Multiple sequence alignment - TraesCS2A01G489200

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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 TraesCS2A01G489200 chr2A 100.000 2564 0 0 1 2564 723101425 723103988 0.000000e+00 4735
1 TraesCS2A01G489200 chr2A 82.958 1555 208 36 39 1571 712539279 712537760 0.000000e+00 1351
2 TraesCS2A01G489200 chr2A 87.500 392 43 6 26 414 723512007 723512395 5.030000e-122 448
3 TraesCS2A01G489200 chr2B 92.315 2173 102 25 2 2124 712002400 712004557 0.000000e+00 3027
4 TraesCS2A01G489200 chr2B 84.064 1619 201 33 41 1621 689777660 689776061 0.000000e+00 1507
5 TraesCS2A01G489200 chr2B 87.755 392 44 4 25 414 712360189 712360578 3.010000e-124 455
6 TraesCS2A01G489200 chr2B 79.703 404 71 10 12 408 712840876 712841275 5.400000e-72 281
7 TraesCS2A01G489200 chr2D 94.771 1683 49 11 2 1645 588498549 588500231 0.000000e+00 2584
8 TraesCS2A01G489200 chr2D 92.431 938 36 12 1643 2562 588500354 588501274 0.000000e+00 1306
9 TraesCS2A01G489200 chr2D 85.188 1168 153 13 41 1203 573952372 573951220 0.000000e+00 1181
10 TraesCS2A01G489200 chr2D 78.520 1122 194 40 27 1113 588735971 588737080 0.000000e+00 693
11 TraesCS2A01G489200 chr5B 87.580 314 37 2 2252 2564 174880184 174880496 1.880000e-96 363
12 TraesCS2A01G489200 chr5A 86.984 315 37 3 2254 2564 461592117 461592431 4.060000e-93 351
13 TraesCS2A01G489200 chr5A 85.669 314 44 1 2252 2564 205006428 205006741 1.900000e-86 329
14 TraesCS2A01G489200 chr3D 87.713 293 34 2 2273 2564 570601034 570601325 8.790000e-90 340
15 TraesCS2A01G489200 chr6B 84.395 314 46 3 2252 2563 150473052 150472740 3.210000e-79 305
16 TraesCS2A01G489200 chr1B 82.540 315 48 6 2252 2562 2138519 2138830 1.170000e-68 270
17 TraesCS2A01G489200 chr4B 80.573 314 58 3 2252 2563 184857312 184857624 3.300000e-59 239
18 TraesCS2A01G489200 chr7D 88.764 89 9 1 2254 2341 167593078 167593166 9.700000e-20 108


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 TraesCS2A01G489200 chr2A 723101425 723103988 2563 False 4735 4735 100.000 1 2564 1 chr2A.!!$F1 2563
1 TraesCS2A01G489200 chr2A 712537760 712539279 1519 True 1351 1351 82.958 39 1571 1 chr2A.!!$R1 1532
2 TraesCS2A01G489200 chr2B 712002400 712004557 2157 False 3027 3027 92.315 2 2124 1 chr2B.!!$F1 2122
3 TraesCS2A01G489200 chr2B 689776061 689777660 1599 True 1507 1507 84.064 41 1621 1 chr2B.!!$R1 1580
4 TraesCS2A01G489200 chr2D 588498549 588501274 2725 False 1945 2584 93.601 2 2562 2 chr2D.!!$F2 2560
5 TraesCS2A01G489200 chr2D 573951220 573952372 1152 True 1181 1181 85.188 41 1203 1 chr2D.!!$R1 1162
6 TraesCS2A01G489200 chr2D 588735971 588737080 1109 False 693 693 78.520 27 1113 1 chr2D.!!$F1 1086

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
852 894 0.313987 AGTCTGTTGACATCGACGCA 59.686 50.0 0.0 0.0 45.2 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2253 2485 1.11715 TGCCCTACAATCGTACCCTC 58.883 55.0 0.0 0.0 0.0 4.3 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
188 192 2.740714 GCACACCATCTCGTTCGCC 61.741 63.158 0.00 0.00 0.00 5.54
609 651 2.805845 GTCATACGGACGCTATGTGTT 58.194 47.619 11.26 0.00 36.65 3.32
775 817 2.030628 GCTATCTACCGCCTGAAGAGAC 60.031 54.545 0.00 0.00 0.00 3.36
852 894 0.313987 AGTCTGTTGACATCGACGCA 59.686 50.000 0.00 0.00 45.20 5.24
978 1020 2.055042 GCTCTCTCAGGAGGCGGAA 61.055 63.158 0.00 0.00 39.86 4.30
1015 1057 8.781951 TCAGAGGGTTTATGGAGAAAATATCTT 58.218 33.333 0.00 0.00 38.96 2.40
1140 1182 2.198406 GATAGTTGCGGCATTGTCGTA 58.802 47.619 12.79 4.70 31.29 3.43
1203 1245 0.250252 TGTCGCTGTGCATGGAAGAA 60.250 50.000 0.00 0.00 0.00 2.52
1277 1340 4.141528 GGATGATGTTGTGGAGAAGGAGAT 60.142 45.833 0.00 0.00 0.00 2.75
1286 1349 0.755686 GAGAAGGAGATGGATGCGGT 59.244 55.000 0.00 0.00 0.00 5.68
1824 2019 6.441093 TTGACAATCACTATGGAAGCATTC 57.559 37.500 0.00 0.00 46.67 2.67
1927 2122 1.290955 CCAACACATTGCTGCAGGG 59.709 57.895 17.12 0.12 34.17 4.45
2047 2263 6.213600 ACTTAAAAGAGAGATGGGCTCAACTA 59.786 38.462 0.00 0.00 46.45 2.24
2127 2343 4.432712 AGTTGATCAACACTGGCAAAAAC 58.567 39.130 33.92 9.02 43.47 2.43
2170 2402 0.976641 TGTCAGCTTCCTCGGTCATT 59.023 50.000 0.00 0.00 0.00 2.57
2213 2445 3.250744 ACGTACAATGGAAGACATGACG 58.749 45.455 0.00 0.00 42.23 4.35
2237 2469 6.592994 CGCACATACATCCTTGATAGATGAAT 59.407 38.462 7.70 0.00 43.15 2.57
2296 2528 7.119846 GCATGAGAACCTAAAGTTGTACATCTT 59.880 37.037 12.48 12.48 39.40 2.40
2342 2575 2.481276 GGCCCCGAAGATAATTTTGTGC 60.481 50.000 0.00 0.00 0.00 4.57
2389 2622 3.517100 ACATACCTCAGCTCAACACAGAT 59.483 43.478 0.00 0.00 0.00 2.90
2411 2644 5.138125 TGAAAATGAGATTTTGTCTGCCC 57.862 39.130 0.00 0.00 42.15 5.36
2412 2645 4.834496 TGAAAATGAGATTTTGTCTGCCCT 59.166 37.500 0.00 0.00 42.15 5.19
2457 2690 1.966563 CGCGGTAACACAAATGAAACG 59.033 47.619 0.00 0.00 0.00 3.60
2487 2720 5.841783 AGTCTCCTAGACCTAATGGATTTCC 59.158 44.000 3.49 0.00 46.18 3.13
2512 2745 7.285788 CAGCAGATTTTTACAAGAAATGTTGC 58.714 34.615 0.00 0.00 43.63 4.17
2525 2758 8.970020 ACAAGAAATGTTGCCATATCATTAAGA 58.030 29.630 0.00 0.00 40.06 2.10
2528 2761 9.584008 AGAAATGTTGCCATATCATTAAGAGAT 57.416 29.630 0.00 0.00 32.52 2.75
2562 2795 2.616376 TGTTCCATGACTTGTTCAACGG 59.384 45.455 0.00 0.00 37.92 4.44
2563 2796 2.875933 GTTCCATGACTTGTTCAACGGA 59.124 45.455 0.00 0.00 37.92 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.466529 CGACGAGGCCATATCGATCTG 60.467 57.143 18.70 1.71 42.76 2.90
143 147 4.373116 AAGATGTCGCGCCACCGT 62.373 61.111 0.00 0.00 36.67 4.83
188 192 2.477176 CCTCTCGCCCTGAGTCTCG 61.477 68.421 0.00 0.00 45.46 4.04
504 546 3.677527 TCCTCGTCGGAGTTGTCC 58.322 61.111 0.00 0.00 38.70 4.02
775 817 1.823828 CGTTTGTCGAGGACGGATAG 58.176 55.000 7.13 0.00 42.86 2.08
852 894 2.441164 AGCGACCTCAGCTCCGAT 60.441 61.111 0.00 0.00 41.83 4.18
978 1020 4.741928 AAACCCTCTGAACCTGGTAAAT 57.258 40.909 0.00 0.00 0.00 1.40
1015 1057 2.426738 GCAAATGCAGGTACTTGGCATA 59.573 45.455 15.99 0.00 45.45 3.14
1140 1182 3.312890 CTCCAGGATTCTACCCACTGAT 58.687 50.000 0.00 0.00 0.00 2.90
1203 1245 0.665369 CTTCGGTGTCCTTAACGCGT 60.665 55.000 5.58 5.58 39.39 6.01
1277 1340 2.031674 ATCATCGCTCACCGCATCCA 62.032 55.000 0.00 0.00 39.08 3.41
1286 1349 4.002982 AGCTACAAACAAATCATCGCTCA 58.997 39.130 0.00 0.00 0.00 4.26
1476 1542 1.111116 ACTCGAACGTCCCCTTCACA 61.111 55.000 0.00 0.00 0.00 3.58
1638 1707 5.281727 TCTATGCGTGTAGAAGCTACAATG 58.718 41.667 8.70 6.36 0.00 2.82
1674 1869 7.394016 TCTGTTCTTTACATCTCCTTTGCATA 58.606 34.615 0.00 0.00 35.85 3.14
1675 1870 6.240894 TCTGTTCTTTACATCTCCTTTGCAT 58.759 36.000 0.00 0.00 35.85 3.96
1676 1871 5.620206 TCTGTTCTTTACATCTCCTTTGCA 58.380 37.500 0.00 0.00 35.85 4.08
1677 1872 6.560253 TTCTGTTCTTTACATCTCCTTTGC 57.440 37.500 0.00 0.00 35.85 3.68
1678 1873 6.205464 TGCTTCTGTTCTTTACATCTCCTTTG 59.795 38.462 0.00 0.00 35.85 2.77
1679 1874 6.299141 TGCTTCTGTTCTTTACATCTCCTTT 58.701 36.000 0.00 0.00 35.85 3.11
1927 2122 4.732784 ACAACATTTTGTATGCGGATGTC 58.267 39.130 0.00 0.00 44.53 3.06
1969 2164 8.939201 TTGCAAACTTCAATGATTCAGTTTTA 57.061 26.923 8.37 0.75 37.36 1.52
2021 2217 4.836825 TGAGCCCATCTCTCTTTTAAGTG 58.163 43.478 0.00 0.00 42.38 3.16
2127 2343 8.973378 ACAAATATGAACACAATTTTGGTTACG 58.027 29.630 0.00 0.00 30.73 3.18
2213 2445 7.918536 ATTCATCTATCAAGGATGTATGTGC 57.081 36.000 0.00 0.00 40.76 4.57
2237 2469 5.105351 CGTACCCTCATGAGCCAATATCATA 60.105 44.000 17.76 0.00 35.64 2.15
2253 2485 1.117150 TGCCCTACAATCGTACCCTC 58.883 55.000 0.00 0.00 0.00 4.30
2319 2551 2.291930 ACAAAATTATCTTCGGGGCCCA 60.292 45.455 26.86 7.03 0.00 5.36
2358 2591 1.407437 GCTGAGGTATGTCCCCAACTG 60.407 57.143 0.00 0.00 36.75 3.16
2389 2622 4.834496 AGGGCAGACAAAATCTCATTTTCA 59.166 37.500 0.00 0.00 40.27 2.69
2411 2644 6.538742 TCAAACACCTCTTTCTCAGTAAACAG 59.461 38.462 0.00 0.00 0.00 3.16
2412 2645 6.315393 GTCAAACACCTCTTTCTCAGTAAACA 59.685 38.462 0.00 0.00 0.00 2.83
2457 2690 7.011382 TCCATTAGGTCTAGGAGACTTATTCC 58.989 42.308 6.58 0.00 44.46 3.01
2487 2720 7.285788 GCAACATTTCTTGTAAAAATCTGCTG 58.714 34.615 0.00 0.00 37.68 4.41


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

AutoCloner maintained by Alex Coulton.