Multiple sequence alignment - TraesCS4B01G372500

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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 TraesCS4B01G372500 chr4B 100.000 3119 0 0 1 3119 657458448 657461566 0.000000e+00 5760.0
1 TraesCS4B01G372500 chr4B 88.435 588 67 1 2531 3118 617432568 617431982 0.000000e+00 708.0
2 TraesCS4B01G372500 chr5A 96.917 1038 31 1 403 1439 698231067 698230030 0.000000e+00 1738.0
3 TraesCS4B01G372500 chr5A 79.268 1722 268 44 616 2271 698218073 698216375 0.000000e+00 1120.0
4 TraesCS4B01G372500 chr5A 92.575 633 31 4 1867 2495 698229995 698229375 0.000000e+00 894.0
5 TraesCS4B01G372500 chr5A 73.282 1295 238 69 616 1848 698319116 698317868 2.940000e-100 375.0
6 TraesCS4B01G372500 chr5A 89.809 157 13 2 2270 2424 653299446 653299601 6.820000e-47 198.0
7 TraesCS4B01G372500 chr7D 79.809 1570 233 52 620 2138 31369571 31368035 0.000000e+00 1066.0
8 TraesCS4B01G372500 chr7D 85.625 160 21 2 2013 2171 31366298 31366140 1.920000e-37 167.0
9 TraesCS4B01G372500 chr1B 93.980 598 34 2 2522 3118 642124130 642124726 0.000000e+00 904.0
10 TraesCS4B01G372500 chr1B 95.291 361 13 2 1 357 19078679 19078319 1.260000e-158 569.0
11 TraesCS4B01G372500 chr1B 95.304 362 12 4 1 357 163082921 163082560 1.260000e-158 569.0
12 TraesCS4B01G372500 chr1B 95.291 361 13 2 1 357 313489915 313489555 1.260000e-158 569.0
13 TraesCS4B01G372500 chr1B 89.873 158 12 3 2270 2425 314565693 314565538 1.900000e-47 200.0
14 TraesCS4B01G372500 chr1B 87.931 174 14 6 2256 2424 436688980 436689151 6.820000e-47 198.0
15 TraesCS4B01G372500 chr6A 93.909 591 35 1 2529 3119 539642071 539641482 0.000000e+00 891.0
16 TraesCS4B01G372500 chr7A 93.570 591 37 1 2529 3119 491259019 491258430 0.000000e+00 880.0
17 TraesCS4B01G372500 chr7A 88.796 598 66 1 2522 3119 606178344 606177748 0.000000e+00 732.0
18 TraesCS4B01G372500 chr2B 90.774 607 53 3 2513 3119 180548388 180548991 0.000000e+00 808.0
19 TraesCS4B01G372500 chr2B 95.556 360 13 2 1 357 119272277 119272636 9.700000e-160 573.0
20 TraesCS4B01G372500 chr6D 90.756 595 52 3 2525 3119 451934302 451933711 0.000000e+00 791.0
21 TraesCS4B01G372500 chr3B 90.017 591 58 1 2529 3119 371704741 371705330 0.000000e+00 763.0
22 TraesCS4B01G372500 chr3B 71.264 522 129 18 1478 1984 17315435 17314920 2.540000e-21 113.0
23 TraesCS4B01G372500 chr1D 85.953 598 82 2 2523 3119 343365600 343366196 3.390000e-179 638.0
24 TraesCS4B01G372500 chr6B 95.568 361 12 2 1 357 491632714 491632354 2.700000e-160 575.0
25 TraesCS4B01G372500 chr2A 95.304 362 13 2 1 358 732164251 732163890 3.490000e-159 571.0
26 TraesCS4B01G372500 chr2A 95.291 361 13 2 1 357 82188538 82188178 1.260000e-158 569.0
27 TraesCS4B01G372500 chr2A 90.625 160 11 4 2270 2426 240465868 240466026 3.150000e-50 209.0
28 TraesCS4B01G372500 chr5B 95.291 361 13 2 1 357 642056168 642055808 1.260000e-158 569.0
29 TraesCS4B01G372500 chr5B 95.291 361 13 2 1 357 709520583 709520943 1.260000e-158 569.0
30 TraesCS4B01G372500 chr5B 77.379 557 105 15 1555 2105 43894600 43894059 8.400000e-81 311.0
31 TraesCS4B01G372500 chr5B 75.000 732 126 42 1143 1836 43896883 43896171 5.090000e-73 285.0
32 TraesCS4B01G372500 chr5B 81.620 321 53 5 1478 1792 43899264 43898944 8.580000e-66 261.0
33 TraesCS4B01G372500 chr5B 80.386 311 49 10 567 871 43900162 43899858 3.130000e-55 226.0
34 TraesCS4B01G372500 chr5B 84.000 75 12 0 924 998 43899835 43899761 4.310000e-09 73.1
35 TraesCS4B01G372500 chr4D 83.013 624 90 11 1508 2124 509373762 509373148 4.550000e-153 551.0
36 TraesCS4B01G372500 chr4D 80.028 716 111 13 1577 2271 509383881 509383177 4.640000e-138 501.0
37 TraesCS4B01G372500 chr4D 80.216 556 89 12 1021 1573 509384896 509384359 6.270000e-107 398.0
38 TraesCS4B01G372500 chr4D 74.852 843 154 48 1033 1837 509380212 509379390 2.320000e-86 329.0
39 TraesCS4B01G372500 chr4D 77.920 548 78 24 468 999 509376124 509375604 5.060000e-78 302.0
40 TraesCS4B01G372500 chr4D 80.528 303 48 8 567 859 509380681 509380380 4.050000e-54 222.0
41 TraesCS4B01G372500 chr4D 89.809 157 13 3 2270 2424 75266754 75266909 6.820000e-47 198.0
42 TraesCS4B01G372500 chr4D 89.809 157 12 2 2270 2424 508222910 508222756 6.820000e-47 198.0
43 TraesCS4B01G372500 chr4A 84.932 219 33 0 1743 1961 697333344 697333126 4.050000e-54 222.0
44 TraesCS4B01G372500 chr4A 79.476 229 37 7 1953 2172 697331848 697331621 1.500000e-33 154.0
45 TraesCS4B01G372500 chr3D 87.135 171 19 3 2270 2438 612268604 612268435 1.140000e-44 191.0
46 TraesCS4B01G372500 chr3D 88.608 158 15 2 2270 2425 537154708 537154864 4.110000e-44 189.0


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 TraesCS4B01G372500 chr4B 657458448 657461566 3118 False 5760.000000 5760 100.000000 1 3119 1 chr4B.!!$F1 3118
1 TraesCS4B01G372500 chr4B 617431982 617432568 586 True 708.000000 708 88.435000 2531 3118 1 chr4B.!!$R1 587
2 TraesCS4B01G372500 chr5A 698229375 698231067 1692 True 1316.000000 1738 94.746000 403 2495 2 chr5A.!!$R3 2092
3 TraesCS4B01G372500 chr5A 698216375 698218073 1698 True 1120.000000 1120 79.268000 616 2271 1 chr5A.!!$R1 1655
4 TraesCS4B01G372500 chr5A 698317868 698319116 1248 True 375.000000 375 73.282000 616 1848 1 chr5A.!!$R2 1232
5 TraesCS4B01G372500 chr7D 31366140 31369571 3431 True 616.500000 1066 82.717000 620 2171 2 chr7D.!!$R1 1551
6 TraesCS4B01G372500 chr1B 642124130 642124726 596 False 904.000000 904 93.980000 2522 3118 1 chr1B.!!$F2 596
7 TraesCS4B01G372500 chr6A 539641482 539642071 589 True 891.000000 891 93.909000 2529 3119 1 chr6A.!!$R1 590
8 TraesCS4B01G372500 chr7A 491258430 491259019 589 True 880.000000 880 93.570000 2529 3119 1 chr7A.!!$R1 590
9 TraesCS4B01G372500 chr7A 606177748 606178344 596 True 732.000000 732 88.796000 2522 3119 1 chr7A.!!$R2 597
10 TraesCS4B01G372500 chr2B 180548388 180548991 603 False 808.000000 808 90.774000 2513 3119 1 chr2B.!!$F2 606
11 TraesCS4B01G372500 chr6D 451933711 451934302 591 True 791.000000 791 90.756000 2525 3119 1 chr6D.!!$R1 594
12 TraesCS4B01G372500 chr3B 371704741 371705330 589 False 763.000000 763 90.017000 2529 3119 1 chr3B.!!$F1 590
13 TraesCS4B01G372500 chr1D 343365600 343366196 596 False 638.000000 638 85.953000 2523 3119 1 chr1D.!!$F1 596
14 TraesCS4B01G372500 chr5B 43894059 43900162 6103 True 231.220000 311 79.677000 567 2105 5 chr5B.!!$R2 1538
15 TraesCS4B01G372500 chr4D 509373148 509384896 11748 True 383.833333 551 79.426167 468 2271 6 chr4D.!!$R2 1803

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
844 9172 1.227853 ACGGTCAACACCAAGCTCC 60.228 57.895 0.0 0.0 44.02 4.70 F
1264 10939 1.072266 AGGTAATGTTGCAGGGGACA 58.928 50.000 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1704 11501 0.253044 AGACCCATGGACCATGAACG 59.747 55.000 32.16 21.07 43.81 3.95 R
2799 19075 1.139853 AGATTCCGATGCAGAACCCTC 59.860 52.381 0.00 0.00 0.00 4.30 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
19 20 2.914695 TAGTTACCACCACTTGCGTT 57.085 45.000 0.00 0.00 0.00 4.84
22 23 2.098443 AGTTACCACCACTTGCGTTTTG 59.902 45.455 0.00 0.00 0.00 2.44
23 24 1.752683 TACCACCACTTGCGTTTTGT 58.247 45.000 0.00 0.00 0.00 2.83
26 27 2.034053 ACCACCACTTGCGTTTTGTATG 59.966 45.455 0.00 0.00 0.00 2.39
27 28 2.034053 CCACCACTTGCGTTTTGTATGT 59.966 45.455 0.00 0.00 0.00 2.29
28 29 3.490078 CCACCACTTGCGTTTTGTATGTT 60.490 43.478 0.00 0.00 0.00 2.71
29 30 3.485378 CACCACTTGCGTTTTGTATGTTG 59.515 43.478 0.00 0.00 0.00 3.33
30 31 3.129638 ACCACTTGCGTTTTGTATGTTGT 59.870 39.130 0.00 0.00 0.00 3.32
31 32 4.335874 ACCACTTGCGTTTTGTATGTTGTA 59.664 37.500 0.00 0.00 0.00 2.41
32 33 4.673311 CCACTTGCGTTTTGTATGTTGTAC 59.327 41.667 0.00 0.00 0.00 2.90
33 34 4.374538 CACTTGCGTTTTGTATGTTGTACG 59.625 41.667 0.00 0.00 0.00 3.67
34 35 4.034279 ACTTGCGTTTTGTATGTTGTACGT 59.966 37.500 0.00 0.00 0.00 3.57
35 36 5.233902 ACTTGCGTTTTGTATGTTGTACGTA 59.766 36.000 0.00 0.00 0.00 3.57
36 37 5.253334 TGCGTTTTGTATGTTGTACGTAG 57.747 39.130 0.00 0.00 0.00 3.51
38 39 5.917447 TGCGTTTTGTATGTTGTACGTAGTA 59.083 36.000 0.00 0.00 45.11 1.82
52 53 4.771590 ACGTAGTATCTGTCAAAACCGA 57.228 40.909 0.00 0.00 41.94 4.69
53 54 4.730657 ACGTAGTATCTGTCAAAACCGAG 58.269 43.478 0.00 0.00 41.94 4.63
54 55 4.456911 ACGTAGTATCTGTCAAAACCGAGA 59.543 41.667 0.00 0.00 41.94 4.04
55 56 5.048504 ACGTAGTATCTGTCAAAACCGAGAA 60.049 40.000 0.00 0.00 41.94 2.87
56 57 6.034591 CGTAGTATCTGTCAAAACCGAGAAT 58.965 40.000 0.00 0.00 0.00 2.40
61 62 4.951254 TCTGTCAAAACCGAGAATGTGTA 58.049 39.130 0.00 0.00 0.00 2.90
63 64 3.491639 TGTCAAAACCGAGAATGTGTACG 59.508 43.478 0.00 0.00 0.00 3.67
64 65 3.492011 GTCAAAACCGAGAATGTGTACGT 59.508 43.478 0.00 0.00 0.00 3.57
65 66 3.491639 TCAAAACCGAGAATGTGTACGTG 59.508 43.478 0.00 0.00 0.00 4.49
66 67 2.806608 AACCGAGAATGTGTACGTGT 57.193 45.000 0.00 0.00 0.00 4.49
67 68 3.921119 AACCGAGAATGTGTACGTGTA 57.079 42.857 0.00 0.00 0.00 2.90
68 69 3.482722 ACCGAGAATGTGTACGTGTAG 57.517 47.619 0.00 0.00 0.00 2.74
70 71 4.002982 ACCGAGAATGTGTACGTGTAGTA 58.997 43.478 0.00 0.00 0.00 1.82
71 72 4.637534 ACCGAGAATGTGTACGTGTAGTAT 59.362 41.667 0.00 0.00 37.69 2.12
72 73 4.968181 CCGAGAATGTGTACGTGTAGTATG 59.032 45.833 0.00 0.00 37.69 2.39
73 74 5.448225 CCGAGAATGTGTACGTGTAGTATGT 60.448 44.000 0.00 0.00 37.69 2.29
74 75 6.238184 CCGAGAATGTGTACGTGTAGTATGTA 60.238 42.308 0.00 0.00 37.69 2.29
75 76 6.844779 CGAGAATGTGTACGTGTAGTATGTAG 59.155 42.308 0.00 0.00 37.69 2.74
76 77 7.465111 CGAGAATGTGTACGTGTAGTATGTAGT 60.465 40.741 0.00 0.00 37.69 2.73
77 78 8.722480 AGAATGTGTACGTGTAGTATGTAGTA 57.278 34.615 0.00 0.00 37.69 1.82
78 79 9.334947 AGAATGTGTACGTGTAGTATGTAGTAT 57.665 33.333 0.00 0.00 37.69 2.12
195 196 9.646427 TTCACAAATATAACAAAAACTATGGGC 57.354 29.630 0.00 0.00 0.00 5.36
197 198 9.301153 CACAAATATAACAAAAACTATGGGCTC 57.699 33.333 0.00 0.00 0.00 4.70
198 199 9.030452 ACAAATATAACAAAAACTATGGGCTCA 57.970 29.630 0.00 0.00 0.00 4.26
203 204 5.520376 ACAAAAACTATGGGCTCATATGC 57.480 39.130 6.77 0.00 35.53 3.14
204 205 4.955450 ACAAAAACTATGGGCTCATATGCA 59.045 37.500 6.77 0.00 35.53 3.96
206 207 6.098695 ACAAAAACTATGGGCTCATATGCAAT 59.901 34.615 6.77 0.00 35.53 3.56
207 208 6.736110 AAAACTATGGGCTCATATGCAATT 57.264 33.333 6.77 0.00 35.53 2.32
208 209 6.736110 AAACTATGGGCTCATATGCAATTT 57.264 33.333 6.77 1.06 35.53 1.82
209 210 6.736110 AACTATGGGCTCATATGCAATTTT 57.264 33.333 6.77 0.00 35.53 1.82
306 307 9.928618 AGTACCACATGCTAGTATATGAGATAT 57.071 33.333 0.06 0.00 0.00 1.63
307 308 9.958234 GTACCACATGCTAGTATATGAGATATG 57.042 37.037 0.06 0.00 0.00 1.78
308 309 8.601047 ACCACATGCTAGTATATGAGATATGT 57.399 34.615 0.06 0.00 0.00 2.29
309 310 8.473219 ACCACATGCTAGTATATGAGATATGTG 58.527 37.037 0.06 17.04 38.35 3.21
310 311 7.924947 CCACATGCTAGTATATGAGATATGTGG 59.075 40.741 22.27 22.27 44.41 4.17
311 312 7.924947 CACATGCTAGTATATGAGATATGTGGG 59.075 40.741 16.64 0.00 36.81 4.61
312 313 7.070447 ACATGCTAGTATATGAGATATGTGGGG 59.930 40.741 9.68 0.00 0.00 4.96
313 314 6.503041 TGCTAGTATATGAGATATGTGGGGT 58.497 40.000 0.00 0.00 0.00 4.95
314 315 7.648770 TGCTAGTATATGAGATATGTGGGGTA 58.351 38.462 0.00 0.00 0.00 3.69
319 320 9.476928 AGTATATGAGATATGTGGGGTAACTAC 57.523 37.037 0.00 0.00 0.00 2.73
320 321 7.735326 ATATGAGATATGTGGGGTAACTACC 57.265 40.000 0.00 0.00 45.71 3.18
343 344 3.412386 CCGGATGGTAGGATGGATTTTC 58.588 50.000 0.00 0.00 0.00 2.29
344 345 3.412386 CGGATGGTAGGATGGATTTTCC 58.588 50.000 0.00 0.00 36.96 3.13
346 347 3.399305 GGATGGTAGGATGGATTTTCCCT 59.601 47.826 0.00 0.00 35.03 4.20
347 348 4.601857 GGATGGTAGGATGGATTTTCCCTA 59.398 45.833 0.00 0.00 35.03 3.53
348 349 5.254032 GGATGGTAGGATGGATTTTCCCTAT 59.746 44.000 0.00 0.00 35.03 2.57
350 351 7.129504 GGATGGTAGGATGGATTTTCCCTATAT 59.870 40.741 0.00 0.00 35.03 0.86
351 352 9.225682 GATGGTAGGATGGATTTTCCCTATATA 57.774 37.037 0.00 0.00 35.03 0.86
381 382 9.628746 ATTCCGTACACAATAAAAATAACAACC 57.371 29.630 0.00 0.00 0.00 3.77
382 383 8.162878 TCCGTACACAATAAAAATAACAACCA 57.837 30.769 0.00 0.00 0.00 3.67
383 384 8.074972 TCCGTACACAATAAAAATAACAACCAC 58.925 33.333 0.00 0.00 0.00 4.16
384 385 7.861372 CCGTACACAATAAAAATAACAACCACA 59.139 33.333 0.00 0.00 0.00 4.17
385 386 8.897809 CGTACACAATAAAAATAACAACCACAG 58.102 33.333 0.00 0.00 0.00 3.66
388 389 9.959749 ACACAATAAAAATAACAACCACAGTAG 57.040 29.630 0.00 0.00 0.00 2.57
389 390 9.405587 CACAATAAAAATAACAACCACAGTAGG 57.594 33.333 0.00 0.00 0.00 3.18
390 391 8.085909 ACAATAAAAATAACAACCACAGTAGGC 58.914 33.333 0.00 0.00 0.00 3.93
392 393 6.664428 AAAAATAACAACCACAGTAGGCAT 57.336 33.333 0.00 0.00 0.00 4.40
393 394 5.643379 AAATAACAACCACAGTAGGCATG 57.357 39.130 0.00 0.00 0.00 4.06
395 396 2.949177 ACAACCACAGTAGGCATGAA 57.051 45.000 0.00 0.00 0.00 2.57
396 397 3.439857 ACAACCACAGTAGGCATGAAT 57.560 42.857 0.00 0.00 0.00 2.57
397 398 3.347216 ACAACCACAGTAGGCATGAATC 58.653 45.455 0.00 0.00 0.00 2.52
399 400 2.200081 ACCACAGTAGGCATGAATCCT 58.800 47.619 0.00 0.00 37.72 3.24
400 401 2.092753 ACCACAGTAGGCATGAATCCTG 60.093 50.000 0.00 0.00 35.21 3.86
432 433 7.826260 ATAAAAACAACAACAAACTGGACTG 57.174 32.000 0.00 0.00 0.00 3.51
810 9129 2.092882 GTTCCCGGAGTTCTTCGCG 61.093 63.158 0.73 0.00 0.00 5.87
811 9130 2.567497 TTCCCGGAGTTCTTCGCGT 61.567 57.895 0.73 0.00 0.00 6.01
844 9172 1.227853 ACGGTCAACACCAAGCTCC 60.228 57.895 0.00 0.00 44.02 4.70
895 9226 4.511246 AGATACGCCCGGGGTCGA 62.511 66.667 28.34 16.26 39.00 4.20
900 9231 4.587189 CGCCCGGGGTCGAGATTC 62.587 72.222 25.28 0.00 39.00 2.52
931 9262 1.557443 CTTCGTTCGTGACCACTGCC 61.557 60.000 0.00 0.00 0.00 4.85
1264 10939 1.072266 AGGTAATGTTGCAGGGGACA 58.928 50.000 0.00 0.00 0.00 4.02
1439 11174 7.093945 CCACCACTAGCTTGTTTTACCATAATT 60.094 37.037 0.00 0.00 0.00 1.40
1463 11219 5.932619 AAGGTTCATTGGGCTTATTTACC 57.067 39.130 0.00 0.00 0.00 2.85
1466 11227 5.598417 AGGTTCATTGGGCTTATTTACCATC 59.402 40.000 0.00 0.00 33.63 3.51
1472 11233 8.664992 TCATTGGGCTTATTTACCATCTATGTA 58.335 33.333 0.00 0.00 33.63 2.29
1474 11235 8.685838 TTGGGCTTATTTACCATCTATGTAAC 57.314 34.615 0.00 0.00 33.63 2.50
1525 11287 2.993899 GAGGACAAGTACCGTGTGATTG 59.006 50.000 4.60 0.00 0.00 2.67
1528 11290 3.432252 GGACAAGTACCGTGTGATTGAAG 59.568 47.826 4.60 0.00 0.00 3.02
1545 11332 2.483877 TGAAGCACCAATCGACATGAAC 59.516 45.455 0.00 0.00 0.00 3.18
1546 11333 1.078709 AGCACCAATCGACATGAACG 58.921 50.000 0.00 5.16 0.00 3.95
1704 11501 2.512301 GCGAGCGTCAGATCAGCAC 61.512 63.158 0.00 0.00 34.36 4.40
1844 16222 7.970614 TGACGATGTAGATGACAATATAGATGC 59.029 37.037 0.00 0.00 42.78 3.91
1846 16224 7.148239 ACGATGTAGATGACAATATAGATGCGA 60.148 37.037 0.00 0.00 42.78 5.10
1856 16234 1.800805 ATAGATGCGATTCAAGGGCG 58.199 50.000 0.00 0.00 0.00 6.13
1862 16240 1.153823 CGATTCAAGGGCGTCGTCT 60.154 57.895 0.00 0.00 0.00 4.18
1864 16242 1.140407 GATTCAAGGGCGTCGTCTCG 61.140 60.000 0.00 0.00 0.00 4.04
1865 16243 2.558554 ATTCAAGGGCGTCGTCTCGG 62.559 60.000 0.00 0.00 0.00 4.63
1875 16253 1.332686 CGTCGTCTCGGTGGATATGAA 59.667 52.381 0.00 0.00 0.00 2.57
1925 16303 3.977134 TCTCTTCTTGAGCAGCTTCAT 57.023 42.857 0.00 0.00 42.38 2.57
2085 16467 1.083489 CGTACACGCCATGTTGGATT 58.917 50.000 0.00 0.00 40.96 3.01
2281 18551 9.832445 AATTAAGCATCTATCTCCGTTTCTAAA 57.168 29.630 0.00 0.00 0.00 1.85
2364 18634 8.654230 TGAGTATAGATTCACTCATTTTGCTC 57.346 34.615 0.44 0.00 44.70 4.26
2365 18635 7.712639 TGAGTATAGATTCACTCATTTTGCTCC 59.287 37.037 0.44 0.00 44.70 4.70
2366 18636 5.998454 ATAGATTCACTCATTTTGCTCCG 57.002 39.130 0.00 0.00 0.00 4.63
2367 18637 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2368 18638 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2369 18639 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2370 18640 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2371 18641 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2372 18642 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2373 18643 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2389 18659 6.921857 CCGTATGTAGTCCGTATTTGAATCTT 59.078 38.462 0.00 0.00 0.00 2.40
2391 18661 8.814235 CGTATGTAGTCCGTATTTGAATCTTTT 58.186 33.333 0.00 0.00 0.00 2.27
2441 18714 8.577048 AAGTAGTAGCTAGTATGAACAAGTCA 57.423 34.615 11.44 0.00 41.67 3.41
2495 18768 5.971763 ACTGGCTATTAACTCTCAACTGAG 58.028 41.667 0.00 0.00 43.36 3.35
2508 18781 6.364945 TCTCAACTGAGAGATGTACGTATG 57.635 41.667 5.29 0.00 45.48 2.39
2509 18782 5.880887 TCTCAACTGAGAGATGTACGTATGT 59.119 40.000 5.29 0.00 45.48 2.29
2510 18783 5.880341 TCAACTGAGAGATGTACGTATGTG 58.120 41.667 0.00 0.00 0.00 3.21
2511 18784 5.646360 TCAACTGAGAGATGTACGTATGTGA 59.354 40.000 0.00 0.00 0.00 3.58
2512 18785 5.487153 ACTGAGAGATGTACGTATGTGAC 57.513 43.478 0.00 0.00 0.00 3.67
2572 18847 0.037046 TTAGGGTTTCGAGCGGAACC 60.037 55.000 21.83 21.83 33.42 3.62
2575 18850 1.301479 GGTTTCGAGCGGAACCTGT 60.301 57.895 22.46 0.00 33.42 4.00
2718 18993 2.612604 GAAGAGAAGCTCGGGAAACTC 58.387 52.381 0.00 0.00 35.36 3.01
2799 19075 1.823899 GAAGTGGCTATTGGCGGGG 60.824 63.158 0.00 0.00 42.94 5.73
2892 19169 1.196012 GGGGACTCCAGTTTCGATCT 58.804 55.000 0.00 0.00 35.00 2.75
2905 19182 5.068460 CAGTTTCGATCTATGGGAGAGAACT 59.932 44.000 0.00 0.00 37.70 3.01
2916 19193 1.433534 GAGAGAACTCCTTTGTGGCG 58.566 55.000 0.00 0.00 37.19 5.69
2931 19208 1.548269 GTGGCGGAATTTGAATCCCAA 59.452 47.619 0.00 0.00 33.13 4.12
2940 19217 1.087202 TTGAATCCCAACGCGATCGG 61.087 55.000 15.93 2.29 40.69 4.18
2964 19241 1.274703 GGATCTGGGAAGGCTCACCA 61.275 60.000 9.44 9.44 39.06 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.744137 ACTACGTACAACATACAAAACGCA 59.256 37.500 0.00 0.00 33.87 5.24
15 16 5.254669 ACTACGTACAACATACAAAACGC 57.745 39.130 0.00 0.00 33.87 4.84
16 17 8.309019 CAGATACTACGTACAACATACAAAACG 58.691 37.037 0.00 0.00 36.48 3.60
18 19 9.345517 GACAGATACTACGTACAACATACAAAA 57.654 33.333 0.00 0.00 0.00 2.44
19 20 8.513774 TGACAGATACTACGTACAACATACAAA 58.486 33.333 0.00 0.00 0.00 2.83
22 23 8.900511 TTTGACAGATACTACGTACAACATAC 57.099 34.615 0.00 0.00 0.00 2.39
23 24 9.345517 GTTTTGACAGATACTACGTACAACATA 57.654 33.333 0.00 0.00 0.00 2.29
26 27 6.183359 CGGTTTTGACAGATACTACGTACAAC 60.183 42.308 0.00 0.00 0.00 3.32
27 28 5.858049 CGGTTTTGACAGATACTACGTACAA 59.142 40.000 0.00 0.00 0.00 2.41
28 29 5.181056 TCGGTTTTGACAGATACTACGTACA 59.819 40.000 0.00 0.00 0.00 2.90
29 30 5.631026 TCGGTTTTGACAGATACTACGTAC 58.369 41.667 0.00 0.00 0.00 3.67
30 31 5.643348 TCTCGGTTTTGACAGATACTACGTA 59.357 40.000 0.00 0.00 0.00 3.57
31 32 4.456911 TCTCGGTTTTGACAGATACTACGT 59.543 41.667 0.00 0.00 0.00 3.57
32 33 4.978186 TCTCGGTTTTGACAGATACTACG 58.022 43.478 0.00 0.00 0.00 3.51
33 34 6.812160 ACATTCTCGGTTTTGACAGATACTAC 59.188 38.462 0.00 0.00 0.00 2.73
34 35 6.811665 CACATTCTCGGTTTTGACAGATACTA 59.188 38.462 0.00 0.00 0.00 1.82
35 36 5.639506 CACATTCTCGGTTTTGACAGATACT 59.360 40.000 0.00 0.00 0.00 2.12
36 37 5.408604 ACACATTCTCGGTTTTGACAGATAC 59.591 40.000 0.00 0.00 0.00 2.24
37 38 5.547465 ACACATTCTCGGTTTTGACAGATA 58.453 37.500 0.00 0.00 0.00 1.98
38 39 4.389374 ACACATTCTCGGTTTTGACAGAT 58.611 39.130 0.00 0.00 0.00 2.90
39 40 3.804036 ACACATTCTCGGTTTTGACAGA 58.196 40.909 0.00 0.00 0.00 3.41
41 42 3.491639 CGTACACATTCTCGGTTTTGACA 59.508 43.478 0.00 0.00 0.00 3.58
42 43 3.492011 ACGTACACATTCTCGGTTTTGAC 59.508 43.478 0.00 0.00 0.00 3.18
43 44 3.491639 CACGTACACATTCTCGGTTTTGA 59.508 43.478 0.00 0.00 0.00 2.69
44 45 3.246699 ACACGTACACATTCTCGGTTTTG 59.753 43.478 0.00 0.00 0.00 2.44
46 47 3.102052 ACACGTACACATTCTCGGTTT 57.898 42.857 0.00 0.00 0.00 3.27
47 48 2.806608 ACACGTACACATTCTCGGTT 57.193 45.000 0.00 0.00 0.00 4.44
49 50 3.482722 ACTACACGTACACATTCTCGG 57.517 47.619 0.00 0.00 0.00 4.63
50 51 5.566623 ACATACTACACGTACACATTCTCG 58.433 41.667 0.00 0.00 0.00 4.04
51 52 7.692088 ACTACATACTACACGTACACATTCTC 58.308 38.462 0.00 0.00 0.00 2.87
52 53 7.621428 ACTACATACTACACGTACACATTCT 57.379 36.000 0.00 0.00 0.00 2.40
169 170 9.646427 GCCCATAGTTTTTGTTATATTTGTGAA 57.354 29.630 0.00 0.00 0.00 3.18
170 171 9.030452 AGCCCATAGTTTTTGTTATATTTGTGA 57.970 29.630 0.00 0.00 0.00 3.58
171 172 9.301153 GAGCCCATAGTTTTTGTTATATTTGTG 57.699 33.333 0.00 0.00 0.00 3.33
172 173 9.030452 TGAGCCCATAGTTTTTGTTATATTTGT 57.970 29.630 0.00 0.00 0.00 2.83
178 179 7.287466 TGCATATGAGCCCATAGTTTTTGTTAT 59.713 33.333 6.97 0.00 38.53 1.89
181 182 4.955450 TGCATATGAGCCCATAGTTTTTGT 59.045 37.500 6.97 0.00 38.53 2.83
185 186 6.736110 AAATTGCATATGAGCCCATAGTTT 57.264 33.333 6.97 0.00 38.53 2.66
186 187 6.736110 AAAATTGCATATGAGCCCATAGTT 57.264 33.333 6.97 0.00 38.53 2.24
187 188 6.736110 AAAAATTGCATATGAGCCCATAGT 57.264 33.333 6.97 0.00 38.53 2.12
280 281 9.928618 ATATCTCATATACTAGCATGTGGTACT 57.071 33.333 0.34 0.00 0.00 2.73
282 283 9.700831 ACATATCTCATATACTAGCATGTGGTA 57.299 33.333 0.34 0.17 0.00 3.25
283 284 8.473219 CACATATCTCATATACTAGCATGTGGT 58.527 37.037 14.90 0.00 37.92 4.16
287 288 7.070447 ACCCCACATATCTCATATACTAGCATG 59.930 40.741 0.00 0.00 0.00 4.06
291 292 9.702253 AGTTACCCCACATATCTCATATACTAG 57.298 37.037 0.00 0.00 0.00 2.57
293 294 9.476928 GTAGTTACCCCACATATCTCATATACT 57.523 37.037 0.00 0.00 0.00 2.12
294 295 8.693625 GGTAGTTACCCCACATATCTCATATAC 58.306 40.741 0.00 0.00 40.53 1.47
296 297 7.253421 TGGTAGTTACCCCACATATCTCATAT 58.747 38.462 5.90 0.00 45.87 1.78
298 299 5.473273 TGGTAGTTACCCCACATATCTCAT 58.527 41.667 5.90 0.00 45.87 2.90
299 300 4.886163 TGGTAGTTACCCCACATATCTCA 58.114 43.478 5.90 0.00 45.87 3.27
308 309 0.043032 ATCCGGTGGTAGTTACCCCA 59.957 55.000 0.00 0.00 45.87 4.96
309 310 0.466963 CATCCGGTGGTAGTTACCCC 59.533 60.000 0.00 5.97 45.87 4.95
310 311 0.466963 CCATCCGGTGGTAGTTACCC 59.533 60.000 13.21 0.00 45.87 3.69
321 322 6.278687 GGAAAATCCATCCTACCATCCGGT 62.279 50.000 0.00 0.00 42.28 5.28
322 323 3.412386 GAAAATCCATCCTACCATCCGG 58.588 50.000 0.00 0.00 38.77 5.14
323 324 3.412386 GGAAAATCCATCCTACCATCCG 58.588 50.000 0.00 0.00 36.28 4.18
325 326 4.731313 AGGGAAAATCCATCCTACCATC 57.269 45.455 0.00 0.00 38.64 3.51
355 356 9.628746 GGTTGTTATTTTTATTGTGTACGGAAT 57.371 29.630 0.00 0.00 0.00 3.01
357 358 8.074972 GTGGTTGTTATTTTTATTGTGTACGGA 58.925 33.333 0.00 0.00 0.00 4.69
359 360 8.783999 TGTGGTTGTTATTTTTATTGTGTACG 57.216 30.769 0.00 0.00 0.00 3.67
360 361 9.738832 ACTGTGGTTGTTATTTTTATTGTGTAC 57.261 29.630 0.00 0.00 0.00 2.90
363 364 9.405587 CCTACTGTGGTTGTTATTTTTATTGTG 57.594 33.333 0.00 0.00 0.00 3.33
364 365 8.085909 GCCTACTGTGGTTGTTATTTTTATTGT 58.914 33.333 0.00 0.00 0.00 2.71
367 368 7.768807 TGCCTACTGTGGTTGTTATTTTTAT 57.231 32.000 0.00 0.00 0.00 1.40
369 370 6.266558 TCATGCCTACTGTGGTTGTTATTTTT 59.733 34.615 0.00 0.00 0.00 1.94
370 371 5.772672 TCATGCCTACTGTGGTTGTTATTTT 59.227 36.000 0.00 0.00 0.00 1.82
372 373 4.917385 TCATGCCTACTGTGGTTGTTATT 58.083 39.130 0.00 0.00 0.00 1.40
373 374 4.568072 TCATGCCTACTGTGGTTGTTAT 57.432 40.909 0.00 0.00 0.00 1.89
374 375 4.359434 TTCATGCCTACTGTGGTTGTTA 57.641 40.909 0.00 0.00 0.00 2.41
375 376 2.949177 TCATGCCTACTGTGGTTGTT 57.051 45.000 0.00 0.00 0.00 2.83
376 377 2.949177 TTCATGCCTACTGTGGTTGT 57.051 45.000 0.00 0.00 0.00 3.32
377 378 2.684881 GGATTCATGCCTACTGTGGTTG 59.315 50.000 0.00 0.00 0.00 3.77
378 379 2.578021 AGGATTCATGCCTACTGTGGTT 59.422 45.455 0.00 0.00 32.92 3.67
379 380 2.092753 CAGGATTCATGCCTACTGTGGT 60.093 50.000 0.00 0.00 33.51 4.16
380 381 2.171237 TCAGGATTCATGCCTACTGTGG 59.829 50.000 6.50 0.00 33.51 4.17
381 382 3.548745 TCAGGATTCATGCCTACTGTG 57.451 47.619 6.50 0.00 33.51 3.66
382 383 4.263462 TGTTTCAGGATTCATGCCTACTGT 60.263 41.667 6.50 0.00 33.51 3.55
383 384 4.264253 TGTTTCAGGATTCATGCCTACTG 58.736 43.478 0.00 1.22 33.51 2.74
384 385 4.574674 TGTTTCAGGATTCATGCCTACT 57.425 40.909 0.00 0.00 33.51 2.57
385 386 6.942532 TTATGTTTCAGGATTCATGCCTAC 57.057 37.500 0.00 0.00 33.51 3.18
387 388 8.537728 TTTATTATGTTTCAGGATTCATGCCT 57.462 30.769 0.00 0.00 35.75 4.75
388 389 9.598517 TTTTTATTATGTTTCAGGATTCATGCC 57.401 29.630 0.00 0.00 0.00 4.40
432 433 4.996344 AGAAAAGTAACGAGCCTAGCTAC 58.004 43.478 0.00 0.00 39.88 3.58
895 9226 3.744987 CGAAGTACTCGTTGTCGAATCT 58.255 45.455 7.94 0.00 45.61 2.40
931 9262 1.153005 GGAGCAAGAGGAGGCCATG 60.153 63.158 5.01 0.00 0.00 3.66
1439 11174 6.954684 TGGTAAATAAGCCCAATGAACCTTTA 59.045 34.615 0.00 0.00 0.00 1.85
1472 11233 8.160106 GGGATATCCTACAAGATCAAATCAGTT 58.840 37.037 21.18 0.00 35.95 3.16
1474 11235 7.915930 AGGGATATCCTACAAGATCAAATCAG 58.084 38.462 21.18 0.00 45.98 2.90
1525 11287 2.474526 CGTTCATGTCGATTGGTGCTTC 60.475 50.000 7.11 0.00 0.00 3.86
1528 11290 0.521242 GCGTTCATGTCGATTGGTGC 60.521 55.000 14.71 0.00 0.00 5.01
1545 11332 2.693591 TCTTCCTAGGTAAGTCATGGCG 59.306 50.000 9.08 0.00 0.00 5.69
1546 11333 4.345257 TGATCTTCCTAGGTAAGTCATGGC 59.655 45.833 9.08 0.00 0.00 4.40
1704 11501 0.253044 AGACCCATGGACCATGAACG 59.747 55.000 32.16 21.07 43.81 3.95
1773 16151 3.753294 TCTTCGACTCTTGCTTCCTTT 57.247 42.857 0.00 0.00 0.00 3.11
1777 16155 3.249917 CCTCTTCTTCGACTCTTGCTTC 58.750 50.000 0.00 0.00 0.00 3.86
1844 16222 1.140407 GAGACGACGCCCTTGAATCG 61.140 60.000 0.00 0.00 40.39 3.34
1846 16224 1.153823 CGAGACGACGCCCTTGAAT 60.154 57.895 0.00 0.00 0.00 2.57
1856 16234 2.358267 ACTTCATATCCACCGAGACGAC 59.642 50.000 0.00 0.00 0.00 4.34
1862 16240 4.283337 TCCAAGTACTTCATATCCACCGA 58.717 43.478 4.77 0.00 0.00 4.69
1864 16242 7.012421 GTGAAATCCAAGTACTTCATATCCACC 59.988 40.741 4.77 0.00 30.96 4.61
1865 16243 7.012421 GGTGAAATCCAAGTACTTCATATCCAC 59.988 40.741 4.77 9.96 30.96 4.02
1875 16253 5.255397 TGAATGGGTGAAATCCAAGTACT 57.745 39.130 0.00 0.00 37.87 2.73
1925 16303 0.909610 AGCGTCCCATTCTTCTCCCA 60.910 55.000 0.00 0.00 0.00 4.37
2120 16505 6.546484 CATACCCAGGTTCCAGATAATTGAT 58.454 40.000 0.00 0.00 0.00 2.57
2225 18483 5.710513 AAAACATGTGCAAGAATCTAGCA 57.289 34.783 0.00 0.00 35.63 3.49
2363 18633 5.833406 TTCAAATACGGACTACATACGGA 57.167 39.130 0.00 0.00 0.00 4.69
2364 18634 6.444633 AGATTCAAATACGGACTACATACGG 58.555 40.000 0.00 0.00 0.00 4.02
2365 18635 7.925703 AAGATTCAAATACGGACTACATACG 57.074 36.000 0.00 0.00 0.00 3.06
2420 18693 8.067751 TGATTGACTTGTTCATACTAGCTACT 57.932 34.615 0.00 0.00 32.84 2.57
2441 18714 1.938577 CAAGCGCTGCTCATACTGATT 59.061 47.619 12.58 0.00 38.25 2.57
2466 18739 6.360370 TGAGAGTTAATAGCCAGTCTTTGT 57.640 37.500 0.00 0.00 0.00 2.83
2504 18777 2.915738 AACTCCTCGTCGTCACATAC 57.084 50.000 0.00 0.00 0.00 2.39
2505 18778 3.928727 AAAACTCCTCGTCGTCACATA 57.071 42.857 0.00 0.00 0.00 2.29
2506 18779 2.814280 AAAACTCCTCGTCGTCACAT 57.186 45.000 0.00 0.00 0.00 3.21
2507 18780 2.589798 AAAAACTCCTCGTCGTCACA 57.410 45.000 0.00 0.00 0.00 3.58
2572 18847 3.490793 ATCCGATGAGCGCCGACAG 62.491 63.158 2.29 0.00 39.11 3.51
2575 18850 2.907407 AGATCCGATGAGCGCCGA 60.907 61.111 2.29 0.00 39.11 5.54
2582 18857 2.106938 GCCGTGCAGATCCGATGA 59.893 61.111 0.00 0.00 0.00 2.92
2799 19075 1.139853 AGATTCCGATGCAGAACCCTC 59.860 52.381 0.00 0.00 0.00 4.30
2905 19182 1.988293 TCAAATTCCGCCACAAAGGA 58.012 45.000 0.00 0.00 41.22 3.36
2916 19193 1.470890 TCGCGTTGGGATTCAAATTCC 59.529 47.619 5.77 0.00 37.08 3.01
2931 19208 3.480225 GATCCGTTCCCGATCGCGT 62.480 63.158 10.32 0.00 35.63 6.01
2940 19217 1.153147 GCCTTCCCAGATCCGTTCC 60.153 63.158 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.