Multiple sequence alignment - TraesCS2A01G164400

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 TraesCS2A01G164400 chr2A 100.000 2522 0 0 1 2522 116699630 116697109 0.000000e+00 4658.0
1 TraesCS2A01G164400 chr2A 92.104 2495 182 10 37 2522 116832460 116829972 0.000000e+00 3502.0
2 TraesCS2A01G164400 chr2A 97.917 48 1 0 1 48 625139865 625139818 1.610000e-12 84.2
3 TraesCS2A01G164400 chr2D 92.308 2535 165 14 6 2522 115150859 115148337 0.000000e+00 3574.0
4 TraesCS2A01G164400 chr2D 84.241 1561 216 19 880 2424 44139949 44138403 0.000000e+00 1493.0
5 TraesCS2A01G164400 chr2D 84.702 621 70 18 150 766 192139611 192140210 4.640000e-167 597.0
6 TraesCS2A01G164400 chr2D 85.391 575 69 11 241 813 245074935 245075496 1.300000e-162 582.0
7 TraesCS2A01G164400 chr2B 91.647 2526 184 14 5 2519 165929360 165926851 0.000000e+00 3470.0
8 TraesCS2A01G164400 chr2B 91.502 2530 185 17 3 2519 165779683 165777171 0.000000e+00 3454.0
9 TraesCS2A01G164400 chr2B 100.000 30 0 0 55 84 191740351 191740380 3.500000e-04 56.5
10 TraesCS2A01G164400 chr4A 87.891 735 88 1 880 1614 735146447 735147180 0.000000e+00 863.0
11 TraesCS2A01G164400 chr4A 87.755 735 89 1 880 1614 735936559 735937292 0.000000e+00 857.0
12 TraesCS2A01G164400 chr4A 85.306 735 87 7 880 1614 736968624 736969337 0.000000e+00 739.0
13 TraesCS2A01G164400 chr4A 85.306 735 87 7 880 1614 736995739 736996452 0.000000e+00 739.0
14 TraesCS2A01G164400 chr7D 85.653 697 76 17 77 766 375036856 375037535 0.000000e+00 712.0
15 TraesCS2A01G164400 chr7D 95.918 49 2 0 1 49 486173846 486173894 2.080000e-11 80.5
16 TraesCS2A01G164400 chr7A 83.972 705 89 19 83 779 30158038 30157350 0.000000e+00 654.0
17 TraesCS2A01G164400 chr7A 83.573 694 99 12 77 766 421486623 421487305 9.840000e-179 636.0
18 TraesCS2A01G164400 chr7B 93.443 61 4 0 755 815 187599569 187599629 9.610000e-15 91.6
19 TraesCS2A01G164400 chr6D 92.727 55 4 0 1 55 161756247 161756193 2.080000e-11 80.5
20 TraesCS2A01G164400 chr3A 90.164 61 6 0 755 815 696406774 696406834 2.080000e-11 80.5
21 TraesCS2A01G164400 chr1B 95.918 49 2 0 1 49 169688914 169688866 2.080000e-11 80.5
22 TraesCS2A01G164400 chr1B 90.164 61 5 1 1 61 538306785 538306844 7.480000e-11 78.7
23 TraesCS2A01G164400 chr1B 100.000 30 0 0 55 84 668060926 668060897 3.500000e-04 56.5
24 TraesCS2A01G164400 chr1A 92.593 54 3 1 1 54 419162910 419162858 2.690000e-10 76.8
25 TraesCS2A01G164400 chr6A 97.059 34 1 0 54 87 359061050 359061017 9.740000e-05 58.4
26 TraesCS2A01G164400 chr6A 100.000 31 0 0 54 84 551860602 551860632 9.740000e-05 58.4
27 TraesCS2A01G164400 chr5B 100.000 31 0 0 54 84 121687328 121687298 9.740000e-05 58.4


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 TraesCS2A01G164400 chr2A 116697109 116699630 2521 True 4658 4658 100.000 1 2522 1 chr2A.!!$R1 2521
1 TraesCS2A01G164400 chr2A 116829972 116832460 2488 True 3502 3502 92.104 37 2522 1 chr2A.!!$R2 2485
2 TraesCS2A01G164400 chr2D 115148337 115150859 2522 True 3574 3574 92.308 6 2522 1 chr2D.!!$R2 2516
3 TraesCS2A01G164400 chr2D 44138403 44139949 1546 True 1493 1493 84.241 880 2424 1 chr2D.!!$R1 1544
4 TraesCS2A01G164400 chr2D 192139611 192140210 599 False 597 597 84.702 150 766 1 chr2D.!!$F1 616
5 TraesCS2A01G164400 chr2D 245074935 245075496 561 False 582 582 85.391 241 813 1 chr2D.!!$F2 572
6 TraesCS2A01G164400 chr2B 165926851 165929360 2509 True 3470 3470 91.647 5 2519 1 chr2B.!!$R2 2514
7 TraesCS2A01G164400 chr2B 165777171 165779683 2512 True 3454 3454 91.502 3 2519 1 chr2B.!!$R1 2516
8 TraesCS2A01G164400 chr4A 735146447 735147180 733 False 863 863 87.891 880 1614 1 chr4A.!!$F1 734
9 TraesCS2A01G164400 chr4A 735936559 735937292 733 False 857 857 87.755 880 1614 1 chr4A.!!$F2 734
10 TraesCS2A01G164400 chr4A 736968624 736969337 713 False 739 739 85.306 880 1614 1 chr4A.!!$F3 734
11 TraesCS2A01G164400 chr4A 736995739 736996452 713 False 739 739 85.306 880 1614 1 chr4A.!!$F4 734
12 TraesCS2A01G164400 chr7D 375036856 375037535 679 False 712 712 85.653 77 766 1 chr7D.!!$F1 689
13 TraesCS2A01G164400 chr7A 30157350 30158038 688 True 654 654 83.972 83 779 1 chr7A.!!$R1 696
14 TraesCS2A01G164400 chr7A 421486623 421487305 682 False 636 636 83.573 77 766 1 chr7A.!!$F1 689

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
379 383 1.003355 CTTCATGGTGTCCCGCACT 60.003 57.895 0.0 0.0 46.86 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2148 0.663153 CCCGCTTCCGATTTGAATCC 59.337 55.0 0.0 0.0 36.29 3.01 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
35 36 5.447624 AAAAACCGTTTGTATAGCAGCTT 57.552 34.783 0.00 0.00 0.00 3.74
45 46 4.900684 TGTATAGCAGCTTGTTGTACCAA 58.099 39.130 0.00 0.00 27.31 3.67
52 53 2.884639 AGCTTGTTGTACCAATGACCAC 59.115 45.455 0.00 0.00 0.00 4.16
103 104 8.259411 AGAAATTTTGCATGAATGGCTATTACA 58.741 29.630 0.00 0.00 0.00 2.41
108 109 4.202000 TGCATGAATGGCTATTACAAACGG 60.202 41.667 0.00 0.00 0.00 4.44
207 210 4.826274 ATGTAGCTTGTCTGGCTTTCTA 57.174 40.909 0.00 0.00 40.74 2.10
208 211 3.926616 TGTAGCTTGTCTGGCTTTCTAC 58.073 45.455 0.00 0.00 40.74 2.59
281 284 4.452733 CTGACGACCCGCCTTCCC 62.453 72.222 0.00 0.00 0.00 3.97
379 383 1.003355 CTTCATGGTGTCCCGCACT 60.003 57.895 0.00 0.00 46.86 4.40
386 390 3.635191 TGTCCCGCACTGCATCCA 61.635 61.111 1.11 0.00 0.00 3.41
417 421 1.011968 GTGCAGATGCGTACGACCAA 61.012 55.000 21.65 0.69 45.83 3.67
421 425 1.393539 CAGATGCGTACGACCAAAAGG 59.606 52.381 21.65 0.00 0.00 3.11
425 429 2.496111 TGCGTACGACCAAAAGGAAAT 58.504 42.857 21.65 0.00 0.00 2.17
516 520 9.406828 TGATAGTAATAAATGACATAGTGCGTC 57.593 33.333 0.00 0.00 0.00 5.19
625 634 6.369615 TGATCTCACATATATGGTGCGATTTG 59.630 38.462 16.96 3.85 39.90 2.32
642 651 8.730427 GTGCGATTTGTAAATTCTTAATTACCG 58.270 33.333 0.00 0.00 0.00 4.02
748 762 5.813513 AATGAGCAAGGGAAAATTCAGTT 57.186 34.783 0.00 0.00 0.00 3.16
753 767 3.573967 GCAAGGGAAAATTCAGTTGGAGA 59.426 43.478 8.11 0.00 0.00 3.71
793 807 1.120530 CCGGAGTACCAGGCTAACAT 58.879 55.000 0.00 0.00 35.59 2.71
965 980 6.442885 TCATCATCCATGGCTATAAGAGATGT 59.557 38.462 6.96 0.00 33.16 3.06
1007 1022 5.470098 TGCATCTTTTGTGTTCTCTCTTACC 59.530 40.000 0.00 0.00 0.00 2.85
1015 1030 3.006967 GTGTTCTCTCTTACCTGCCTTCA 59.993 47.826 0.00 0.00 0.00 3.02
1016 1031 3.646162 TGTTCTCTCTTACCTGCCTTCAA 59.354 43.478 0.00 0.00 0.00 2.69
1063 1078 4.118168 ACCCTCAATGTGACAATCCTTT 57.882 40.909 0.00 0.00 0.00 3.11
1154 1170 3.057033 AGAACAATGCACTTCCTCAATGC 60.057 43.478 0.00 0.00 39.88 3.56
1317 1338 1.073722 TGCAAAGAGCTCAGTGGGG 59.926 57.895 17.77 0.00 45.94 4.96
1361 1382 0.178981 AGGCTGAATGTGTTGTGGCT 60.179 50.000 0.00 0.00 0.00 4.75
1578 1601 5.105146 TGCCAAGTTGTCTTTATGTTTTGGT 60.105 36.000 1.45 0.00 36.93 3.67
1709 1737 6.370994 TGTGTTGCAAAAATGATGTGTTCTTT 59.629 30.769 0.00 0.00 0.00 2.52
1716 1744 7.614908 CAAAAATGATGTGTTCTTTGTGACTG 58.385 34.615 0.00 0.00 0.00 3.51
1772 1805 1.686052 GATCATGAGACTCGCTCCCTT 59.314 52.381 0.09 0.00 43.26 3.95
1787 1820 6.650120 TCGCTCCCTTATTTTCTGAAGTAAT 58.350 36.000 0.00 0.00 0.00 1.89
1789 1822 8.262227 TCGCTCCCTTATTTTCTGAAGTAATAA 58.738 33.333 6.94 6.94 0.00 1.40
1820 1853 5.564550 ACAAAGAAGATGTGTGAGCCTAAT 58.435 37.500 0.00 0.00 0.00 1.73
1821 1854 5.413833 ACAAAGAAGATGTGTGAGCCTAATG 59.586 40.000 0.00 0.00 0.00 1.90
1931 1964 4.530553 TGGAACTCTTATAAGTCTGGTGCA 59.469 41.667 12.19 10.60 0.00 4.57
1937 1970 5.516044 TCTTATAAGTCTGGTGCACTCCTA 58.484 41.667 17.98 0.17 0.00 2.94
1956 1989 3.053291 GTGACCGCGGCCAAATGA 61.053 61.111 28.58 0.00 0.00 2.57
1963 1996 2.952978 ACCGCGGCCAAATGAAATAATA 59.047 40.909 28.58 0.00 0.00 0.98
2106 2139 3.319689 TGTGGACTCGAATGCGGATATAA 59.680 43.478 0.00 0.00 38.28 0.98
2130 2163 2.351726 GACCACGGATTCAAATCGGAAG 59.648 50.000 14.85 8.97 38.61 3.46
2158 2191 2.949644 AGACTTGGACCGAAAACCAAAG 59.050 45.455 0.00 0.00 44.03 2.77
2254 2287 7.147689 TGGCCTTGCATGAATCAATTAGTTAAT 60.148 33.333 3.32 0.00 0.00 1.40
2291 2324 5.296780 TGATTTAGGCTAAAATCCGAGCTTG 59.703 40.000 22.42 0.00 42.63 4.01
2441 2475 9.860898 GCTAGGATTGTTTTACTCAAAAATCAT 57.139 29.630 0.00 0.00 39.22 2.45
2511 2545 8.962884 ATAATCCGTATTTGCATGCTATATGA 57.037 30.769 20.33 15.42 0.00 2.15
2514 2548 7.770801 TCCGTATTTGCATGCTATATGATAC 57.229 36.000 20.33 14.01 0.00 2.24
2515 2549 6.761242 TCCGTATTTGCATGCTATATGATACC 59.239 38.462 20.33 3.47 0.00 2.73
2516 2550 6.292328 CCGTATTTGCATGCTATATGATACCG 60.292 42.308 20.33 13.31 0.00 4.02
2517 2551 6.255670 CGTATTTGCATGCTATATGATACCGT 59.744 38.462 20.33 0.00 0.00 4.83
2518 2552 7.434013 CGTATTTGCATGCTATATGATACCGTA 59.566 37.037 20.33 0.00 0.00 4.02
2519 2553 6.961359 TTTGCATGCTATATGATACCGTAC 57.039 37.500 20.33 0.00 0.00 3.67
2520 2554 5.006153 TGCATGCTATATGATACCGTACC 57.994 43.478 20.33 0.00 0.00 3.34
2521 2555 4.142026 TGCATGCTATATGATACCGTACCC 60.142 45.833 20.33 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 1.699634 AGCAGTTGGTAGTGTGGTCAT 59.300 47.619 0.00 0.00 0.00 3.06
52 53 3.197766 TCCTAATGGAGCAGTTGGTAGTG 59.802 47.826 0.00 0.00 37.46 2.74
80 81 8.667463 GTTTGTAATAGCCATTCATGCAAAATT 58.333 29.630 0.00 0.00 0.00 1.82
103 104 0.665369 CTTGGTAGTCGTCGCCGTTT 60.665 55.000 0.00 0.00 35.01 3.60
108 109 2.872370 ACAATACTTGGTAGTCGTCGC 58.128 47.619 0.00 0.00 35.78 5.19
163 166 3.256383 TCTGAAATCAAGTGTGGCCATTG 59.744 43.478 9.72 10.36 0.00 2.82
379 383 4.193893 CCCCTGCGGATGGATGCA 62.194 66.667 0.00 0.00 39.13 3.96
399 403 0.319986 TTTGGTCGTACGCATCTGCA 60.320 50.000 11.24 0.00 42.21 4.41
494 498 7.489160 TCTGACGCACTATGTCATTTATTACT 58.511 34.615 0.00 0.00 44.70 2.24
495 499 7.694388 TCTGACGCACTATGTCATTTATTAC 57.306 36.000 0.00 0.00 44.70 1.89
748 762 0.487325 TTCCTCTCACCACCTCTCCA 59.513 55.000 0.00 0.00 0.00 3.86
753 767 4.663334 GGTTTTATTTCCTCTCACCACCT 58.337 43.478 0.00 0.00 0.00 4.00
815 830 9.607285 CAATATATGTGTGACATGATGTTGATG 57.393 33.333 0.00 0.00 39.53 3.07
929 944 5.818336 GCCATGGATGATGATATCTGAAGAG 59.182 44.000 18.40 0.00 33.31 2.85
965 980 4.233632 TGCACATCCAAATGGTCTATGA 57.766 40.909 6.61 0.00 37.19 2.15
1007 1022 6.537301 TCAAGTAATATACGGTTTGAAGGCAG 59.463 38.462 0.00 0.00 0.00 4.85
1015 1030 6.990349 CCCATGTCTCAAGTAATATACGGTTT 59.010 38.462 0.00 0.00 0.00 3.27
1016 1031 6.325545 TCCCATGTCTCAAGTAATATACGGTT 59.674 38.462 0.00 0.00 0.00 4.44
1063 1078 5.880332 GTGGCATGAGGAGTAGAAAACATAA 59.120 40.000 0.00 0.00 0.00 1.90
1117 1133 5.627503 GCATTGTTCTTGCAGGGGATTATTT 60.628 40.000 0.00 0.00 39.90 1.40
1154 1170 3.741344 GGCTAGCAAACGTATAGACCATG 59.259 47.826 18.24 0.00 0.00 3.66
1199 1219 8.712228 AGGGACAAAAGAAAAGAATGTAAGAT 57.288 30.769 0.00 0.00 0.00 2.40
1200 1220 8.533569 AAGGGACAAAAGAAAAGAATGTAAGA 57.466 30.769 0.00 0.00 0.00 2.10
1275 1296 2.912956 TCTTGGCCTCTGAACCTACAAT 59.087 45.455 3.32 0.00 0.00 2.71
1317 1338 1.931172 ACAACGTGAAGCGGTATATGC 59.069 47.619 0.00 0.00 46.52 3.14
1444 1466 6.585389 ACACGTTTCTTCTTTAACACTCTC 57.415 37.500 0.00 0.00 0.00 3.20
1578 1601 9.891828 GTTAGATATTCATGTGTGTGTTTTGAA 57.108 29.630 0.00 0.00 0.00 2.69
1709 1737 5.478407 CGGATATATATGCAACCAGTCACA 58.522 41.667 13.86 0.00 0.00 3.58
1787 1820 7.335673 TCACACATCTTCTTTGTTCACTTGTTA 59.664 33.333 0.00 0.00 0.00 2.41
1789 1822 5.647658 TCACACATCTTCTTTGTTCACTTGT 59.352 36.000 0.00 0.00 0.00 3.16
1931 1964 3.003113 GCCGCGGTCACTTAGGAGT 62.003 63.158 28.70 0.00 36.25 3.85
1937 1970 2.282180 ATTTGGCCGCGGTCACTT 60.282 55.556 35.74 20.58 0.00 3.16
1963 1996 7.290014 AGGGTTTACAAAATGAATGTTCTCCTT 59.710 33.333 0.00 0.00 32.27 3.36
2054 2087 6.406370 TCAATATCGGATCCGCAATTAATCT 58.594 36.000 29.62 6.31 39.59 2.40
2059 2092 3.691118 CCATCAATATCGGATCCGCAATT 59.309 43.478 29.62 24.64 39.59 2.32
2062 2095 1.066215 CCCATCAATATCGGATCCGCA 60.066 52.381 29.62 19.20 39.59 5.69
2068 2101 2.774809 TCCACAACCCATCAATATCGGA 59.225 45.455 0.00 0.00 0.00 4.55
2106 2139 1.734163 GATTTGAATCCGTGGTCCGT 58.266 50.000 0.00 0.00 33.66 4.69
2115 2148 0.663153 CCCGCTTCCGATTTGAATCC 59.337 55.000 0.00 0.00 36.29 3.01
2263 2296 8.540388 AGCTCGGATTTTAGCCTAAATCATATA 58.460 33.333 17.80 4.68 43.24 0.86
2441 2475 8.533657 TGTCTAAGAGTTTCAAACCGGATAATA 58.466 33.333 9.46 0.00 0.00 0.98
2497 2531 5.416083 GGTACGGTATCATATAGCATGCAA 58.584 41.667 21.98 5.05 0.00 4.08


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

AutoCloner maintained by Alex Coulton.