Multiple sequence alignment - TraesCS3B01G284400

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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 TraesCS3B01G284400 chr3B 100.000 2428 0 0 1 2428 455491039 455493466 0.000000e+00 4484.0
1 TraesCS3B01G284400 chr3B 95.521 1563 61 6 261 1819 589660408 589658851 0.000000e+00 2490.0
2 TraesCS3B01G284400 chr3B 91.189 488 28 8 1216 1700 648407840 648408315 0.000000e+00 649.0
3 TraesCS3B01G284400 chr7B 96.220 1561 52 5 261 1819 336258982 336260537 0.000000e+00 2549.0
4 TraesCS3B01G284400 chr7B 95.503 845 32 5 3 846 345988400 345989239 0.000000e+00 1345.0
5 TraesCS3B01G284400 chr7B 92.672 655 40 1 850 1496 345989364 345990018 0.000000e+00 937.0
6 TraesCS3B01G284400 chr7B 94.399 607 34 0 1821 2427 349965402 349966008 0.000000e+00 933.0
7 TraesCS3B01G284400 chr7B 97.521 121 3 0 1699 1819 20342487 20342367 8.800000e-50 207.0
8 TraesCS3B01G284400 chr5B 95.836 1561 58 5 261 1819 22034571 22033016 0.000000e+00 2516.0
9 TraesCS3B01G284400 chr5B 95.583 1562 60 7 261 1819 463404250 463402695 0.000000e+00 2494.0
10 TraesCS3B01G284400 chr5B 91.803 488 25 8 1216 1700 389236451 389236926 0.000000e+00 665.0
11 TraesCS3B01G284400 chr6B 95.131 1561 68 6 261 1819 587741804 587743358 0.000000e+00 2455.0
12 TraesCS3B01G284400 chr6B 92.008 488 24 8 1216 1700 185001922 185002397 0.000000e+00 671.0
13 TraesCS3B01G284400 chr6B 96.694 121 4 0 1699 1819 185006571 185006691 4.090000e-48 202.0
14 TraesCS3B01G284400 chr5A 91.243 1199 94 8 3 1197 337891996 337890805 0.000000e+00 1622.0
15 TraesCS3B01G284400 chr2A 91.167 1200 97 7 3 1197 347861541 347862736 0.000000e+00 1620.0
16 TraesCS3B01G284400 chr2A 94.408 608 34 0 1821 2428 408795999 408796606 0.000000e+00 935.0
17 TraesCS3B01G284400 chr2A 94.234 607 35 0 1821 2427 752240774 752240168 0.000000e+00 928.0
18 TraesCS3B01G284400 chr2A 93.821 615 37 1 1814 2428 408797311 408797924 0.000000e+00 924.0
19 TraesCS3B01G284400 chr7A 91.023 1192 94 13 3 1189 354945171 354946354 0.000000e+00 1596.0
20 TraesCS3B01G284400 chr1A 93.495 661 32 4 3 662 327384283 327383633 0.000000e+00 972.0
21 TraesCS3B01G284400 chr2B 94.003 617 36 1 1813 2428 195375882 195375266 0.000000e+00 933.0
22 TraesCS3B01G284400 chr2B 89.959 488 34 8 1216 1700 746311632 746311157 1.230000e-172 616.0
23 TraesCS3B01G284400 chr2B 89.388 490 33 11 1216 1700 388577254 388576779 1.240000e-167 599.0
24 TraesCS3B01G284400 chr2B 97.521 121 3 0 1699 1819 746309299 746309179 8.800000e-50 207.0
25 TraesCS3B01G284400 chr2B 96.694 121 4 0 1699 1819 388574857 388574737 4.090000e-48 202.0
26 TraesCS3B01G284400 chr1D 94.234 607 35 0 1821 2427 305006280 305006886 0.000000e+00 928.0
27 TraesCS3B01G284400 chr1D 93.700 619 37 2 1810 2428 128012245 128012861 0.000000e+00 926.0
28 TraesCS3B01G284400 chr1D 92.255 581 38 4 622 1197 93821145 93821723 0.000000e+00 817.0
29 TraesCS3B01G284400 chr1D 93.873 408 17 1 3 410 93820414 93820813 2.060000e-170 608.0
30 TraesCS3B01G284400 chr4D 94.079 608 36 0 1821 2428 204852936 204853543 0.000000e+00 924.0
31 TraesCS3B01G284400 chr6D 93.659 615 39 0 1813 2427 254068122 254068736 0.000000e+00 920.0
32 TraesCS3B01G284400 chr6D 80.620 129 15 4 1261 1381 239528414 239528540 9.240000e-15 91.6


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 TraesCS3B01G284400 chr3B 455491039 455493466 2427 False 4484.0 4484 100.0000 1 2428 1 chr3B.!!$F1 2427
1 TraesCS3B01G284400 chr3B 589658851 589660408 1557 True 2490.0 2490 95.5210 261 1819 1 chr3B.!!$R1 1558
2 TraesCS3B01G284400 chr7B 336258982 336260537 1555 False 2549.0 2549 96.2200 261 1819 1 chr7B.!!$F1 1558
3 TraesCS3B01G284400 chr7B 345988400 345990018 1618 False 1141.0 1345 94.0875 3 1496 2 chr7B.!!$F3 1493
4 TraesCS3B01G284400 chr7B 349965402 349966008 606 False 933.0 933 94.3990 1821 2427 1 chr7B.!!$F2 606
5 TraesCS3B01G284400 chr5B 22033016 22034571 1555 True 2516.0 2516 95.8360 261 1819 1 chr5B.!!$R1 1558
6 TraesCS3B01G284400 chr5B 463402695 463404250 1555 True 2494.0 2494 95.5830 261 1819 1 chr5B.!!$R2 1558
7 TraesCS3B01G284400 chr6B 587741804 587743358 1554 False 2455.0 2455 95.1310 261 1819 1 chr6B.!!$F3 1558
8 TraesCS3B01G284400 chr5A 337890805 337891996 1191 True 1622.0 1622 91.2430 3 1197 1 chr5A.!!$R1 1194
9 TraesCS3B01G284400 chr2A 347861541 347862736 1195 False 1620.0 1620 91.1670 3 1197 1 chr2A.!!$F1 1194
10 TraesCS3B01G284400 chr2A 408795999 408797924 1925 False 929.5 935 94.1145 1814 2428 2 chr2A.!!$F2 614
11 TraesCS3B01G284400 chr2A 752240168 752240774 606 True 928.0 928 94.2340 1821 2427 1 chr2A.!!$R1 606
12 TraesCS3B01G284400 chr7A 354945171 354946354 1183 False 1596.0 1596 91.0230 3 1189 1 chr7A.!!$F1 1186
13 TraesCS3B01G284400 chr1A 327383633 327384283 650 True 972.0 972 93.4950 3 662 1 chr1A.!!$R1 659
14 TraesCS3B01G284400 chr2B 195375266 195375882 616 True 933.0 933 94.0030 1813 2428 1 chr2B.!!$R1 615
15 TraesCS3B01G284400 chr2B 746309179 746311632 2453 True 411.5 616 93.7400 1216 1819 2 chr2B.!!$R3 603
16 TraesCS3B01G284400 chr2B 388574737 388577254 2517 True 400.5 599 93.0410 1216 1819 2 chr2B.!!$R2 603
17 TraesCS3B01G284400 chr1D 305006280 305006886 606 False 928.0 928 94.2340 1821 2427 1 chr1D.!!$F2 606
18 TraesCS3B01G284400 chr1D 128012245 128012861 616 False 926.0 926 93.7000 1810 2428 1 chr1D.!!$F1 618
19 TraesCS3B01G284400 chr1D 93820414 93821723 1309 False 712.5 817 93.0640 3 1197 2 chr1D.!!$F3 1194
20 TraesCS3B01G284400 chr4D 204852936 204853543 607 False 924.0 924 94.0790 1821 2428 1 chr4D.!!$F1 607
21 TraesCS3B01G284400 chr6D 254068122 254068736 614 False 920.0 920 93.6590 1813 2427 1 chr6D.!!$F2 614

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
126 127 1.065854 AGTTGCAGAGAGTATGGGCAC 60.066 52.381 0.0 0.0 33.66 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1717 3930 0.387112 CACATGTGCCGCGTTGATTT 60.387 50.0 13.94 0.0 0.0 2.17 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
126 127 1.065854 AGTTGCAGAGAGTATGGGCAC 60.066 52.381 0.00 0.00 33.66 5.01
202 203 4.365514 TCTCCTTGTACCAAATGAAGCA 57.634 40.909 0.00 0.00 0.00 3.91
248 249 2.378038 GTGCATCAAATGGCTTCCCTA 58.622 47.619 0.00 0.00 0.00 3.53
697 820 8.984764 GTACAACTTACTGAATGACATGTGTTA 58.015 33.333 1.15 0.00 0.00 2.41
772 896 5.757850 ATTTGACTGAACCTGAACTGAAC 57.242 39.130 0.00 0.00 0.00 3.18
782 906 5.036117 ACCTGAACTGAACTTTAGCTCAA 57.964 39.130 0.00 0.00 0.00 3.02
1116 1367 2.350738 TGACCTCGTCATCAGTGCA 58.649 52.632 0.00 0.00 37.67 4.57
1129 1380 2.256306 TCAGTGCATCCCTCTTGTACA 58.744 47.619 0.00 0.00 32.83 2.90
1179 1430 2.203523 ATGCAACAGCTGGGCACA 60.204 55.556 29.84 17.72 40.83 4.57
1225 1476 8.243961 TCATTTTGATTTTCTTACCTTGGTGA 57.756 30.769 2.03 0.00 0.00 4.02
1412 1680 2.524394 ACGAGGCAGACAGGTGGT 60.524 61.111 0.00 0.00 0.00 4.16
1417 1685 4.269523 GCAGACAGGTGGTGGGCA 62.270 66.667 0.00 0.00 0.00 5.36
1523 1791 1.873591 GATTGGTGTCGTGCAGTTCTT 59.126 47.619 0.00 0.00 0.00 2.52
1525 1793 1.860676 TGGTGTCGTGCAGTTCTTAC 58.139 50.000 0.00 0.00 0.00 2.34
1538 1808 5.048364 TGCAGTTCTTACTTGTTTTGTGTGT 60.048 36.000 0.00 0.00 30.26 3.72
1539 1809 5.286082 GCAGTTCTTACTTGTTTTGTGTGTG 59.714 40.000 0.00 0.00 30.26 3.82
1540 1810 6.378582 CAGTTCTTACTTGTTTTGTGTGTGT 58.621 36.000 0.00 0.00 30.26 3.72
1558 1828 2.161410 GTGTGTGTGTGTTGTGTGATGT 59.839 45.455 0.00 0.00 0.00 3.06
1595 1866 0.673644 CGACAAGTTAGCCCCCACAG 60.674 60.000 0.00 0.00 0.00 3.66
1663 1934 5.185828 TCTTCATCTCCGATGTTTTCTCTCA 59.814 40.000 4.01 0.00 0.00 3.27
1717 3930 2.953648 TGGTCGAGTGTAGTGAACAAGA 59.046 45.455 0.00 0.00 40.63 3.02
1807 4020 2.461110 GCACCGGCCACATTACTCG 61.461 63.158 0.00 0.00 0.00 4.18
1819 4032 1.854743 CATTACTCGTCATGCCACTCG 59.145 52.381 0.00 0.00 0.00 4.18
1824 4037 0.821517 TCGTCATGCCACTCGGTAAT 59.178 50.000 0.00 0.00 33.28 1.89
1879 4092 0.539901 GCGGGATCTAGACTGGCCTA 60.540 60.000 3.32 0.00 0.00 3.93
1912 4125 3.495001 ACTAGTCTTTTCTGCGCACTTTC 59.505 43.478 5.66 0.00 0.00 2.62
1979 4192 5.397899 CCCATCCTGAAATTACTCCAAGCTA 60.398 44.000 0.00 0.00 0.00 3.32
2073 4286 8.125733 AGTACTCTATCATCCCTAATAAGCCAT 58.874 37.037 0.00 0.00 0.00 4.40
2095 4308 2.172717 GCTATCACATACACCCCCACTT 59.827 50.000 0.00 0.00 0.00 3.16
2107 4320 1.497161 CCCCACTTAGAGGAACCGAT 58.503 55.000 0.00 0.00 0.00 4.18
2234 5765 0.961019 AACATGATTGCGCACCTGTT 59.039 45.000 11.12 12.66 0.00 3.16
2391 5922 4.363990 CCTCACTCGTGCGCACCT 62.364 66.667 33.23 14.29 0.00 4.00
2416 5947 1.835712 AACTTCCCGGTCGGTCACT 60.836 57.895 8.67 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.190327 TCACGCATAAACTGGTTGGAATG 59.810 43.478 0.00 0.00 0.00 2.67
15 16 4.621068 ATCATCACGCATAAACTGGTTG 57.379 40.909 0.00 0.00 0.00 3.77
151 152 9.212641 CTCTCTTCAAAGATCTTAATGACAACA 57.787 33.333 8.75 0.00 33.93 3.33
202 203 4.026744 TCTACAGAAGCCTTGTAGCATCT 58.973 43.478 12.57 0.00 41.26 2.90
221 222 2.091720 AGCCATTTGATGCACCCATCTA 60.092 45.455 0.00 0.00 46.43 1.98
330 331 7.809806 GCACTGTAAAAAGAGCTTATGTTTCAT 59.190 33.333 0.00 0.00 31.83 2.57
647 770 6.891908 ACTTGGATAGTTAACTGATTGCCAAT 59.108 34.615 18.56 0.53 31.29 3.16
697 820 3.952323 CTGGACCAGCTTTCATTCATGAT 59.048 43.478 8.99 0.00 36.56 2.45
772 896 5.947228 TGTCAAATGAGGTTGAGCTAAAG 57.053 39.130 0.00 0.00 38.17 1.85
782 906 6.017109 GTGTGTATCTGTTTGTCAAATGAGGT 60.017 38.462 0.40 0.36 0.00 3.85
1051 1302 0.679505 AACGAGCACTGGAAGCAGTA 59.320 50.000 0.00 0.00 37.60 2.74
1116 1367 1.640917 ACACGGTGTACAAGAGGGAT 58.359 50.000 12.96 0.00 0.00 3.85
1179 1430 1.961180 GCACCCAGTAGAGCGGACAT 61.961 60.000 0.00 0.00 0.00 3.06
1412 1680 1.000233 CCCCTATTGTTGCTGCCCA 60.000 57.895 0.00 0.00 0.00 5.36
1417 1685 0.965363 CGCCAACCCCTATTGTTGCT 60.965 55.000 0.00 0.00 41.33 3.91
1523 1791 4.276183 ACACACACACACACAAAACAAGTA 59.724 37.500 0.00 0.00 0.00 2.24
1525 1793 3.424861 CACACACACACACACAAAACAAG 59.575 43.478 0.00 0.00 0.00 3.16
1538 1808 2.431454 ACATCACACAACACACACACA 58.569 42.857 0.00 0.00 0.00 3.72
1539 1809 3.868661 TCTACATCACACAACACACACAC 59.131 43.478 0.00 0.00 0.00 3.82
1540 1810 4.130286 TCTACATCACACAACACACACA 57.870 40.909 0.00 0.00 0.00 3.72
1558 1828 1.787058 TCGGATCCTCCTTCCCATCTA 59.213 52.381 10.75 0.00 33.30 1.98
1595 1866 4.662145 CAGAAGTTCTCCAACAACACAAC 58.338 43.478 1.26 0.00 34.60 3.32
1663 1934 1.721487 CGATCCGCGCTCCATTTTT 59.279 52.632 5.56 0.00 0.00 1.94
1717 3930 0.387112 CACATGTGCCGCGTTGATTT 60.387 50.000 13.94 0.00 0.00 2.17
1807 4020 0.657840 GCATTACCGAGTGGCATGAC 59.342 55.000 0.00 0.00 39.70 3.06
1819 4032 1.747745 GTGTGTCCGGGGCATTACC 60.748 63.158 3.85 0.00 37.93 2.85
1879 4092 7.276658 CGCAGAAAAGACTAGTATTGATCTGTT 59.723 37.037 28.67 12.56 34.16 3.16
1912 4125 1.812922 GGTGCGCATGAGTGAGGAG 60.813 63.158 15.91 0.00 0.00 3.69
1979 4192 4.829492 AGAACTCCAAAGTTAAGCATGCTT 59.171 37.500 33.70 33.70 45.80 3.91
2073 4286 1.488812 GTGGGGGTGTATGTGATAGCA 59.511 52.381 0.00 0.00 0.00 3.49
2234 5765 1.735018 CGGTTACATGGATGTTTGCGA 59.265 47.619 0.00 0.00 41.97 5.10
2302 5833 1.823169 GCCAGGAGTAACGACCACCA 61.823 60.000 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.