Multiple sequence alignment - TraesCS2D01G143400

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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 TraesCS2D01G143400 chr2D 100.000 2621 0 0 1 2621 84780838 84778218 0.000000e+00 4841
1 TraesCS2D01G143400 chr2D 96.276 2390 66 8 253 2621 85408973 85406586 0.000000e+00 3899
2 TraesCS2D01G143400 chr2D 96.243 2289 59 10 358 2621 84938076 84935790 0.000000e+00 3725
3 TraesCS2D01G143400 chr2D 90.696 1236 55 10 72 1296 85252199 85251013 0.000000e+00 1591
4 TraesCS2D01G143400 chr2D 92.905 888 45 4 412 1298 85703786 85702916 0.000000e+00 1275
5 TraesCS2D01G143400 chr2D 92.099 848 53 8 1781 2621 85703010 85702170 0.000000e+00 1182
6 TraesCS2D01G143400 chr2B 94.268 1727 61 11 6 1711 136639399 136637690 0.000000e+00 2606
7 TraesCS2D01G143400 chr2B 94.444 1476 61 8 253 1711 137622677 137621206 0.000000e+00 2252
8 TraesCS2D01G143400 chr2B 94.850 1437 58 4 290 1711 136815293 136813858 0.000000e+00 2230
9 TraesCS2D01G143400 chr2B 94.543 1411 59 6 290 1684 137014950 137013542 0.000000e+00 2163
10 TraesCS2D01G143400 chr2B 93.943 842 44 4 1781 2621 137348518 137347683 0.000000e+00 1266
11 TraesCS2D01G143400 chr2B 93.824 842 45 4 1781 2621 137813679 137812844 0.000000e+00 1260
12 TraesCS2D01G143400 chr2A 93.151 1241 38 6 397 1615 85613727 85612512 0.000000e+00 1777
13 TraesCS2D01G143400 chr2A 93.151 1241 38 6 397 1615 85927152 85925937 0.000000e+00 1777
14 TraesCS2D01G143400 chr2A 93.042 848 43 10 1780 2621 84144427 84145264 0.000000e+00 1225
15 TraesCS2D01G143400 chr2A 92.899 845 47 6 1781 2621 84229107 84229942 0.000000e+00 1216
16 TraesCS2D01G143400 chr2A 88.346 266 15 6 10 272 85613974 85613722 3.280000e-79 305
17 TraesCS2D01G143400 chr2A 88.346 266 15 6 10 272 85811492 85811240 3.280000e-79 305
18 TraesCS2D01G143400 chr2A 88.550 262 14 6 14 272 85927395 85927147 1.180000e-78 303
19 TraesCS2D01G143400 chr4A 92.990 1241 40 6 397 1615 349806780 349805565 0.000000e+00 1766
20 TraesCS2D01G143400 chr4A 88.346 266 15 6 10 272 349807027 349806775 3.280000e-79 305
21 TraesCS2D01G143400 chr5B 91.732 1270 66 14 60 1298 321478605 321477344 0.000000e+00 1727
22 TraesCS2D01G143400 chr7A 93.942 1007 48 5 296 1298 618195480 618194483 0.000000e+00 1509
23 TraesCS2D01G143400 chr7A 93.824 842 47 4 1781 2621 618194577 618193740 0.000000e+00 1262
24 TraesCS2D01G143400 chr7A 93.750 80 4 1 1605 1684 627006928 627006850 4.580000e-23 119
25 TraesCS2D01G143400 chr5D 91.617 847 56 7 1781 2621 283109566 283108729 0.000000e+00 1157
26 TraesCS2D01G143400 chr5D 91.314 449 29 4 60 505 283110760 283110319 2.890000e-169 604
27 TraesCS2D01G143400 chr7D 82.719 434 47 13 1369 1776 518766779 518767210 6.900000e-96 361
28 TraesCS2D01G143400 chrUn 88.346 266 15 6 10 272 354326316 354326064 3.280000e-79 305
29 TraesCS2D01G143400 chr7B 93.642 173 5 1 1615 1781 588876413 588876241 1.200000e-63 254


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 TraesCS2D01G143400 chr2D 84778218 84780838 2620 True 4841.0 4841 100.0000 1 2621 1 chr2D.!!$R1 2620
1 TraesCS2D01G143400 chr2D 85406586 85408973 2387 True 3899.0 3899 96.2760 253 2621 1 chr2D.!!$R4 2368
2 TraesCS2D01G143400 chr2D 84935790 84938076 2286 True 3725.0 3725 96.2430 358 2621 1 chr2D.!!$R2 2263
3 TraesCS2D01G143400 chr2D 85251013 85252199 1186 True 1591.0 1591 90.6960 72 1296 1 chr2D.!!$R3 1224
4 TraesCS2D01G143400 chr2D 85702170 85703786 1616 True 1228.5 1275 92.5020 412 2621 2 chr2D.!!$R5 2209
5 TraesCS2D01G143400 chr2B 136637690 136639399 1709 True 2606.0 2606 94.2680 6 1711 1 chr2B.!!$R1 1705
6 TraesCS2D01G143400 chr2B 137621206 137622677 1471 True 2252.0 2252 94.4440 253 1711 1 chr2B.!!$R5 1458
7 TraesCS2D01G143400 chr2B 136813858 136815293 1435 True 2230.0 2230 94.8500 290 1711 1 chr2B.!!$R2 1421
8 TraesCS2D01G143400 chr2B 137013542 137014950 1408 True 2163.0 2163 94.5430 290 1684 1 chr2B.!!$R3 1394
9 TraesCS2D01G143400 chr2B 137347683 137348518 835 True 1266.0 1266 93.9430 1781 2621 1 chr2B.!!$R4 840
10 TraesCS2D01G143400 chr2B 137812844 137813679 835 True 1260.0 1260 93.8240 1781 2621 1 chr2B.!!$R6 840
11 TraesCS2D01G143400 chr2A 84144427 84145264 837 False 1225.0 1225 93.0420 1780 2621 1 chr2A.!!$F1 841
12 TraesCS2D01G143400 chr2A 84229107 84229942 835 False 1216.0 1216 92.8990 1781 2621 1 chr2A.!!$F2 840
13 TraesCS2D01G143400 chr2A 85612512 85613974 1462 True 1041.0 1777 90.7485 10 1615 2 chr2A.!!$R2 1605
14 TraesCS2D01G143400 chr2A 85925937 85927395 1458 True 1040.0 1777 90.8505 14 1615 2 chr2A.!!$R3 1601
15 TraesCS2D01G143400 chr4A 349805565 349807027 1462 True 1035.5 1766 90.6680 10 1615 2 chr4A.!!$R1 1605
16 TraesCS2D01G143400 chr5B 321477344 321478605 1261 True 1727.0 1727 91.7320 60 1298 1 chr5B.!!$R1 1238
17 TraesCS2D01G143400 chr7A 618193740 618195480 1740 True 1385.5 1509 93.8830 296 2621 2 chr7A.!!$R2 2325
18 TraesCS2D01G143400 chr5D 283108729 283110760 2031 True 880.5 1157 91.4655 60 2621 2 chr5D.!!$R1 2561

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
441 469 0.690192 TCATTTCCAGTTCAGCCGGA 59.310 50.0 5.05 0.0 0.0 5.14 F
1037 1146 0.394565 GCCTCTGATATTGCCTCCGT 59.605 55.0 0.00 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1492 1613 0.663568 GACTTGGTCACGTCGGAGTG 60.664 60.000 0.0 5.08 43.11 3.51 R
2537 2670 1.804748 CTTTAACTCACCAAGACGCCC 59.195 52.381 0.0 0.00 0.00 6.13 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
218 222 3.462021 GATCTCTGGGAAATCAACGAGG 58.538 50.000 0.00 0.00 0.00 4.63
441 469 0.690192 TCATTTCCAGTTCAGCCGGA 59.310 50.000 5.05 0.00 0.00 5.14
530 591 1.140407 CGGCTCCAACTCGATTCGTC 61.140 60.000 5.89 0.00 0.00 4.20
811 872 3.371063 AGCGCCGTCTCGAGGAAA 61.371 61.111 13.56 0.00 0.00 3.13
1037 1146 0.394565 GCCTCTGATATTGCCTCCGT 59.605 55.000 0.00 0.00 0.00 4.69
1067 1176 4.982701 GCCTGCCACCACCTTGCT 62.983 66.667 0.00 0.00 0.00 3.91
1492 1613 0.179045 CAACGACCCCTGGATCCATC 60.179 60.000 16.63 9.04 0.00 3.51
1673 1795 3.409026 AGCTTCTTGGTGGTAGTCTTG 57.591 47.619 0.00 0.00 0.00 3.02
2026 2148 1.202651 GGCTGCGTCCAGTGGTATTAT 60.203 52.381 9.54 0.00 41.26 1.28
2079 2204 5.314923 ACCATGCACACATAAGTTTCATC 57.685 39.130 0.00 0.00 33.67 2.92
2364 2495 0.798771 GGCACGAGACAGAGCGTAAG 60.799 60.000 0.00 0.00 38.92 2.34
2520 2653 7.826690 TCCTGTAAAATTAATCTTGGCTGAAC 58.173 34.615 0.00 0.00 0.00 3.18
2537 2670 4.201990 GCTGAACTGGATTCTTAGGCATTG 60.202 45.833 0.00 0.00 38.25 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 146 4.247380 CTGCATCCCTCCCGGCTC 62.247 72.222 0.00 0.00 0.00 4.70
148 151 4.554036 GACGGCTGCATCCCTCCC 62.554 72.222 0.00 0.00 0.00 4.30
178 182 3.710722 CCGAACAGCAGCTCCCCT 61.711 66.667 0.00 0.00 0.00 4.79
218 222 1.522580 GAGATCTTCAGGTGGCGCC 60.523 63.158 22.73 22.73 37.58 6.53
441 469 1.751924 GACTCGGATTACCAGCTGTCT 59.248 52.381 13.81 0.00 35.59 3.41
835 896 4.699522 GAGTTCTTGGGCGGCCGT 62.700 66.667 28.70 2.08 0.00 5.68
865 926 2.764128 ACGCCCTCCATGGTCGAT 60.764 61.111 12.58 0.83 0.00 3.59
1492 1613 0.663568 GACTTGGTCACGTCGGAGTG 60.664 60.000 0.00 5.08 43.11 3.51
1673 1795 1.066908 CCGACTCTTCTCCTCTGATGC 59.933 57.143 0.00 0.00 0.00 3.91
1916 2038 2.677228 CCATCCCCCTTCTTGCGT 59.323 61.111 0.00 0.00 0.00 5.24
2026 2148 4.806286 GCAACTAAAAGACTAGGGAAGGCA 60.806 45.833 0.00 0.00 34.57 4.75
2079 2204 6.578023 CAGAACCTAGAGGGACAAAGATTAG 58.422 44.000 0.00 0.00 40.27 1.73
2364 2495 3.308878 ATTTTGCGGCGAGTGCGTC 62.309 57.895 12.98 0.00 44.10 5.19
2520 2653 1.959282 GCCCAATGCCTAAGAATCCAG 59.041 52.381 0.00 0.00 0.00 3.86
2537 2670 1.804748 CTTTAACTCACCAAGACGCCC 59.195 52.381 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.