Multiple sequence alignment - TraesCS2A01G034500

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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 TraesCS2A01G034500 chr2A 100.000 2633 0 0 1 2633 15154709 15152077 0.000000e+00 4863
1 TraesCS2A01G034500 chr2D 96.705 2610 56 10 35 2622 13130487 13127886 0.000000e+00 4316
2 TraesCS2A01G034500 chr7A 83.889 180 21 7 1817 1992 47875555 47875380 5.830000e-37 165
3 TraesCS2A01G034500 chr7A 81.429 210 29 7 1802 2006 563500616 563500412 2.100000e-36 163
4 TraesCS2A01G034500 chr7A 82.584 178 25 5 1817 1992 715125804 715125631 4.540000e-33 152
5 TraesCS2A01G034500 chr3D 82.540 189 30 2 1808 1995 93614897 93614711 2.100000e-36 163
6 TraesCS2A01G034500 chr1A 82.632 190 25 6 1807 1992 49000174 49000359 7.540000e-36 161
7 TraesCS2A01G034500 chr5A 83.240 179 25 3 1817 1993 490309717 490309892 2.710000e-35 159
8 TraesCS2A01G034500 chr5A 83.146 178 19 8 1817 1989 398285794 398285965 4.540000e-33 152
9 TraesCS2A01G034500 chr3B 82.418 182 25 5 1817 1992 738760578 738760398 4.540000e-33 152


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 TraesCS2A01G034500 chr2A 15152077 15154709 2632 True 4863 4863 100.000 1 2633 1 chr2A.!!$R1 2632
1 TraesCS2A01G034500 chr2D 13127886 13130487 2601 True 4316 4316 96.705 35 2622 1 chr2D.!!$R1 2587

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
27 28 0.320683 CATGGCCGACTGTCAGTTCA 60.321 55.0 7.0 4.58 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1671 1676 2.237643 AGGACACACACCACAACTGTTA 59.762 45.455 0.0 0.0 0.0 2.41 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
17 18 3.813596 GTGGATGACATGGCCGAC 58.186 61.111 0.00 0.00 0.00 4.79
18 19 1.221840 GTGGATGACATGGCCGACT 59.778 57.895 0.00 0.00 0.00 4.18
19 20 1.091771 GTGGATGACATGGCCGACTG 61.092 60.000 0.00 0.00 0.00 3.51
20 21 1.221840 GGATGACATGGCCGACTGT 59.778 57.895 0.00 5.20 0.00 3.55
21 22 0.811616 GGATGACATGGCCGACTGTC 60.812 60.000 20.32 20.32 41.69 3.51
23 24 1.293179 TGACATGGCCGACTGTCAG 59.707 57.895 23.97 0.00 45.01 3.51
24 25 1.293498 GACATGGCCGACTGTCAGT 59.707 57.895 21.55 4.81 41.13 3.41
25 26 0.320771 GACATGGCCGACTGTCAGTT 60.321 55.000 21.55 0.00 41.13 3.16
26 27 0.320771 ACATGGCCGACTGTCAGTTC 60.321 55.000 7.00 0.00 0.00 3.01
27 28 0.320683 CATGGCCGACTGTCAGTTCA 60.321 55.000 7.00 4.58 0.00 3.18
28 29 0.615331 ATGGCCGACTGTCAGTTCAT 59.385 50.000 7.00 6.59 0.00 2.57
29 30 0.396435 TGGCCGACTGTCAGTTCATT 59.604 50.000 7.00 0.00 0.00 2.57
30 31 0.798776 GGCCGACTGTCAGTTCATTG 59.201 55.000 7.00 0.00 0.00 2.82
31 32 0.798776 GCCGACTGTCAGTTCATTGG 59.201 55.000 7.00 5.96 0.00 3.16
32 33 0.798776 CCGACTGTCAGTTCATTGGC 59.201 55.000 7.00 0.00 0.00 4.52
33 34 0.439985 CGACTGTCAGTTCATTGGCG 59.560 55.000 7.00 0.16 0.00 5.69
77 78 7.302524 GCTAGATATAAGGACGATATAGCTGC 58.697 42.308 0.00 0.00 37.40 5.25
99 100 0.997932 GCGACATCACTTGAGCAGAG 59.002 55.000 0.00 0.00 34.39 3.35
114 115 3.603671 GAGCCGGGGGTAGTAGCG 61.604 72.222 2.18 0.00 0.00 4.26
124 125 1.622312 GGGTAGTAGCGGATTAAGGGG 59.378 57.143 0.00 0.00 0.00 4.79
235 236 4.450053 GCTGTAGGAAGAAGCTGAATGAT 58.550 43.478 0.00 0.00 34.05 2.45
273 274 0.592637 CAGCGGTCTGTGCAAAATCA 59.407 50.000 0.00 0.00 35.61 2.57
314 315 4.506758 TGGGTTACTGTTAAATAGTCGGC 58.493 43.478 0.00 0.00 0.00 5.54
460 461 8.196771 GGGATATATGTTGTGCTTTTGATTTCA 58.803 33.333 0.00 0.00 0.00 2.69
597 602 5.866335 TGGCTGTACCGTGTTTTAATAAG 57.134 39.130 0.00 0.00 43.94 1.73
713 718 2.997986 GTCCAACCGTCGTGTATGATTT 59.002 45.455 0.00 0.00 0.00 2.17
765 770 5.870978 GTCAAGAACAAAGCCGTATAGGTAA 59.129 40.000 0.00 0.00 43.70 2.85
766 771 6.537660 GTCAAGAACAAAGCCGTATAGGTAAT 59.462 38.462 0.00 0.00 43.70 1.89
767 772 7.065443 GTCAAGAACAAAGCCGTATAGGTAATT 59.935 37.037 0.00 0.00 43.70 1.40
768 773 8.259411 TCAAGAACAAAGCCGTATAGGTAATTA 58.741 33.333 0.00 0.00 43.70 1.40
769 774 8.548721 CAAGAACAAAGCCGTATAGGTAATTAG 58.451 37.037 0.00 0.00 43.70 1.73
770 775 7.215085 AGAACAAAGCCGTATAGGTAATTAGG 58.785 38.462 0.00 0.00 43.70 2.69
771 776 6.490241 ACAAAGCCGTATAGGTAATTAGGT 57.510 37.500 0.00 0.00 43.70 3.08
772 777 7.601705 ACAAAGCCGTATAGGTAATTAGGTA 57.398 36.000 0.00 0.00 43.70 3.08
933 938 5.006153 TGTGAAGAAGAGAGAAACAACGA 57.994 39.130 0.00 0.00 0.00 3.85
1125 1130 3.718210 GACATCCGACGTCCCTGGC 62.718 68.421 10.58 3.26 0.00 4.85
1404 1409 4.343323 CATGGCACGGACACCCCA 62.343 66.667 0.00 0.00 34.14 4.96
1468 1473 1.599606 CGACAGCTCCCAGCACTACT 61.600 60.000 0.00 0.00 45.56 2.57
1670 1675 7.462731 CAGGTCGTCCGTATACTCTATATTTC 58.537 42.308 0.56 0.00 39.05 2.17
1671 1676 7.333921 CAGGTCGTCCGTATACTCTATATTTCT 59.666 40.741 0.56 0.00 39.05 2.52
1695 1700 1.145156 TTGTGGTGTGTGTCCTCCG 59.855 57.895 0.00 0.00 0.00 4.63
1836 1841 3.903714 TGTAGGGCATATGTAGATGTGCT 59.096 43.478 18.81 5.30 44.11 4.40
1841 1846 5.738909 GGGCATATGTAGATGTGCTCTAAT 58.261 41.667 18.81 0.00 42.47 1.73
1861 1866 9.539825 CTCTAATTATTGCACATCTAAGTGACT 57.460 33.333 0.00 0.00 42.05 3.41
1873 1878 8.777413 CACATCTAAGTGACTCAATCTCAAAAA 58.223 33.333 0.00 0.00 42.05 1.94
1912 1917 5.662211 AAGACAAAAGAAAATGCATGCAC 57.338 34.783 25.37 10.53 0.00 4.57
1919 1924 4.025015 AGAAAATGCATGCACGAATCTC 57.975 40.909 25.37 13.44 0.00 2.75
1963 1973 8.458052 TGTGTCTTAAATGTGCAATACTTATGG 58.542 33.333 0.00 0.00 0.00 2.74
2010 2020 9.026074 CAAAACTGATTAACAAAATACACCGTT 57.974 29.630 0.00 0.00 0.00 4.44
2037 2047 2.185310 AATGTCGCCCCCTCAGACAC 62.185 60.000 0.00 0.00 45.99 3.67
2177 2188 0.774276 TTTGGAGGGGTGCACACATA 59.226 50.000 22.94 0.00 0.00 2.29
2244 2255 0.250901 TGGTTCCTGAAAGCTGCTCC 60.251 55.000 1.00 0.00 36.31 4.70
2270 2281 6.617782 AGTCATGCTACAAGATATAGGCAT 57.382 37.500 0.00 0.00 40.38 4.40
2406 2417 0.606673 GTGGACTCAGTGGGGCTTTC 60.607 60.000 0.00 0.00 0.00 2.62
2438 2449 3.812053 GCAAGTGATTCACTCAACTCTGT 59.188 43.478 19.23 0.00 44.62 3.41
2460 2471 1.475751 CCCTAGTGCCCTACTGCAATG 60.476 57.143 0.00 0.00 44.11 2.82
2480 2491 6.128172 GCAATGCTTTCACTTGATAGTAGTGT 60.128 38.462 13.48 0.00 42.77 3.55
2501 2512 5.345741 GTGTATGCAACATTCGAAAATTGCT 59.654 36.000 32.39 24.53 46.06 3.91
2508 2519 6.237648 GCAACATTCGAAAATTGCTATTGGAG 60.238 38.462 28.80 9.52 43.26 3.86
2589 2612 5.382618 ACTTTTGGACATCAAAGATGCTC 57.617 39.130 6.90 4.53 45.00 4.26
2622 2645 7.322664 AGATGCATGTAAAATTTCGTTCCATT 58.677 30.769 2.46 0.00 0.00 3.16
2623 2646 8.465999 AGATGCATGTAAAATTTCGTTCCATTA 58.534 29.630 2.46 0.00 0.00 1.90
2624 2647 7.804614 TGCATGTAAAATTTCGTTCCATTAC 57.195 32.000 0.00 0.00 0.00 1.89
2625 2648 7.371159 TGCATGTAAAATTTCGTTCCATTACA 58.629 30.769 0.00 0.00 37.57 2.41
2626 2649 8.031864 TGCATGTAAAATTTCGTTCCATTACAT 58.968 29.630 10.57 10.57 41.89 2.29
2627 2650 8.531530 GCATGTAAAATTTCGTTCCATTACATC 58.468 33.333 12.34 7.27 40.22 3.06
2628 2651 9.787532 CATGTAAAATTTCGTTCCATTACATCT 57.212 29.630 12.34 0.00 40.22 2.90
2629 2652 9.787532 ATGTAAAATTTCGTTCCATTACATCTG 57.212 29.630 10.57 0.00 38.78 2.90
2630 2653 7.753132 TGTAAAATTTCGTTCCATTACATCTGC 59.247 33.333 0.00 0.00 30.68 4.26
2631 2654 4.536364 ATTTCGTTCCATTACATCTGCG 57.464 40.909 0.00 0.00 0.00 5.18
2632 2655 1.934589 TCGTTCCATTACATCTGCGG 58.065 50.000 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.091771 CAGTCGGCCATGTCATCCAC 61.092 60.000 2.24 0.00 0.00 4.02
1 2 1.221566 CAGTCGGCCATGTCATCCA 59.778 57.895 2.24 0.00 0.00 3.41
2 3 0.811616 GACAGTCGGCCATGTCATCC 60.812 60.000 21.74 1.85 44.21 3.51
3 4 2.682893 GACAGTCGGCCATGTCATC 58.317 57.895 21.74 1.71 44.21 2.92
4 5 4.941609 GACAGTCGGCCATGTCAT 57.058 55.556 21.74 0.00 44.21 3.06
6 7 0.320771 AACTGACAGTCGGCCATGTC 60.321 55.000 20.49 20.49 44.88 3.06
7 8 0.320771 GAACTGACAGTCGGCCATGT 60.321 55.000 8.93 3.88 0.00 3.21
8 9 0.320683 TGAACTGACAGTCGGCCATG 60.321 55.000 8.93 0.00 0.00 3.66
9 10 0.615331 ATGAACTGACAGTCGGCCAT 59.385 50.000 8.93 10.14 0.00 4.40
10 11 0.396435 AATGAACTGACAGTCGGCCA 59.604 50.000 8.93 8.26 0.00 5.36
11 12 0.798776 CAATGAACTGACAGTCGGCC 59.201 55.000 8.93 0.00 0.00 6.13
12 13 0.798776 CCAATGAACTGACAGTCGGC 59.201 55.000 8.93 2.49 0.00 5.54
13 14 0.798776 GCCAATGAACTGACAGTCGG 59.201 55.000 8.93 7.94 0.00 4.79
14 15 0.439985 CGCCAATGAACTGACAGTCG 59.560 55.000 8.93 2.31 0.00 4.18
15 16 1.728971 CTCGCCAATGAACTGACAGTC 59.271 52.381 8.93 3.49 0.00 3.51
16 17 1.609061 CCTCGCCAATGAACTGACAGT 60.609 52.381 1.07 1.07 0.00 3.55
17 18 1.081892 CCTCGCCAATGAACTGACAG 58.918 55.000 0.00 0.00 0.00 3.51
18 19 0.321564 CCCTCGCCAATGAACTGACA 60.322 55.000 0.00 0.00 0.00 3.58
19 20 1.648467 GCCCTCGCCAATGAACTGAC 61.648 60.000 0.00 0.00 0.00 3.51
20 21 1.377202 GCCCTCGCCAATGAACTGA 60.377 57.895 0.00 0.00 0.00 3.41
21 22 1.372087 GAGCCCTCGCCAATGAACTG 61.372 60.000 0.00 0.00 34.57 3.16
22 23 1.078143 GAGCCCTCGCCAATGAACT 60.078 57.895 0.00 0.00 34.57 3.01
23 24 2.464459 CGAGCCCTCGCCAATGAAC 61.464 63.158 4.63 0.00 46.50 3.18
24 25 2.125147 CGAGCCCTCGCCAATGAA 60.125 61.111 4.63 0.00 46.50 2.57
33 34 2.125350 CAGTCTTGGCGAGCCCTC 60.125 66.667 12.05 0.00 34.56 4.30
77 78 2.456119 GCTCAAGTGATGTCGCCGG 61.456 63.158 0.00 0.00 0.00 6.13
88 89 3.710722 CCCCGGCTCTGCTCAAGT 61.711 66.667 0.00 0.00 0.00 3.16
124 125 2.438075 CTGCTCAAGCTGCCTCCC 60.438 66.667 3.32 0.00 42.66 4.30
235 236 3.448301 GCTGGGTTGAAATCCAATGATCA 59.552 43.478 0.00 0.00 37.08 2.92
273 274 7.839680 AACCCATGAAGAGTTAGTTTCATTT 57.160 32.000 0.00 0.00 40.93 2.32
314 315 8.567948 CATGCTAACTAAAACATATTAGTGGGG 58.432 37.037 0.86 0.00 43.52 4.96
562 563 4.923871 CGGTACAGCCATAGATGTTCATAC 59.076 45.833 0.00 0.00 40.49 2.39
597 602 4.377738 GCCGTTTCTAAACACGTTCATTTC 59.622 41.667 6.41 0.00 38.81 2.17
697 702 3.777478 CTGGTAAATCATACACGACGGT 58.223 45.455 0.00 0.00 0.00 4.83
713 718 6.662865 TTGAAAATGAAAGAATGGCTGGTA 57.337 33.333 0.00 0.00 0.00 3.25
765 770 6.808829 CATGCAATGTTGGATTGTACCTAAT 58.191 36.000 0.00 0.00 40.20 1.73
766 771 6.206395 CATGCAATGTTGGATTGTACCTAA 57.794 37.500 0.00 0.00 40.20 2.69
767 772 5.833406 CATGCAATGTTGGATTGTACCTA 57.167 39.130 0.00 0.00 40.20 3.08
768 773 4.724074 CATGCAATGTTGGATTGTACCT 57.276 40.909 0.00 0.00 40.20 3.08
837 842 0.386352 TTCGCGACGACACTAACCTG 60.386 55.000 9.15 0.00 34.89 4.00
1404 1409 6.986817 GCACATATAAGTACACCTCAATCACT 59.013 38.462 0.00 0.00 0.00 3.41
1670 1675 2.612212 GGACACACACCACAACTGTTAG 59.388 50.000 0.00 0.00 0.00 2.34
1671 1676 2.237643 AGGACACACACCACAACTGTTA 59.762 45.455 0.00 0.00 0.00 2.41
1695 1700 4.740695 TGCAAATACGGTAGCAAAACAAAC 59.259 37.500 0.00 0.00 33.48 2.93
1800 1805 2.557056 GCCCTACAAAGACCCTTTGTTC 59.443 50.000 24.30 11.70 42.10 3.18
1836 1841 9.534565 GAGTCACTTAGATGTGCAATAATTAGA 57.465 33.333 0.00 0.00 37.81 2.10
1841 1846 8.043113 AGATTGAGTCACTTAGATGTGCAATAA 58.957 33.333 0.00 0.00 37.81 1.40
1905 1910 4.340894 TTTAACAGAGATTCGTGCATGC 57.659 40.909 11.82 11.82 0.00 4.06
1912 1917 9.218359 CATGTCATTCATTTTAACAGAGATTCG 57.782 33.333 0.00 0.00 34.09 3.34
2020 2030 3.311110 GTGTCTGAGGGGGCGACA 61.311 66.667 0.00 0.00 35.49 4.35
2037 2047 4.627467 CCTACAACAAGTCTCTTGAATCCG 59.373 45.833 15.04 2.96 0.00 4.18
2177 2188 3.245122 ACAATGTCGGTTATCCTGGGTTT 60.245 43.478 0.00 0.00 0.00 3.27
2270 2281 6.288941 TGGTTAACTAGATCCAACGATCAA 57.711 37.500 5.42 0.00 46.42 2.57
2386 2397 1.062488 AAAGCCCCACTGAGTCCACT 61.062 55.000 0.00 0.00 0.00 4.00
2406 2417 4.946157 AGTGAATCACTTGCCTAATCTTGG 59.054 41.667 10.56 0.00 42.59 3.61
2438 2449 2.367202 GCAGTAGGGCACTAGGGCA 61.367 63.158 20.77 0.00 45.66 5.36
2460 2471 6.535150 TGCATACACTACTATCAAGTGAAAGC 59.465 38.462 10.02 9.82 45.89 3.51
2480 2491 7.222417 CCAATAGCAATTTTCGAATGTTGCATA 59.778 33.333 31.85 24.48 46.92 3.14
2501 2512 0.106708 GATGTGCTCGGGCTCCAATA 59.893 55.000 9.62 0.00 39.59 1.90
2508 2519 0.319125 GCTAGTAGATGTGCTCGGGC 60.319 60.000 0.00 0.00 39.26 6.13
2557 2580 9.533253 CTTTGATGTCCAAAAGTTTTAGATTGT 57.467 29.630 0.00 0.00 43.50 2.71
2560 2583 9.918630 CATCTTTGATGTCCAAAAGTTTTAGAT 57.081 29.630 0.00 0.15 43.50 1.98
2564 2587 6.585416 AGCATCTTTGATGTCCAAAAGTTTT 58.415 32.000 8.98 0.00 43.50 2.43
2568 2591 4.461781 AGGAGCATCTTTGATGTCCAAAAG 59.538 41.667 20.30 3.20 43.50 2.27
2589 2612 7.641411 CGAAATTTTACATGCATCTAGAACAGG 59.359 37.037 0.00 2.74 0.00 4.00


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

AutoCloner maintained by Alex Coulton.