGATTTAGCTGCTAAAC 59.410 38.462 30.77 24.01 38.51 2.01
3165 5298 2.439409 AGCTGCTAAACATGCATGTGA 58.561 42.857 31.98 21.31 41.61 3.58
3169 5302 4.274214 GCTGCTAAACATGCATGTGATAGA 59.726 41.667 34.80 24.77 41.61 1.98
3179 5312 4.686972 TGCATGTGATAGAGCAACTCTAC 58.313 43.478 6.48 0.00 44.47 2.59
3182 5315 3.708451 TGTGATAGAGCAACTCTACCCA 58.292 45.455 6.48 5.68 44.47 4.51
3189 5323 5.048846 AGAGCAACTCTACCCAAGAAAAA 57.951 39.130 0.00 0.00 39.28 1.94
3214 5348 6.183360 AAAAACTGGTTTTTCTCTCTAACCGG 60.183 38.462 15.65 0.00 46.30 5.28
3220 5354 5.416947 GTTTTTCTCTCTAACCGGCATCTA 58.583 41.667 0.00 0.00 0.00 1.98
3233 5367 0.743097 GCATCTAGCCAAAGCCCAAG 59.257 55.000 0.00 0.00 41.25 3.61
3240 5374 2.118679 AGCCAAAGCCCAAGAAAACTT 58.881 42.857 0.00 0.00 41.25 2.66
3282 5416 7.068839 AGAGGTAAATACATCAGTAGTGTCTGG 59.931 40.741 7.84 0.00 39.29 3.86
3289 5423 2.598565 TCAGTAGTGTCTGGACTTGCT 58.401 47.619 0.00 1.53 36.25 3.91
3335 5469 8.455682 CCTAAAGTTGAAAAATATGCCGAACTA 58.544 33.333 0.00 0.00 0.00 2.24
3381 5515 4.511454 TGCAAATACGGTGCTAATCTCATC 59.489 41.667 0.00 0.00 42.69 2.92
3382 5516 4.752101 GCAAATACGGTGCTAATCTCATCT 59.248 41.667 0.00 0.00 39.00 2.90
3383 5517 5.333645 GCAAATACGGTGCTAATCTCATCTG 60.334 44.000 0.00 0.00 39.00 2.90
3384 5518 5.537300 AATACGGTGCTAATCTCATCTGT 57.463 39.130 0.00 0.00 0.00 3.41
3500 5635 2.092323 GCCTTTATGACAAGTGGTCCC 58.908 52.381 0.00 0.00 46.38 4.46
3501 5636 2.554344 GCCTTTATGACAAGTGGTCCCA 60.554 50.000 0.00 0.00 46.38 4.37
3502 5637 3.877735 GCCTTTATGACAAGTGGTCCCAT 60.878 47.826 0.00 0.00 46.38 4.00
3503 5638 4.627741 GCCTTTATGACAAGTGGTCCCATA 60.628 45.833 0.00 0.00 46.38 2.74
3549 5684 7.841915 AATTGAAATTAAAAATAGTGCCCGG 57.158 32.000 0.00 0.00 0.00 5.73
3551 5686 6.347859 TGAAATTAAAAATAGTGCCCGGTT 57.652 33.333 0.00 0.00 0.00 4.44
3563 5698 1.139095 CCCGGTTAGAGACGAGCAC 59.861 63.158 0.00 0.00 0.00 4.40
3565 5700 0.456221 CCGGTTAGAGACGAGCACAT 59.544 55.000 0.00 0.00 0.00 3.21
3593 5728 1.134670 AGGTTGAAGAGAGCATACGCC 60.135 52.381 0.00 0.00 39.83 5.68
3612 5747 2.513666 ACCACTGCACCACACACG 60.514 61.111 0.00 0.00 0.00 4.49
3620 5755 1.006832 GCACCACACACGGTATGATC 58.993 55.000 0.00 0.00 37.07 2.92
3624 5759 0.645355 CACACACGGTATGATCGCAC 59.355 55.000 0.00 0.00 0.00 5.34
3634 5769 0.396139 ATGATCGCACCTTTGGCCAT 60.396 50.000 6.09 0.00 0.00 4.40
3651 5796 8.830201 TTTGGCCATTACATATTAATGAATGC 57.170 30.769 6.09 10.78 37.15 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.006832 CTGTAAATCTCCCGCAACCG 58.993 55.000 0.00 0.00 0.00 4.44
3 4 1.339727 ACCTGTAAATCTCCCGCAACC 60.340 52.381 0.00 0.00 0.00 3.77
6 7 0.539986 GGACCTGTAAATCTCCCGCA 59.460 55.000 0.00 0.00 0.00 5.69
7 8 0.539986 TGGACCTGTAAATCTCCCGC 59.460 55.000 0.00 0.00 0.00 6.13
8 9 1.134491 GGTGGACCTGTAAATCTCCCG 60.134 57.143 0.00 0.00 0.00 5.14
9 10 2.197465 AGGTGGACCTGTAAATCTCCC 58.803 52.381 0.00 0.00 46.55 4.30
21 22 1.285078 AGGCCATCTTTAAGGTGGACC 59.715 52.381 25.28 23.26 42.22 4.46
22 23 2.808906 AGGCCATCTTTAAGGTGGAC 57.191 50.000 26.79 24.47 41.53 4.02
23 24 4.855340 CTTTAGGCCATCTTTAAGGTGGA 58.145 43.478 26.79 4.22 34.94 4.02
24 25 3.381590 GCTTTAGGCCATCTTTAAGGTGG 59.618 47.826 19.28 19.28 36.09 4.61
25 26 3.065371 CGCTTTAGGCCATCTTTAAGGTG 59.935 47.826 5.01 0.00 37.74 4.00
26 27 3.279434 CGCTTTAGGCCATCTTTAAGGT 58.721 45.455 5.01 0.00 37.74 3.50
27 28 2.033424 GCGCTTTAGGCCATCTTTAAGG 59.967 50.000 5.01 0.00 37.74 2.69
39 40 5.585820 TTTTTAATAAGGGGCGCTTTAGG 57.414 39.130 22.38 0.00 0.00 2.69
62 63 1.067212 GTGGTCGAGTCTGTGAGTGTT 59.933 52.381 0.00 0.00 0.00 3.32
145 146 0.679002 AGCAGCACTTACTGGCCATG 60.679 55.000 5.51 1.36 38.16 3.66
148 149 0.890996 AACAGCAGCACTTACTGGCC 60.891 55.000 0.00 0.00 38.16 5.36
149 150 0.954452 AAACAGCAGCACTTACTGGC 59.046 50.000 0.00 0.00 38.16 4.85
150 151 2.221169 TCAAACAGCAGCACTTACTGG 58.779 47.619 0.00 0.00 38.16 4.00
152 153 3.947834 ACTTTCAAACAGCAGCACTTACT 59.052 39.130 0.00 0.00 0.00 2.24
153 154 4.292977 ACTTTCAAACAGCAGCACTTAC 57.707 40.909 0.00 0.00 0.00 2.34
154 155 4.397730 TCAACTTTCAAACAGCAGCACTTA 59.602 37.500 0.00 0.00 0.00 2.24
155 156 3.193267 TCAACTTTCAAACAGCAGCACTT 59.807 39.130 0.00 0.00 0.00 3.16
156 157 2.754552 TCAACTTTCAAACAGCAGCACT 59.245 40.909 0.00 0.00 0.00 4.40
173 176 4.031426 CGATGAACTAGTAGGCGTTTCAAC 59.969 45.833 0.00 1.09 0.00 3.18
174 177 4.171005 CGATGAACTAGTAGGCGTTTCAA 58.829 43.478 0.00 0.00 0.00 2.69
175 178 3.192001 ACGATGAACTAGTAGGCGTTTCA 59.808 43.478 0.00 2.99 0.00 2.69
176 179 3.546670 CACGATGAACTAGTAGGCGTTTC 59.453 47.826 0.00 0.00 0.00 2.78
177 180 3.508762 CACGATGAACTAGTAGGCGTTT 58.491 45.455 0.00 0.00 0.00 3.60
210 220 2.678336 GTTAAACCCTGGCGATCAGAAG 59.322 50.000 7.63 2.41 46.18 2.85
211 221 2.706890 GTTAAACCCTGGCGATCAGAA 58.293 47.619 7.63 0.00 46.18 3.02
212 222 1.404986 CGTTAAACCCTGGCGATCAGA 60.405 52.381 7.63 0.00 46.18 3.27
213 223 1.006832 CGTTAAACCCTGGCGATCAG 58.993 55.000 0.00 0.00 43.00 2.90
214 224 1.022451 GCGTTAAACCCTGGCGATCA 61.022 55.000 0.00 0.00 0.00 2.92
215 225 0.743345 AGCGTTAAACCCTGGCGATC 60.743 55.000 0.00 0.00 0.00 3.69
238 248 0.389948 CCTTGTATATCGCCTCCGGC 60.390 60.000 0.00 0.00 46.75 6.13
249 259 4.380550 CGATCTAATGGCGCTCCTTGTATA 60.381 45.833 7.64 0.00 0.00 1.47
295 307 1.946475 AAAGTCTCGCCTAGTCCCGC 61.946 60.000 0.00 0.00 0.00 6.13
296 308 0.179134 CAAAGTCTCGCCTAGTCCCG 60.179 60.000 0.00 0.00 0.00 5.14
299 311 5.744819 GTCTTTATCAAAGTCTCGCCTAGTC 59.255 44.000 0.00 0.00 39.52 2.59
300 312 5.185249 TGTCTTTATCAAAGTCTCGCCTAGT 59.815 40.000 0.00 0.00 39.52 2.57
301 313 5.651530 TGTCTTTATCAAAGTCTCGCCTAG 58.348 41.667 0.00 0.00 39.52 3.02
302 314 5.654603 TGTCTTTATCAAAGTCTCGCCTA 57.345 39.130 0.00 0.00 39.52 3.93
534 2502 0.251653 TCCCAGCTCACCTCTACGTT 60.252 55.000 0.00 0.00 0.00 3.99
535 2503 0.681564 CTCCCAGCTCACCTCTACGT 60.682 60.000 0.00 0.00 0.00 3.57
882 2850 4.291369 CGTCCATCAATGGCTACGACATT 61.291 47.826 14.73 0.00 45.57 2.71
1176 3144 6.633668 AATTTCGAGTTCTCACACTAATCG 57.366 37.500 0.79 0.00 0.00 3.34
1200 3168 6.822667 AAGACTCATTTGCACATCACAATA 57.177 33.333 0.00 0.00 0.00 1.90
1203 3171 7.064966 CAGTATAAGACTCATTTGCACATCACA 59.935 37.037 0.00 0.00 35.64 3.58
1212 3180 6.726258 TGTGTGCAGTATAAGACTCATTTG 57.274 37.500 0.00 0.00 35.64 2.32
1240 3211 4.627035 TCACAATACTCGCAACTGATTCTG 59.373 41.667 0.00 0.00 0.00 3.02
1257 3230 4.771577 TGCCATTCATTACTTGGTCACAAT 59.228 37.500 0.00 0.00 35.73 2.71
1316 3337 7.660208 ACACGGTAGAGAAATGAACTTTACATT 59.340 33.333 0.00 0.00 39.25 2.71
1338 3359 2.014128 AGACAAGTTCCACCAAACACG 58.986 47.619 0.00 0.00 0.00 4.49
1420 3455 8.991026 GTCTAAGCGAGTCAGACTCTAATAATA 58.009 37.037 25.11 10.60 42.92 0.98
1428 3463 1.062880 CGGTCTAAGCGAGTCAGACTC 59.937 57.143 19.43 19.43 42.41 3.36
1496 3544 6.252441 TGCACTGAAAACAAAAACAAGTATCG 59.748 34.615 0.00 0.00 0.00 2.92
1532 3580 4.432712 ACTAGGTTTCGTACACAAACGTT 58.567 39.130 14.43 0.00 43.31 3.99
1535 3584 5.284079 TGAGACTAGGTTTCGTACACAAAC 58.716 41.667 8.35 8.35 33.65 2.93
1582 3633 9.777297 ACTTTGACCAAATTTTATATGCAAACT 57.223 25.926 0.00 0.00 0.00 2.66
1584 3635 9.770097 TGACTTTGACCAAATTTTATATGCAAA 57.230 25.926 0.00 0.00 0.00 3.68
1585 3636 9.770097 TTGACTTTGACCAAATTTTATATGCAA 57.230 25.926 0.00 0.00 0.00 4.08
1586 3637 9.421806 CTTGACTTTGACCAAATTTTATATGCA 57.578 29.630 0.00 0.00 0.00 3.96
1587 3638 9.423061 ACTTGACTTTGACCAAATTTTATATGC 57.577 29.630 0.00 0.00 0.00 3.14
1749 3800 7.973944 GTCAACCTTTGTAAAGTTTGATCAACT 59.026 33.333 16.72 6.20 45.13 3.16
1750 3801 7.973944 AGTCAACCTTTGTAAAGTTTGATCAAC 59.026 33.333 16.72 3.85 45.13 3.18
1751 3802 8.062065 AGTCAACCTTTGTAAAGTTTGATCAA 57.938 30.769 16.72 3.38 45.13 2.57
1752 3803 7.639113 AGTCAACCTTTGTAAAGTTTGATCA 57.361 32.000 16.72 0.00 45.13 2.92
1753 3804 8.926715 AAAGTCAACCTTTGTAAAGTTTGATC 57.073 30.769 16.72 11.87 45.13 2.92
1769 3820 9.455847 GCATATAAGATTTGATCAAAGTCAACC 57.544 33.333 24.17 10.10 37.80 3.77
1772 3823 9.617523 TCTGCATATAAGATTTGATCAAAGTCA 57.382 29.630 24.17 11.02 33.32 3.41
1773 3824 9.875675 GTCTGCATATAAGATTTGATCAAAGTC 57.124 33.333 24.17 19.70 33.32 3.01
1774 3825 9.624373 AGTCTGCATATAAGATTTGATCAAAGT 57.376 29.630 24.17 14.86 33.32 2.66
1803 3854 8.721133 AACAATTTAGTACTCCCTCCATTTTT 57.279 30.769 0.00 0.00 0.00 1.94
1804 3855 8.721133 AAACAATTTAGTACTCCCTCCATTTT 57.279 30.769 0.00 0.00 0.00 1.82
1805 3856 8.721133 AAAACAATTTAGTACTCCCTCCATTT 57.279 30.769 0.00 0.00 0.00 2.32
1806 3857 8.585018 CAAAAACAATTTAGTACTCCCTCCATT 58.415 33.333 0.00 0.00 0.00 3.16
1807 3858 7.728532 ACAAAAACAATTTAGTACTCCCTCCAT 59.271 33.333 0.00 0.00 0.00 3.41
1808 3859 7.064229 ACAAAAACAATTTAGTACTCCCTCCA 58.936 34.615 0.00 0.00 0.00 3.86
1809 3860 7.520451 ACAAAAACAATTTAGTACTCCCTCC 57.480 36.000 0.00 0.00 0.00 4.30
1810 3861 8.727910 CCTACAAAAACAATTTAGTACTCCCTC 58.272 37.037 0.00 0.00 0.00 4.30
1811 3862 8.442374 TCCTACAAAAACAATTTAGTACTCCCT 58.558 33.333 0.00 0.00 0.00 4.20
1812 3863 8.625786 TCCTACAAAAACAATTTAGTACTCCC 57.374 34.615 0.00 0.00 0.00 4.30
1813 3864 8.235226 GCTCCTACAAAAACAATTTAGTACTCC 58.765 37.037 0.00 0.00 0.00 3.85
1814 3865 8.780249 TGCTCCTACAAAAACAATTTAGTACTC 58.220 33.333 0.00 0.00 0.00 2.59
1815 3866 8.685838 TGCTCCTACAAAAACAATTTAGTACT 57.314 30.769 0.00 0.00 0.00 2.73
1816 3867 9.394477 CTTGCTCCTACAAAAACAATTTAGTAC 57.606 33.333 0.00 0.00 0.00 2.73
1817 3868 8.079809 GCTTGCTCCTACAAAAACAATTTAGTA 58.920 33.333 0.00 0.00 0.00 1.82
1818 3869 6.923508 GCTTGCTCCTACAAAAACAATTTAGT 59.076 34.615 0.00 0.00 0.00 2.24
1819 3870 6.922957 TGCTTGCTCCTACAAAAACAATTTAG 59.077 34.615 0.00 0.00 0.00 1.85
1820 3871 6.810911 TGCTTGCTCCTACAAAAACAATTTA 58.189 32.000 0.00 0.00 0.00 1.40
1821 3872 5.669477 TGCTTGCTCCTACAAAAACAATTT 58.331 33.333 0.00 0.00 0.00 1.82
1829 3880 0.038166 CCCCTGCTTGCTCCTACAAA 59.962 55.000 0.00 0.00 0.00 2.83
2884 5011 3.234630 TAGGCAGCACCACCACGAC 62.235 63.158 0.00 0.00 43.14 4.34
3037 5170 0.723414 CAGGTAACGCTGAGCATGTG 59.277 55.000 4.88 0.00 46.39 3.21
3082 5215 7.490657 TGATTACACCCTTTAGTGACATACT 57.509 36.000 0.00 0.00 40.34 2.12
3083 5216 8.448615 GTTTGATTACACCCTTTAGTGACATAC 58.551 37.037 0.00 0.00 40.34 2.39
3084 5217 7.332430 CGTTTGATTACACCCTTTAGTGACATA 59.668 37.037 0.00 0.00 40.34 2.29
3085 5218 6.148811 CGTTTGATTACACCCTTTAGTGACAT 59.851 38.462 0.00 0.00 40.34 3.06
3086 5219 5.467399 CGTTTGATTACACCCTTTAGTGACA 59.533 40.000 0.00 0.00 40.34 3.58
3087 5220 5.106830 CCGTTTGATTACACCCTTTAGTGAC 60.107 44.000 0.00 0.00 40.34 3.67
3088 5221 4.998672 CCGTTTGATTACACCCTTTAGTGA 59.001 41.667 0.00 0.00 40.34 3.41
3089 5222 4.379082 GCCGTTTGATTACACCCTTTAGTG 60.379 45.833 0.00 0.00 43.65 2.74
3090 5223 3.754850 GCCGTTTGATTACACCCTTTAGT 59.245 43.478 0.00 0.00 0.00 2.24
3091 5224 3.181514 CGCCGTTTGATTACACCCTTTAG 60.182 47.826 0.00 0.00 0.00 1.85
3092 5225 2.743126 CGCCGTTTGATTACACCCTTTA 59.257 45.455 0.00 0.00 0.00 1.85
3093 5226 1.538075 CGCCGTTTGATTACACCCTTT 59.462 47.619 0.00 0.00 0.00 3.11
3094 5227 1.161843 CGCCGTTTGATTACACCCTT 58.838 50.000 0.00 0.00 0.00 3.95
3096 5229 0.167251 CACGCCGTTTGATTACACCC 59.833 55.000 0.00 0.00 0.00 4.61
3097 5230 0.167251 CCACGCCGTTTGATTACACC 59.833 55.000 0.00 0.00 0.00 4.16
3150 5283 5.996669 TGCTCTATCACATGCATGTTTAG 57.003 39.130 29.48 27.68 39.39 1.85
3155 5288 4.127907 AGAGTTGCTCTATCACATGCATG 58.872 43.478 25.09 25.09 39.28 4.06
3165 5298 6.374417 TTTTCTTGGGTAGAGTTGCTCTAT 57.626 37.500 8.83 0.00 43.69 1.98
3193 5327 3.806157 GCCGGTTAGAGAGAAAAACCAGT 60.806 47.826 1.90 0.00 42.31 4.00
3214 5348 0.743097 CTTGGGCTTTGGCTAGATGC 59.257 55.000 0.00 0.00 41.94 3.91
3220 5354 1.793414 AGTTTTCTTGGGCTTTGGCT 58.207 45.000 0.00 0.00 38.73 4.75
3224 5358 5.661312 ACTCCTTTAAGTTTTCTTGGGCTTT 59.339 36.000 0.00 0.00 40.70 3.51
3225 5359 5.208890 ACTCCTTTAAGTTTTCTTGGGCTT 58.791 37.500 0.00 0.00 40.70 4.35
3227 5361 6.644248 TTACTCCTTTAAGTTTTCTTGGGC 57.356 37.500 0.00 0.00 40.70 5.36
3274 5408 2.540383 TCCATAGCAAGTCCAGACACT 58.460 47.619 0.00 0.00 0.00 3.55
3282 5416 5.886960 AAAGTGAACATCCATAGCAAGTC 57.113 39.130 0.00 0.00 0.00 3.01
3326 5460 4.753107 CCAAGTTTTAGAACTAGTTCGGCA 59.247 41.667 25.92 14.75 45.18 5.69
3381 5515 4.793731 CAGCACACTACACGTCTAATACAG 59.206 45.833 0.00 0.00 0.00 2.74
3382 5516 4.456566 TCAGCACACTACACGTCTAATACA 59.543 41.667 0.00 0.00 0.00 2.29
3383 5517 4.978186 TCAGCACACTACACGTCTAATAC 58.022 43.478 0.00 0.00 0.00 1.89
3384 5518 5.124936 ACATCAGCACACTACACGTCTAATA 59.875 40.000 0.00 0.00 0.00 0.98
3478 5613 2.488153 GGACCACTTGTCATAAAGGCAC 59.512 50.000 0.00 0.00 46.38 5.01
3481 5616 3.433306 TGGGACCACTTGTCATAAAGG 57.567 47.619 0.00 0.00 46.38 3.11
3549 5684 2.164624 AGGTCATGTGCTCGTCTCTAAC 59.835 50.000 0.00 0.00 0.00 2.34
3551 5686 1.745653 CAGGTCATGTGCTCGTCTCTA 59.254 52.381 0.00 0.00 0.00 2.43
3593 5728 2.203001 TGTGTGGTGCAGTGGTCG 60.203 61.111 0.00 0.00 0.00 4.79
3612 5747 0.663153 GCCAAAGGTGCGATCATACC 59.337 55.000 7.18 7.18 37.23 2.73
3620 5755 0.817013 ATGTAATGGCCAAAGGTGCG 59.183 50.000 10.96 0.00 0.00 5.34
3624 5759 9.426837 CATTCATTAATATGTAATGGCCAAAGG 57.573 33.333 10.96 0.00 36.03 3.11
3651 5796 4.524328 AGCACCAGAATCCCTTTTGTTTAG 59.476 41.667 0.00 0.00 0.00 1.85
3661 5806 2.223572 CGCATTTAAGCACCAGAATCCC 60.224 50.000 0.00 0.00 0.00 3.85
3720 5893 8.833231 TTACAGACCTTTTACATTTCTCTCTG 57.167 34.615 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.