Multiple sequence alignment - TraesCS6A01G232800

Loading Multiple Alignment...

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 TraesCS6A01G232800 chr6A 100.000 2549 0 0 1 2549 440264714 440267262 0.000000e+00 4708.0
1 TraesCS6A01G232800 chr6A 93.010 701 48 1 1266 1965 125236293 125235593 0.000000e+00 1022.0
2 TraesCS6A01G232800 chr6A 92.713 494 29 2 776 1269 125245641 125245155 0.000000e+00 706.0
3 TraesCS6A01G232800 chr5A 87.867 1772 201 7 780 2548 123309451 123311211 0.000000e+00 2069.0
4 TraesCS6A01G232800 chr3D 86.839 1778 217 10 776 2548 502952227 502953992 0.000000e+00 1971.0
5 TraesCS6A01G232800 chr1D 88.122 1448 165 7 777 2219 439631840 439633285 0.000000e+00 1714.0
6 TraesCS6A01G232800 chr1D 79.769 1557 301 6 995 2548 302922561 302921016 0.000000e+00 1118.0
7 TraesCS6A01G232800 chr1D 85.030 334 36 9 2217 2548 439644947 439645268 6.800000e-86 327.0
8 TraesCS6A01G232800 chr1D 87.143 70 6 3 210 277 453462063 453462131 2.720000e-10 76.8
9 TraesCS6A01G232800 chr2A 83.230 1777 281 8 775 2548 760305556 760303794 0.000000e+00 1615.0
10 TraesCS6A01G232800 chr6D 79.382 1780 334 20 776 2548 27723825 27725578 0.000000e+00 1223.0
11 TraesCS6A01G232800 chr6D 93.036 718 33 12 1 704 305744010 305744724 0.000000e+00 1033.0
12 TraesCS6A01G232800 chr6D 90.000 70 6 1 209 277 83202372 83202303 3.490000e-14 89.8
13 TraesCS6A01G232800 chr2D 82.748 1252 207 9 775 2022 630844292 630845538 0.000000e+00 1107.0
14 TraesCS6A01G232800 chr2D 84.878 410 47 7 2084 2491 630886084 630886480 1.420000e-107 399.0
15 TraesCS6A01G232800 chr2D 73.177 768 197 7 1004 1767 650873781 650874543 4.180000e-68 268.0
16 TraesCS6A01G232800 chr6B 94.215 484 21 4 264 747 470817715 470817239 0.000000e+00 732.0
17 TraesCS6A01G232800 chr6B 91.255 263 18 4 1 259 470819131 470818870 1.120000e-93 353.0
18 TraesCS6A01G232800 chr6B 77.447 470 91 12 2040 2506 91043008 91043465 1.500000e-67 267.0
19 TraesCS6A01G232800 chr6B 91.429 70 5 1 209 277 158187037 158186968 7.510000e-16 95.3
20 TraesCS6A01G232800 chr5B 79.135 1040 207 10 1265 2299 311068050 311067016 0.000000e+00 710.0
21 TraesCS6A01G232800 chr5B 80.159 378 70 5 771 1145 311070192 311069817 6.950000e-71 278.0
22 TraesCS6A01G232800 chr3A 85.333 75 10 1 209 282 19200641 19200567 2.720000e-10 76.8
23 TraesCS6A01G232800 chr3A 85.333 75 10 1 209 282 19224081 19224007 2.720000e-10 76.8
24 TraesCS6A01G232800 chr1B 87.143 70 6 3 210 277 623897903 623897971 2.720000e-10 76.8
25 TraesCS6A01G232800 chr1A 85.714 70 7 3 210 277 548395783 548395851 1.270000e-08 71.3


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 TraesCS6A01G232800 chr6A 440264714 440267262 2548 False 4708.0 4708 100.000 1 2549 1 chr6A.!!$F1 2548
1 TraesCS6A01G232800 chr6A 125235593 125236293 700 True 1022.0 1022 93.010 1266 1965 1 chr6A.!!$R1 699
2 TraesCS6A01G232800 chr5A 123309451 123311211 1760 False 2069.0 2069 87.867 780 2548 1 chr5A.!!$F1 1768
3 TraesCS6A01G232800 chr3D 502952227 502953992 1765 False 1971.0 1971 86.839 776 2548 1 chr3D.!!$F1 1772
4 TraesCS6A01G232800 chr1D 439631840 439633285 1445 False 1714.0 1714 88.122 777 2219 1 chr1D.!!$F1 1442
5 TraesCS6A01G232800 chr1D 302921016 302922561 1545 True 1118.0 1118 79.769 995 2548 1 chr1D.!!$R1 1553
6 TraesCS6A01G232800 chr2A 760303794 760305556 1762 True 1615.0 1615 83.230 775 2548 1 chr2A.!!$R1 1773
7 TraesCS6A01G232800 chr6D 27723825 27725578 1753 False 1223.0 1223 79.382 776 2548 1 chr6D.!!$F1 1772
8 TraesCS6A01G232800 chr6D 305744010 305744724 714 False 1033.0 1033 93.036 1 704 1 chr6D.!!$F2 703
9 TraesCS6A01G232800 chr2D 630844292 630845538 1246 False 1107.0 1107 82.748 775 2022 1 chr2D.!!$F1 1247
10 TraesCS6A01G232800 chr2D 650873781 650874543 762 False 268.0 268 73.177 1004 1767 1 chr2D.!!$F3 763
11 TraesCS6A01G232800 chr6B 470817239 470819131 1892 True 542.5 732 92.735 1 747 2 chr6B.!!$R2 746
12 TraesCS6A01G232800 chr5B 311067016 311070192 3176 True 494.0 710 79.647 771 2299 2 chr5B.!!$R1 1528

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
595 1748 1.336148 TGCTGCTATGTTTGTTGCTGC 60.336 47.619 0.0 0.0 45.88 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2497 5394 0.67996 TCGCTCCTGTGATTCCTCGA 60.68 55.0 0.0 0.0 0.0 4.04 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
197 202 5.009210 ACATGCTGTAACAAAATAACGTGGT 59.991 36.000 0.00 0.00 0.00 4.16
201 206 6.183360 TGCTGTAACAAAATAACGTGGTCTTT 60.183 34.615 0.00 0.00 0.00 2.52
256 261 8.821894 ACTGATTTATTTAGCGAGACATTTCTC 58.178 33.333 0.00 0.00 44.50 2.87
317 1470 4.537135 TCGATGGCAGGATTAGAATACC 57.463 45.455 0.00 0.00 0.00 2.73
542 1695 1.544691 GAGACCCAGTAAGCTCGAACA 59.455 52.381 0.00 0.00 0.00 3.18
595 1748 1.336148 TGCTGCTATGTTTGTTGCTGC 60.336 47.619 0.00 0.00 45.88 5.25
725 1878 5.435291 TGTTCCTTCCTACGTTTTGGTTTA 58.565 37.500 0.00 0.00 0.00 2.01
726 1879 5.528320 TGTTCCTTCCTACGTTTTGGTTTAG 59.472 40.000 0.00 0.00 0.00 1.85
992 2148 2.047560 AAGCTCGGTTACGGCCAC 60.048 61.111 2.24 0.00 41.39 5.01
1253 2409 3.691342 CCTCGGCGACTGGGAACA 61.691 66.667 4.99 0.00 39.59 3.18
1303 4196 5.398236 TCAAGGGAAAAATGGTGGTAATCA 58.602 37.500 0.00 0.00 0.00 2.57
1497 4391 8.705048 ACTTTTTCAGAGTCCGTATTAAGATC 57.295 34.615 0.00 0.00 0.00 2.75
1514 4408 1.599542 GATCAATGTCACTAAGCCGCC 59.400 52.381 0.00 0.00 0.00 6.13
1523 4417 1.153901 CTAAGCCGCCGAAGAACGA 60.154 57.895 0.00 0.00 45.77 3.85
1560 4454 2.826725 CAAGAGGTAGAAGGAGGTCGTT 59.173 50.000 0.00 0.00 0.00 3.85
1595 4489 4.764823 CAGGGTTAAGTATGAAAGGTTGCA 59.235 41.667 0.00 0.00 0.00 4.08
1804 4698 2.895424 CGAGGCAGGGGGAACAACT 61.895 63.158 0.00 0.00 0.00 3.16
1813 4707 1.551019 GGGGAACAACTAGGACCGCT 61.551 60.000 0.00 0.00 0.00 5.52
1918 4814 0.105964 TCAAGCTACAGCCGTGTTGT 59.894 50.000 0.00 0.00 43.38 3.32
1938 4834 2.882137 GTTGCCAGCTAGTAACCAAACA 59.118 45.455 1.78 0.00 0.00 2.83
1968 4865 1.616628 AATCTCCTTGCCCTCCCGT 60.617 57.895 0.00 0.00 0.00 5.28
2001 4898 2.354203 CCGGAGAGTCCCTCTTCAAAAG 60.354 54.545 0.00 0.00 41.35 2.27
2048 4945 1.554160 CCACAGATCACTGAGAAGGCT 59.446 52.381 0.00 0.00 46.03 4.58
2149 5046 7.519008 GCAATGAGTATACTATGTTGGAACTGC 60.519 40.741 18.45 8.79 0.00 4.40
2254 5151 2.896685 AGCTCAAATAGAGGGATCTCGG 59.103 50.000 0.00 0.00 44.86 4.63
2310 5207 5.376854 AAAAGCTATGTGGTTAGCAGTTG 57.623 39.130 6.28 0.00 45.72 3.16
2326 5223 1.348036 AGTTGTGGTAGAAGTGGAGGC 59.652 52.381 0.00 0.00 0.00 4.70
2360 5257 6.500684 TTCGGAAAGATTGGAAAGATTCAG 57.499 37.500 0.00 0.00 0.00 3.02
2428 5325 5.159209 GCTGTTGAGGATCTTGTTGATTTG 58.841 41.667 0.00 0.00 35.14 2.32
2441 5338 7.518161 TCTTGTTGATTTGCAAATACGAGTAG 58.482 34.615 26.99 19.29 38.44 2.57
2475 5372 1.963515 GGAGGCACAAGTGAACCAAAT 59.036 47.619 4.04 0.00 0.00 2.32
2514 5411 1.933247 CTTCGAGGAATCACAGGAGC 58.067 55.000 0.00 0.00 0.00 4.70
2536 5433 3.555795 CGAGCACATTACCATGGATAGCT 60.556 47.826 21.47 17.32 34.27 3.32
2539 5436 6.131972 AGCACATTACCATGGATAGCTATT 57.868 37.500 21.47 0.00 34.27 1.73
2548 5445 6.376248 ACCATGGATAGCTATTGGTGATTTT 58.624 36.000 22.35 2.71 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 7.540055 GCGTATCGGCACTAGTAAGTTATAATT 59.460 37.037 0.00 0.0 31.97 1.40
229 234 9.817809 AGAAATGTCTCGCTAAATAAATCAGTA 57.182 29.630 0.00 0.0 0.00 2.74
253 258 3.868757 AGCACGCTATAACAGTTGAGA 57.131 42.857 0.00 0.0 0.00 3.27
286 1439 1.089112 CTGCCATCGATCACAAGCAA 58.911 50.000 0.00 0.0 0.00 3.91
317 1470 4.397103 GTCTAATAAAACCGGACAAAGGGG 59.603 45.833 9.46 0.0 0.00 4.79
498 1651 7.064229 TCCTAGTATTTTGGGTCAAACTTTGT 58.936 34.615 1.44 0.0 32.79 2.83
756 1909 8.711170 TGAGGGGAAAACTTATTCGTATCTATT 58.289 33.333 0.00 0.0 0.00 1.73
757 1910 8.148999 GTGAGGGGAAAACTTATTCGTATCTAT 58.851 37.037 0.00 0.0 0.00 1.98
758 1911 7.495055 GTGAGGGGAAAACTTATTCGTATCTA 58.505 38.462 0.00 0.0 0.00 1.98
759 1912 6.346896 GTGAGGGGAAAACTTATTCGTATCT 58.653 40.000 0.00 0.0 0.00 1.98
760 1913 5.233689 CGTGAGGGGAAAACTTATTCGTATC 59.766 44.000 0.00 0.0 0.00 2.24
761 1914 5.114081 CGTGAGGGGAAAACTTATTCGTAT 58.886 41.667 0.00 0.0 0.00 3.06
762 1915 4.021192 ACGTGAGGGGAAAACTTATTCGTA 60.021 41.667 0.00 0.0 0.00 3.43
763 1916 3.244318 ACGTGAGGGGAAAACTTATTCGT 60.244 43.478 0.00 0.0 0.00 3.85
764 1917 3.332034 ACGTGAGGGGAAAACTTATTCG 58.668 45.455 0.00 0.0 0.00 3.34
765 1918 5.353400 CCTAACGTGAGGGGAAAACTTATTC 59.647 44.000 11.67 0.0 32.39 1.75
766 1919 5.250982 CCTAACGTGAGGGGAAAACTTATT 58.749 41.667 11.67 0.0 32.39 1.40
767 1920 4.840271 CCTAACGTGAGGGGAAAACTTAT 58.160 43.478 11.67 0.0 32.39 1.73
768 1921 4.276058 CCTAACGTGAGGGGAAAACTTA 57.724 45.455 11.67 0.0 32.39 2.24
769 1922 3.136009 CCTAACGTGAGGGGAAAACTT 57.864 47.619 11.67 0.0 32.39 2.66
880 2034 2.835431 CCCTCAGATCGTCGCCCT 60.835 66.667 0.00 0.0 0.00 5.19
919 2074 3.315191 CCGAAGAAGAAAAGGTTTCTGCA 59.685 43.478 10.61 0.0 34.09 4.41
922 2077 2.885266 GCCCGAAGAAGAAAAGGTTTCT 59.115 45.455 0.00 0.0 35.25 2.52
992 2148 3.490793 ATCGCCTCCATGTCGCTCG 62.491 63.158 0.00 0.0 0.00 5.03
1253 2409 2.081161 GGCCCCTCCTCCATCACAT 61.081 63.158 0.00 0.0 0.00 3.21
1303 4196 3.620427 TGTAAAGCCATCATACGGTGT 57.380 42.857 0.00 0.0 0.00 4.16
1497 4391 0.739462 TCGGCGGCTTAGTGACATTG 60.739 55.000 7.21 0.0 0.00 2.82
1546 4440 5.633655 ATCTCTCTAACGACCTCCTTCTA 57.366 43.478 0.00 0.0 0.00 2.10
1560 4454 9.488762 TCATACTTAACCCTGAAAATCTCTCTA 57.511 33.333 0.00 0.0 0.00 2.43
1595 4489 1.146930 CACACAGTGCACCAGTCCT 59.853 57.895 14.63 0.0 0.00 3.85
1804 4698 4.412843 TCATCATATGGTTAGCGGTCCTA 58.587 43.478 2.13 0.0 0.00 2.94
1813 4707 4.996758 CGCAAGGTCATCATCATATGGTTA 59.003 41.667 2.13 0.0 0.00 2.85
1918 4814 2.882137 GTGTTTGGTTACTAGCTGGCAA 59.118 45.455 0.00 0.0 0.00 4.52
1938 4834 2.586792 GAGATTGCTGCCTCCGGT 59.413 61.111 0.00 0.0 0.00 5.28
1968 4865 1.200519 CTCTCCGGTATTGTTGGGGA 58.799 55.000 0.00 0.0 0.00 4.81
2001 4898 4.576463 TGACTTGTTTCTCTTTGGCTCTTC 59.424 41.667 0.00 0.0 0.00 2.87
2048 4945 2.840038 TGCTGCAGGATTCTTCTCCTTA 59.160 45.455 17.12 0.0 43.33 2.69
2122 5019 7.495606 CAGTTCCAACATAGTATACTCATTGCA 59.504 37.037 9.12 0.0 0.00 4.08
2223 5120 8.964533 TCCCTCTATTTGAGCTTCTAAGATAT 57.035 34.615 0.00 0.0 41.35 1.63
2234 5131 2.028567 CCCGAGATCCCTCTATTTGAGC 60.029 54.545 0.00 0.0 41.35 4.26
2254 5151 6.051179 AGAGTACCTACCAAATTCTCAACC 57.949 41.667 0.00 0.0 0.00 3.77
2310 5207 1.757699 CTAGGCCTCCACTTCTACCAC 59.242 57.143 9.68 0.0 0.00 4.16
2338 5235 5.560724 ACTGAATCTTTCCAATCTTTCCGA 58.439 37.500 0.00 0.0 0.00 4.55
2339 5236 5.886960 ACTGAATCTTTCCAATCTTTCCG 57.113 39.130 0.00 0.0 0.00 4.30
2340 5237 9.631452 CTTTTACTGAATCTTTCCAATCTTTCC 57.369 33.333 0.00 0.0 0.00 3.13
2343 5240 9.971922 CAACTTTTACTGAATCTTTCCAATCTT 57.028 29.630 0.00 0.0 0.00 2.40
2344 5241 9.354673 TCAACTTTTACTGAATCTTTCCAATCT 57.645 29.630 0.00 0.0 0.00 2.40
2345 5242 9.965824 TTCAACTTTTACTGAATCTTTCCAATC 57.034 29.630 0.00 0.0 0.00 2.67
2346 5243 9.971922 CTTCAACTTTTACTGAATCTTTCCAAT 57.028 29.630 0.00 0.0 31.40 3.16
2403 5300 4.025040 TCAACAAGATCCTCAACAGCAT 57.975 40.909 0.00 0.0 0.00 3.79
2428 5325 5.532025 AGACAAAAGCTACTCGTATTTGC 57.468 39.130 5.00 0.0 35.05 3.68
2441 5338 1.340991 TGCCTCCCCATAGACAAAAGC 60.341 52.381 0.00 0.0 0.00 3.51
2475 5372 9.599866 CTCGAAGCATATCCCATGTTTTATATA 57.400 33.333 0.00 0.0 0.00 0.86
2497 5394 0.679960 TCGCTCCTGTGATTCCTCGA 60.680 55.000 0.00 0.0 0.00 4.04
2514 5411 2.738846 GCTATCCATGGTAATGTGCTCG 59.261 50.000 12.58 0.0 31.27 5.03


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

AutoCloner maintained by Alex Coulton.