Multiple sequence alignment - TraesCS2A01G000500

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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 TraesCS2A01G000500 chr2A 100.000 3001 0 0 1 3001 328106 325106 0.000000e+00 5542.0
1 TraesCS2A01G000500 chr2A 86.451 1668 155 41 193 1834 487019098 487020720 0.000000e+00 1762.0
2 TraesCS2A01G000500 chr2A 92.495 533 30 7 2472 3001 130272409 130271884 0.000000e+00 754.0
3 TraesCS2A01G000500 chr2A 92.308 533 30 8 2472 3001 293274544 293274020 0.000000e+00 747.0
4 TraesCS2A01G000500 chr2A 92.120 533 32 7 2472 3001 130280510 130279985 0.000000e+00 743.0
5 TraesCS2A01G000500 chr2A 89.695 262 17 3 1583 1834 487012561 487012822 2.880000e-85 326.0
6 TraesCS2A01G000500 chr1A 93.870 3018 151 19 1 2998 261693453 261696456 0.000000e+00 4518.0
7 TraesCS2A01G000500 chr1A 90.726 1790 135 21 1 1766 248733479 248731697 0.000000e+00 2357.0
8 TraesCS2A01G000500 chr1A 90.452 1791 138 23 1 1766 265097458 265095676 0.000000e+00 2329.0
9 TraesCS2A01G000500 chr1A 89.838 1791 144 20 1 1766 265069807 265068030 0.000000e+00 2265.0
10 TraesCS2A01G000500 chr1A 95.302 1341 52 8 1660 2998 261699817 261701148 0.000000e+00 2117.0
11 TraesCS2A01G000500 chr1A 82.906 1796 203 60 1 1727 66617924 66616164 0.000000e+00 1520.0
12 TraesCS2A01G000500 chr1A 95.050 101 5 0 2383 2483 520133298 520133398 3.100000e-35 159.0
13 TraesCS2A01G000500 chr1A 94.059 101 6 0 2383 2483 520141486 520141586 1.440000e-33 154.0
14 TraesCS2A01G000500 chr1A 94.118 51 3 0 1716 1766 42678254 42678204 8.920000e-11 78.7
15 TraesCS2A01G000500 chr1A 92.157 51 4 0 1716 1766 42702948 42702898 4.150000e-09 73.1
16 TraesCS2A01G000500 chr1A 90.196 51 5 0 1716 1766 42732213 42732163 1.930000e-07 67.6
17 TraesCS2A01G000500 chr3A 92.015 2417 156 15 1 2383 333278442 333276029 0.000000e+00 3360.0
18 TraesCS2A01G000500 chr3A 92.759 2320 142 16 1 2300 333289515 333287202 0.000000e+00 3330.0
19 TraesCS2A01G000500 chr3A 96.577 818 23 3 2186 3001 333275630 333274816 0.000000e+00 1351.0
20 TraesCS2A01G000500 chr3A 96.134 569 19 1 2330 2898 333286961 333286396 0.000000e+00 926.0
21 TraesCS2A01G000500 chr3A 88.462 78 4 3 2302 2376 176228251 176228326 4.120000e-14 89.8
22 TraesCS2A01G000500 chr5A 90.152 1777 143 19 1 1753 166023761 166021993 0.000000e+00 2283.0
23 TraesCS2A01G000500 chr5A 89.888 1790 150 18 1 1766 166015428 166013646 0.000000e+00 2274.0
24 TraesCS2A01G000500 chr5A 89.124 1793 151 27 1 1766 205523953 205525728 0.000000e+00 2191.0
25 TraesCS2A01G000500 chr5A 87.285 1864 165 43 1 1834 111861700 111863521 0.000000e+00 2063.0
26 TraesCS2A01G000500 chr5A 89.566 1591 122 15 1 1554 21708211 21706628 0.000000e+00 1978.0
27 TraesCS2A01G000500 chr5A 93.667 300 18 1 1826 2124 111863630 111863929 5.900000e-122 448.0
28 TraesCS2A01G000500 chr6A 89.582 1795 152 22 1 1766 182820055 182818267 0.000000e+00 2246.0
29 TraesCS2A01G000500 chr6A 89.415 1795 156 20 1 1766 182812050 182810261 0.000000e+00 2231.0
30 TraesCS2A01G000500 chr6A 83.824 1867 220 54 1 1834 243624652 243622835 0.000000e+00 1700.0
31 TraesCS2A01G000500 chr6A 87.267 322 38 3 1826 2145 243622723 243622403 6.110000e-97 364.0
32 TraesCS2A01G000500 chr6A 90.514 253 14 3 1524 1766 397288377 397288125 2.880000e-85 326.0
33 TraesCS2A01G000500 chr7A 83.013 1872 205 65 1 1834 335908205 335910001 0.000000e+00 1591.0
34 TraesCS2A01G000500 chr7A 92.884 534 27 8 2472 3001 552756153 552756679 0.000000e+00 765.0
35 TraesCS2A01G000500 chr7A 93.146 321 21 1 1826 2145 509628094 509628414 1.260000e-128 470.0
36 TraesCS2A01G000500 chr7A 90.462 325 29 2 1826 2148 335910113 335910437 7.690000e-116 427.0
37 TraesCS2A01G000500 chr7A 91.954 87 4 3 2312 2395 350026441 350026355 5.260000e-23 119.0
38 TraesCS2A01G000500 chr7A 90.805 87 5 3 2312 2395 350020256 350020170 2.450000e-21 113.0
39 TraesCS2A01G000500 chr4A 92.322 534 29 9 2472 3001 448936705 448936180 0.000000e+00 749.0
40 TraesCS2A01G000500 chr4A 81.763 828 99 30 1021 1834 267262571 267263360 0.000000e+00 645.0
41 TraesCS2A01G000500 chr4A 84.716 458 54 12 1336 1792 267159121 267159563 7.630000e-121 444.0
42 TraesCS2A01G000500 chr4A 88.785 321 35 1 1826 2145 186644029 186644349 2.800000e-105 392.0
43 TraesCS2A01G000500 chr4A 87.732 269 29 3 1883 2148 267191991 267192258 8.080000e-81 311.0
44 TraesCS2A01G000500 chr4A 89.944 179 18 0 1826 2004 276266517 276266695 6.470000e-57 231.0
45 TraesCS2A01G000500 chr4A 94.898 98 5 0 2386 2483 146933841 146933744 1.440000e-33 154.0
46 TraesCS2A01G000500 chr4A 94.845 97 5 0 2387 2483 540998887 540998983 5.180000e-33 152.0
47 TraesCS2A01G000500 chr4A 93.878 98 6 0 2386 2483 146925652 146925555 6.700000e-32 148.0
48 TraesCS2A01G000500 chr4A 89.333 75 7 1 2302 2376 329607350 329607423 3.190000e-15 93.5


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 TraesCS2A01G000500 chr2A 325106 328106 3000 True 5542.0 5542 100.0000 1 3001 1 chr2A.!!$R1 3000
1 TraesCS2A01G000500 chr2A 487019098 487020720 1622 False 1762.0 1762 86.4510 193 1834 1 chr2A.!!$F2 1641
2 TraesCS2A01G000500 chr2A 130271884 130272409 525 True 754.0 754 92.4950 2472 3001 1 chr2A.!!$R2 529
3 TraesCS2A01G000500 chr2A 293274020 293274544 524 True 747.0 747 92.3080 2472 3001 1 chr2A.!!$R4 529
4 TraesCS2A01G000500 chr2A 130279985 130280510 525 True 743.0 743 92.1200 2472 3001 1 chr2A.!!$R3 529
5 TraesCS2A01G000500 chr1A 261693453 261701148 7695 False 3317.5 4518 94.5860 1 2998 2 chr1A.!!$F3 2997
6 TraesCS2A01G000500 chr1A 248731697 248733479 1782 True 2357.0 2357 90.7260 1 1766 1 chr1A.!!$R5 1765
7 TraesCS2A01G000500 chr1A 265095676 265097458 1782 True 2329.0 2329 90.4520 1 1766 1 chr1A.!!$R7 1765
8 TraesCS2A01G000500 chr1A 265068030 265069807 1777 True 2265.0 2265 89.8380 1 1766 1 chr1A.!!$R6 1765
9 TraesCS2A01G000500 chr1A 66616164 66617924 1760 True 1520.0 1520 82.9060 1 1727 1 chr1A.!!$R4 1726
10 TraesCS2A01G000500 chr3A 333274816 333278442 3626 True 2355.5 3360 94.2960 1 3001 2 chr3A.!!$R1 3000
11 TraesCS2A01G000500 chr3A 333286396 333289515 3119 True 2128.0 3330 94.4465 1 2898 2 chr3A.!!$R2 2897
12 TraesCS2A01G000500 chr5A 166021993 166023761 1768 True 2283.0 2283 90.1520 1 1753 1 chr5A.!!$R3 1752
13 TraesCS2A01G000500 chr5A 166013646 166015428 1782 True 2274.0 2274 89.8880 1 1766 1 chr5A.!!$R2 1765
14 TraesCS2A01G000500 chr5A 205523953 205525728 1775 False 2191.0 2191 89.1240 1 1766 1 chr5A.!!$F1 1765
15 TraesCS2A01G000500 chr5A 21706628 21708211 1583 True 1978.0 1978 89.5660 1 1554 1 chr5A.!!$R1 1553
16 TraesCS2A01G000500 chr5A 111861700 111863929 2229 False 1255.5 2063 90.4760 1 2124 2 chr5A.!!$F2 2123
17 TraesCS2A01G000500 chr6A 182818267 182820055 1788 True 2246.0 2246 89.5820 1 1766 1 chr6A.!!$R2 1765
18 TraesCS2A01G000500 chr6A 182810261 182812050 1789 True 2231.0 2231 89.4150 1 1766 1 chr6A.!!$R1 1765
19 TraesCS2A01G000500 chr6A 243622403 243624652 2249 True 1032.0 1700 85.5455 1 2145 2 chr6A.!!$R4 2144
20 TraesCS2A01G000500 chr7A 335908205 335910437 2232 False 1009.0 1591 86.7375 1 2148 2 chr7A.!!$F3 2147
21 TraesCS2A01G000500 chr7A 552756153 552756679 526 False 765.0 765 92.8840 2472 3001 1 chr7A.!!$F2 529
22 TraesCS2A01G000500 chr4A 448936180 448936705 525 True 749.0 749 92.3220 2472 3001 1 chr4A.!!$R3 529
23 TraesCS2A01G000500 chr4A 267262571 267263360 789 False 645.0 645 81.7630 1021 1834 1 chr4A.!!$F4 813

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
51 52 2.014010 ACCCTACCGTGTAAGGAACA 57.986 50.000 5.91 0.0 34.58 3.18 F
1019 1101 2.242043 CATGGCAGAAAGAAAGGGTGT 58.758 47.619 0.00 0.0 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1049 1131 0.107557 ACCGGAACCAGAACGTTGTT 60.108 50.0 9.46 3.43 0.0 2.83 R
2326 3230 0.396278 CCTCCTGCCCATTTCCTTCC 60.396 60.0 0.00 0.00 0.0 3.46 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
51 52 2.014010 ACCCTACCGTGTAAGGAACA 57.986 50.000 5.91 0.0 34.58 3.18
66 67 4.184649 AGGAACACAAAATCTGGGAACT 57.815 40.909 0.00 0.0 30.48 3.01
83 84 4.440525 GGGAACTTAACACCGATATGACGA 60.441 45.833 0.00 0.0 35.09 4.20
284 318 3.670625 TGAGCAAAAGCGGTAACATAGT 58.329 40.909 0.00 0.0 0.00 2.12
317 351 2.557869 TGCTAGGACAAGGTGGGTTAT 58.442 47.619 0.00 0.0 0.00 1.89
369 406 7.832685 TGATATAGCAAGTGGTAGGTATCGTAT 59.167 37.037 0.00 0.0 29.40 3.06
559 609 2.618709 AGAAGCAACACCGAAAAGAAGG 59.381 45.455 0.00 0.0 0.00 3.46
642 694 5.507149 GCATGTCCGGTTTAAATATGCATGA 60.507 40.000 10.16 0.0 39.25 3.07
657 709 6.123852 TATGCATGACATGGCAAAGTGCAA 62.124 41.667 27.30 16.0 44.20 4.08
696 748 7.408756 AATTAAGTGGAGCTCAATATGCAAA 57.591 32.000 17.19 0.0 0.00 3.68
745 801 9.521503 CACATCAATTATTTAGTTCTCTCTCGA 57.478 33.333 0.00 0.0 0.00 4.04
756 812 9.629878 TTTAGTTCTCTCTCGATTAGGTATTCT 57.370 33.333 0.00 0.0 0.00 2.40
992 1069 5.746307 TGACAAGAGCATTATGAAGCATC 57.254 39.130 0.00 0.0 0.00 3.91
1019 1101 2.242043 CATGGCAGAAAGAAAGGGTGT 58.758 47.619 0.00 0.0 0.00 4.16
1187 1278 2.216331 AAGGCAAAAGCGGGGCAAT 61.216 52.632 0.00 0.0 0.00 3.56
1317 1412 1.595929 GAACGGTTCGGGTCAAGCA 60.596 57.895 4.94 0.0 0.00 3.91
1535 1693 0.906775 CGGTGTAGGGGGTACATGTT 59.093 55.000 2.30 0.0 43.70 2.71
1591 1749 2.879163 CGATCTCGTCAACCCGAAGGA 61.879 57.143 0.00 0.0 42.82 3.36
1592 1750 4.154028 CGATCTCGTCAACCCGAAGGAT 62.154 54.545 0.00 0.0 42.82 3.24
1624 1782 5.012239 ACAATCCACATAGTCATGCACTTT 58.988 37.500 0.00 0.0 36.43 2.66
1700 1868 2.492088 AGTTCTTCGGATGTCGTCATGA 59.508 45.455 0.00 0.0 40.32 3.07
1806 1974 1.091197 TGTGCATGCAGGCATAGTCG 61.091 55.000 30.32 0.0 46.92 4.18
1945 2233 1.512310 CAGACGAGACGAAGGACGC 60.512 63.158 0.00 0.0 46.94 5.19
2041 2329 3.640407 GCAGGTGGTGGAGAGGCA 61.640 66.667 0.00 0.0 0.00 4.75
2282 3186 1.043116 AGATGGGATCGAGCGGTTCA 61.043 55.000 0.00 0.0 0.00 3.18
2300 3204 3.825160 ATGGGAACTGCGTGCGTGT 62.825 57.895 0.00 0.0 0.00 4.49
2709 3827 6.670695 ACTTGAGGCATTTTTGAACCTAAT 57.329 33.333 0.00 0.0 30.95 1.73
2710 3828 7.775053 ACTTGAGGCATTTTTGAACCTAATA 57.225 32.000 0.00 0.0 30.95 0.98
2711 3829 8.189119 ACTTGAGGCATTTTTGAACCTAATAA 57.811 30.769 0.00 0.0 30.95 1.40
2744 3862 5.182001 ACTCCAAAGGATCTGAAATTTGACG 59.818 40.000 0.00 0.0 35.19 4.35
2858 8668 5.730697 AGAAGGAAAGGAGAAGGAGATGATT 59.269 40.000 0.00 0.0 0.00 2.57
2862 8672 6.848631 AGGAAAGGAGAAGGAGATGATTCATA 59.151 38.462 0.00 0.0 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 4.277423 CGGTGTTAAGTTCCCAGATTTTGT 59.723 41.667 0.00 0.00 0.00 2.83
66 67 6.753279 CCTAGTTTTCGTCATATCGGTGTTAA 59.247 38.462 0.00 0.00 0.00 2.01
83 84 0.400594 ACTCTTGCCGCCCTAGTTTT 59.599 50.000 0.00 0.00 0.00 2.43
317 351 1.421268 CCCATAGCCATGTTCAGCCTA 59.579 52.381 0.00 0.00 0.00 3.93
369 406 3.133691 CGCTCTTTTGCTATGCCTATGA 58.866 45.455 0.00 0.00 0.00 2.15
408 445 6.781014 ACCATACCCTCGAAATCACTTCTATA 59.219 38.462 0.00 0.00 31.20 1.31
460 497 4.991687 GTCTTCTTCATGGACTCGTTCTTT 59.008 41.667 0.00 0.00 0.00 2.52
559 609 6.693978 GTGGTGGTTGTTTACTATGTTGTTTC 59.306 38.462 0.00 0.00 0.00 2.78
642 694 1.473080 GGTTGTTGCACTTTGCCATGT 60.473 47.619 0.00 0.00 44.23 3.21
657 709 9.541143 CTCCACTTAATTTGTAATTTTGGTTGT 57.459 29.630 0.00 0.00 0.00 3.32
658 710 8.495148 GCTCCACTTAATTTGTAATTTTGGTTG 58.505 33.333 0.00 0.00 0.00 3.77
662 714 9.474920 TTGAGCTCCACTTAATTTGTAATTTTG 57.525 29.630 12.15 0.00 0.00 2.44
667 719 8.405531 GCATATTGAGCTCCACTTAATTTGTAA 58.594 33.333 12.15 0.00 36.40 2.41
696 748 3.190535 GTGTTTCGTCAATATGCAACCCT 59.809 43.478 0.00 0.00 0.00 4.34
756 812 8.602328 CCACGTTAACCGACATTTAATATTGTA 58.398 33.333 0.00 0.00 40.70 2.41
771 827 0.601841 ACCTCTTGCCACGTTAACCG 60.602 55.000 0.00 0.00 44.03 4.44
779 836 0.253044 TATGCCTCACCTCTTGCCAC 59.747 55.000 0.00 0.00 0.00 5.01
926 996 3.872696 ACTTGTTCATGTCATCCGCATA 58.127 40.909 0.00 0.00 0.00 3.14
1019 1101 0.795698 TTCCGTTATCGTCGTCGTGA 59.204 50.000 1.33 0.00 38.33 4.35
1049 1131 0.107557 ACCGGAACCAGAACGTTGTT 60.108 50.000 9.46 3.43 0.00 2.83
1503 1661 2.307611 TACACCGCACCGAAACACCA 62.308 55.000 0.00 0.00 0.00 4.17
1527 1685 3.309682 CCATGACGACCATCAACATGTAC 59.690 47.826 0.00 0.00 37.29 2.90
1535 1693 2.093711 CCAAGTACCATGACGACCATCA 60.094 50.000 0.00 0.00 31.94 3.07
1591 1749 7.857456 TGACTATGTGGATTGTACCAAGTAAT 58.143 34.615 0.00 0.00 41.87 1.89
1592 1750 7.247456 TGACTATGTGGATTGTACCAAGTAA 57.753 36.000 0.00 0.00 41.87 2.24
1608 1766 5.178061 TCGATGAAAAGTGCATGACTATGT 58.822 37.500 0.00 0.00 36.65 2.29
1624 1782 0.530744 CCGTCAAGTCCCTCGATGAA 59.469 55.000 0.00 0.00 0.00 2.57
1654 1822 1.375523 CACCAAGTCCCACTACCGC 60.376 63.158 0.00 0.00 0.00 5.68
1690 1858 3.917985 CGTGAACAAGTATCATGACGACA 59.082 43.478 0.00 0.00 36.17 4.35
1700 1868 4.863491 ACGACTACAACGTGAACAAGTAT 58.137 39.130 0.00 0.00 42.37 2.12
1806 1974 2.017559 CTCCCCTGTCCCGATTCGTC 62.018 65.000 5.20 0.00 0.00 4.20
1821 1989 1.376553 GACCAGCAGTCAAGCTCCC 60.377 63.158 2.27 0.00 44.54 4.30
1856 2144 2.049156 TCGCGCCTCTGTTCTGTG 60.049 61.111 0.00 0.00 0.00 3.66
2187 2477 1.202651 CCCGAGACCTCTCTCTCTCTC 60.203 61.905 0.93 0.00 40.96 3.20
2188 2478 0.837272 CCCGAGACCTCTCTCTCTCT 59.163 60.000 0.93 0.00 40.96 3.10
2282 3186 3.049674 CACGCACGCAGTTCCCAT 61.050 61.111 0.00 0.00 41.61 4.00
2300 3204 0.823769 CCCTCGATCGATCTCACCCA 60.824 60.000 19.78 0.00 0.00 4.51
2326 3230 0.396278 CCTCCTGCCCATTTCCTTCC 60.396 60.000 0.00 0.00 0.00 3.46
2335 3450 2.367377 CCATCTCCCTCCTGCCCA 60.367 66.667 0.00 0.00 0.00 5.36
2443 3558 2.046892 AGCCGCAACCTGTAGCTG 60.047 61.111 0.00 0.00 31.23 4.24
2709 3827 6.040391 CAGATCCTTTGGAGTTGTTTTGGTTA 59.960 38.462 0.00 0.00 34.05 2.85
2710 3828 4.962362 AGATCCTTTGGAGTTGTTTTGGTT 59.038 37.500 0.00 0.00 34.05 3.67
2711 3829 4.342092 CAGATCCTTTGGAGTTGTTTTGGT 59.658 41.667 0.00 0.00 34.05 3.67
2744 3862 0.402121 ACCTTGCCTTCAACCTCTCC 59.598 55.000 0.00 0.00 0.00 3.71
2858 8668 1.215173 CCCCATGCCTTTGTCCTATGA 59.785 52.381 0.00 0.00 0.00 2.15
2862 8672 0.712380 ATTCCCCATGCCTTTGTCCT 59.288 50.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.