Multiple sequence alignment - TraesCS2D01G065300

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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 TraesCS2D01G065300 chr2D 100.000 2808 0 0 1 2808 27885168 27882361 0.000000e+00 5186.0
1 TraesCS2D01G065300 chr2D 89.822 1012 61 21 1273 2281 27860486 27859514 0.000000e+00 1260.0
2 TraesCS2D01G065300 chr2D 89.796 784 45 12 1414 2197 27853945 27853197 0.000000e+00 972.0
3 TraesCS2D01G065300 chr2D 88.064 687 49 13 496 1152 27854720 27854037 0.000000e+00 784.0
4 TraesCS2D01G065300 chr2D 82.573 855 107 16 1427 2281 27849528 27848716 0.000000e+00 715.0
5 TraesCS2D01G065300 chr2D 82.051 858 103 24 1424 2281 27850872 27850066 0.000000e+00 684.0
6 TraesCS2D01G065300 chr2D 93.779 434 27 0 1388 1821 27901946 27901513 0.000000e+00 652.0
7 TraesCS2D01G065300 chr2D 81.151 504 59 16 742 1223 27861203 27860714 3.420000e-99 372.0
8 TraesCS2D01G065300 chr2D 86.486 111 7 2 2670 2780 27850056 27849954 6.360000e-22 115.0
9 TraesCS2D01G065300 chr2D 75.281 267 50 11 7 271 470067719 470067971 2.290000e-21 113.0
10 TraesCS2D01G065300 chr2D 83.333 102 12 4 2537 2637 364982128 364982225 3.850000e-14 89.8
11 TraesCS2D01G065300 chr2D 89.552 67 6 1 2653 2718 27859523 27859457 1.790000e-12 84.2
12 TraesCS2D01G065300 chr2D 76.978 139 22 7 2290 2427 586398738 586398609 1.400000e-08 71.3
13 TraesCS2D01G065300 chr2A 93.012 2533 120 22 278 2765 30073443 30070923 0.000000e+00 3644.0
14 TraesCS2D01G065300 chr2A 90.089 1009 64 16 1273 2281 30048630 30047658 0.000000e+00 1277.0
15 TraesCS2D01G065300 chr2A 89.447 796 47 11 1414 2209 30021219 30020461 0.000000e+00 970.0
16 TraesCS2D01G065300 chr2A 85.972 720 65 18 496 1183 30021986 30021271 0.000000e+00 737.0
17 TraesCS2D01G065300 chr2A 93.779 434 27 0 1388 1821 30090978 30090545 0.000000e+00 652.0
18 TraesCS2D01G065300 chr2A 93.333 435 27 2 1388 1821 30126666 30126233 2.360000e-180 641.0
19 TraesCS2D01G065300 chr2A 96.552 290 10 0 1 290 30073770 30073481 5.440000e-132 481.0
20 TraesCS2D01G065300 chr2A 82.000 500 58 11 742 1219 30049349 30048860 2.030000e-106 396.0
21 TraesCS2D01G065300 chr2A 89.706 68 4 3 2499 2565 118448036 118447971 1.790000e-12 84.2
22 TraesCS2D01G065300 chr2A 94.545 55 2 1 364 417 622463628 622463682 1.790000e-12 84.2
23 TraesCS2D01G065300 chr2A 94.595 37 2 0 2281 2317 491537794 491537830 1.090000e-04 58.4
24 TraesCS2D01G065300 chr2B 95.587 1201 45 4 799 1992 44311840 44310641 0.000000e+00 1917.0
25 TraesCS2D01G065300 chr2B 89.594 1009 68 15 1273 2281 44286476 44285505 0.000000e+00 1247.0
26 TraesCS2D01G065300 chr2B 87.431 724 52 18 496 1183 44192496 44191776 0.000000e+00 797.0
27 TraesCS2D01G065300 chr2B 87.431 724 52 18 496 1183 44275176 44274456 0.000000e+00 797.0
28 TraesCS2D01G065300 chr2B 91.166 566 27 11 1414 1977 44274404 44273860 0.000000e+00 747.0
29 TraesCS2D01G065300 chr2B 94.872 468 21 1 1414 1881 44191724 44191260 0.000000e+00 728.0
30 TraesCS2D01G065300 chr2B 96.380 442 16 0 2025 2466 44306920 44306479 0.000000e+00 728.0
31 TraesCS2D01G065300 chr2B 93.088 434 30 0 1388 1821 44361214 44360781 1.100000e-178 636.0
32 TraesCS2D01G065300 chr2B 81.414 495 57 14 746 1219 44287186 44286706 3.420000e-99 372.0
33 TraesCS2D01G065300 chr2B 92.265 181 12 2 2630 2808 44306472 44306292 3.590000e-64 255.0
34 TraesCS2D01G065300 chr2B 83.406 229 28 9 496 718 44312060 44311836 1.320000e-48 204.0
35 TraesCS2D01G065300 chr2B 90.991 111 9 1 2670 2780 44188294 44188185 6.270000e-32 148.0
36 TraesCS2D01G065300 chr2B 91.045 67 5 1 2653 2718 44285514 44285448 3.850000e-14 89.8
37 TraesCS2D01G065300 chr2B 79.825 114 10 8 2533 2635 84974886 84974775 1.400000e-08 71.3
38 TraesCS2D01G065300 chr6D 75.926 324 50 21 2255 2569 11072684 11072988 1.050000e-29 141.0
39 TraesCS2D01G065300 chr6D 96.296 54 2 0 371 424 317011517 317011464 3.850000e-14 89.8
40 TraesCS2D01G065300 chr6D 96.078 51 2 0 360 410 31762109 31762059 1.790000e-12 84.2
41 TraesCS2D01G065300 chr6D 94.118 51 3 0 360 410 23431994 23431944 8.340000e-11 78.7
42 TraesCS2D01G065300 chr1D 76.245 261 52 7 5 259 234749616 234749360 2.270000e-26 130.0
43 TraesCS2D01G065300 chr1D 95.000 40 0 2 2721 2760 344627458 344627495 8.400000e-06 62.1
44 TraesCS2D01G065300 chr5D 81.013 158 24 4 2282 2438 61483350 61483502 1.370000e-23 121.0
45 TraesCS2D01G065300 chr3D 84.167 120 19 0 143 262 73425727 73425608 1.770000e-22 117.0
46 TraesCS2D01G065300 chr3D 94.118 51 1 2 370 419 518264176 518264127 3.000000e-10 76.8
47 TraesCS2D01G065300 chr4B 73.704 270 49 19 2307 2569 645313101 645313355 4.980000e-13 86.1
48 TraesCS2D01G065300 chr7D 100.000 45 0 0 370 414 101395202 101395246 1.790000e-12 84.2
49 TraesCS2D01G065300 chr4D 100.000 45 0 0 370 414 466837228 466837184 1.790000e-12 84.2
50 TraesCS2D01G065300 chr5A 82.759 87 12 3 2284 2369 607690179 607690263 1.080000e-09 75.0
51 TraesCS2D01G065300 chrUn 89.831 59 2 4 373 428 478193556 478193613 3.880000e-09 73.1
52 TraesCS2D01G065300 chr6B 84.932 73 9 2 2533 2603 682565723 682565651 3.880000e-09 73.1
53 TraesCS2D01G065300 chr6B 84.286 70 10 1 2501 2569 680771489 680771558 1.810000e-07 67.6
54 TraesCS2D01G065300 chr7B 80.000 95 14 4 2474 2565 523236637 523236545 6.490000e-07 65.8


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 TraesCS2D01G065300 chr2D 27882361 27885168 2807 True 5186.000000 5186 100.000000 1 2808 1 chr2D.!!$R1 2807
1 TraesCS2D01G065300 chr2D 27848716 27854720 6004 True 654.000000 972 85.794000 496 2780 5 chr2D.!!$R4 2284
2 TraesCS2D01G065300 chr2D 27859457 27861203 1746 True 572.066667 1260 86.841667 742 2718 3 chr2D.!!$R5 1976
3 TraesCS2D01G065300 chr2A 30070923 30073770 2847 True 2062.500000 3644 94.782000 1 2765 2 chr2A.!!$R6 2764
4 TraesCS2D01G065300 chr2A 30020461 30021986 1525 True 853.500000 970 87.709500 496 2209 2 chr2A.!!$R4 1713
5 TraesCS2D01G065300 chr2A 30047658 30049349 1691 True 836.500000 1277 86.044500 742 2281 2 chr2A.!!$R5 1539
6 TraesCS2D01G065300 chr2B 44306292 44312060 5768 True 776.000000 1917 91.909500 496 2808 4 chr2B.!!$R6 2312
7 TraesCS2D01G065300 chr2B 44273860 44275176 1316 True 772.000000 797 89.298500 496 1977 2 chr2B.!!$R4 1481
8 TraesCS2D01G065300 chr2B 44285448 44287186 1738 True 569.600000 1247 87.351000 746 2718 3 chr2B.!!$R5 1972
9 TraesCS2D01G065300 chr2B 44188185 44192496 4311 True 557.666667 797 91.098000 496 2780 3 chr2B.!!$R3 2284

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
133 134 0.179018 GTCTTTGCTCCCACACTGGT 60.179 55.0 0.0 0.0 35.17 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 2183 0.319383 CAGAGTCGTGCAGCAGAGTT 60.319 55.0 0.0 0.0 0.0 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
49 50 8.685838 AAGCACCTCAAACATAGTAAAAAGTA 57.314 30.769 0.00 0.00 0.00 2.24
123 124 1.222115 ACGAGCCGTTGTCTTTGCTC 61.222 55.000 0.00 0.00 45.19 4.26
131 132 1.334869 GTTGTCTTTGCTCCCACACTG 59.665 52.381 0.00 0.00 0.00 3.66
133 134 0.179018 GTCTTTGCTCCCACACTGGT 60.179 55.000 0.00 0.00 35.17 4.00
215 216 1.722677 CTCTGGAGCCGTAGTCGTC 59.277 63.158 0.00 0.00 35.01 4.20
240 241 1.409064 TCGAATCCCTGAATCGGTCTG 59.591 52.381 2.14 0.00 35.90 3.51
316 367 1.269831 GGATCCCGGAAGATTGACTCG 60.270 57.143 0.73 0.00 0.00 4.18
319 370 1.476891 TCCCGGAAGATTGACTCGAAG 59.523 52.381 0.73 0.00 0.00 3.79
356 407 1.911269 TCCAAGCGCCACTCCTACA 60.911 57.895 2.29 0.00 0.00 2.74
372 423 7.764901 CCACTCCTACAAGAACTAAAATCCTAC 59.235 40.741 0.00 0.00 0.00 3.18
385 436 5.354842 AAAATCCTACTCCCTCCGTAAAG 57.645 43.478 0.00 0.00 0.00 1.85
394 445 8.645110 CCTACTCCCTCCGTAAAGAAATATAAA 58.355 37.037 0.00 0.00 0.00 1.40
397 448 7.498239 ACTCCCTCCGTAAAGAAATATAAAAGC 59.502 37.037 0.00 0.00 0.00 3.51
637 690 5.335935 CACACTATACGCCTATGAGCATAG 58.664 45.833 9.94 9.94 40.28 2.23
698 753 1.047801 ATTTTGCCCACCCAACTCAC 58.952 50.000 0.00 0.00 0.00 3.51
756 832 4.161377 ACCCAAAAACAAGCAAAGCTAGAA 59.839 37.500 0.00 0.00 38.25 2.10
920 996 4.750098 CACATCTGTACCAAAGAAACGAGT 59.250 41.667 0.00 0.00 0.00 4.18
987 1076 0.398381 GCATCCTCCTCTCCTCCAGT 60.398 60.000 0.00 0.00 0.00 4.00
993 1082 5.068215 TCCTCCTCTCCTCCAGTTAATAG 57.932 47.826 0.00 0.00 0.00 1.73
1211 1321 3.328382 TTCACTTACAGAACATCCCCG 57.672 47.619 0.00 0.00 0.00 5.73
1339 1625 3.055240 CCCATAAGGAGCAATTTTTGGCA 60.055 43.478 0.00 0.00 38.24 4.92
1342 1628 2.103537 AGGAGCAATTTTTGGCATGC 57.896 45.000 9.90 9.90 39.06 4.06
1345 1631 0.035176 AGCAATTTTTGGCATGCCGT 59.965 45.000 30.87 11.96 39.59 5.68
1353 1639 2.121291 TTGGCATGCCGTCTGATTTA 57.879 45.000 30.87 7.94 39.42 1.40
1463 1761 2.354203 GGCATCAAGAAGTTCGAGACCT 60.354 50.000 0.00 0.00 0.00 3.85
1636 1934 1.598701 GGACAATGTGGAAGCTGCCC 61.599 60.000 8.77 3.01 0.00 5.36
1642 1940 0.469705 TGTGGAAGCTGCCCATGTTT 60.470 50.000 8.77 0.00 35.91 2.83
1872 2183 4.695217 GTGAACTTCACTTTTGTCCACA 57.305 40.909 13.77 0.00 43.73 4.17
1876 2201 4.965119 ACTTCACTTTTGTCCACAACTC 57.035 40.909 0.00 0.00 35.28 3.01
1877 2202 4.589908 ACTTCACTTTTGTCCACAACTCT 58.410 39.130 0.00 0.00 35.28 3.24
1878 2203 4.396166 ACTTCACTTTTGTCCACAACTCTG 59.604 41.667 0.00 0.00 35.28 3.35
1879 2204 2.682856 TCACTTTTGTCCACAACTCTGC 59.317 45.455 0.00 0.00 35.28 4.26
1880 2205 2.684881 CACTTTTGTCCACAACTCTGCT 59.315 45.455 0.00 0.00 35.28 4.24
1881 2206 2.684881 ACTTTTGTCCACAACTCTGCTG 59.315 45.455 0.00 0.00 35.28 4.41
1882 2207 1.024271 TTTGTCCACAACTCTGCTGC 58.976 50.000 0.00 0.00 35.28 5.25
1883 2208 0.107263 TTGTCCACAACTCTGCTGCA 60.107 50.000 0.88 0.88 0.00 4.41
1884 2209 0.815213 TGTCCACAACTCTGCTGCAC 60.815 55.000 0.00 0.00 0.00 4.57
1885 2210 1.595109 TCCACAACTCTGCTGCACG 60.595 57.895 0.00 0.00 0.00 5.34
1886 2211 1.595109 CCACAACTCTGCTGCACGA 60.595 57.895 0.00 0.00 0.00 4.35
1887 2212 1.566563 CACAACTCTGCTGCACGAC 59.433 57.895 0.00 0.00 0.00 4.34
1888 2213 0.877649 CACAACTCTGCTGCACGACT 60.878 55.000 0.00 0.00 0.00 4.18
1897 2222 1.777819 CTGCACGACTCTGCTTTCG 59.222 57.895 0.00 0.00 41.14 3.46
2395 9146 4.300189 TGTGTGTGGCTTAATTTGACAC 57.700 40.909 9.40 9.40 43.34 3.67
2429 9180 6.500684 TCCTTGCAAAGTTTCATCATAGAC 57.499 37.500 0.00 0.00 44.25 2.59
2443 9194 6.228995 TCATCATAGACTGGCATTCATCTTC 58.771 40.000 7.63 0.00 0.00 2.87
2471 9226 4.324402 CGGCAATAAACAAATTCAGCACTC 59.676 41.667 0.00 0.00 0.00 3.51
2472 9227 4.627035 GGCAATAAACAAATTCAGCACTCC 59.373 41.667 0.00 0.00 0.00 3.85
2525 10441 9.941325 ATTATTTTTGCATGACTTCCACAAATA 57.059 25.926 0.00 0.00 30.95 1.40
2565 10481 7.551035 ACTTTGCAAGCATTGAAAACATTTA 57.449 28.000 0.00 0.00 46.24 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 2.051076 TCGTTCGGTGTCGTTCGG 60.051 61.111 0.00 0.00 37.69 4.30
123 124 2.066340 TGGCTAGAACCAGTGTGGG 58.934 57.895 0.00 0.00 43.37 4.61
131 132 1.404315 CGACAAGGTCTGGCTAGAACC 60.404 57.143 12.09 10.63 41.79 3.62
133 134 1.919240 TCGACAAGGTCTGGCTAGAA 58.081 50.000 0.00 0.00 34.01 2.10
215 216 1.478137 GATTCAGGGATTCGACGACG 58.522 55.000 0.00 0.00 41.26 5.12
240 241 3.433615 CGAGATTTGGTGTCAGGTTCTTC 59.566 47.826 0.00 0.00 0.00 2.87
316 367 1.077429 ATGGCGGCCCTTCTTCTTC 60.077 57.895 17.97 0.00 0.00 2.87
319 370 1.821332 CAGATGGCGGCCCTTCTTC 60.821 63.158 17.97 5.79 42.11 2.87
356 407 5.128991 CGGAGGGAGTAGGATTTTAGTTCTT 59.871 44.000 0.00 0.00 0.00 2.52
372 423 7.307219 CGCTTTTATATTTCTTTACGGAGGGAG 60.307 40.741 0.00 0.00 0.00 4.30
394 445 8.086522 TGTAAAGAAGTAGTGATCTAAACGCTT 58.913 33.333 0.00 0.00 0.00 4.68
397 448 9.279904 CTCTGTAAAGAAGTAGTGATCTAAACG 57.720 37.037 0.00 0.00 0.00 3.60
547 598 7.710044 TGAATGTCTGCATTTGTACAATGTTTT 59.290 29.630 9.56 0.00 44.61 2.43
637 690 1.597742 TGCTGGCTCACTCTTGAAAC 58.402 50.000 0.00 0.00 0.00 2.78
678 733 2.158385 AGTGAGTTGGGTGGGCAAAATA 60.158 45.455 0.00 0.00 0.00 1.40
698 753 3.005554 ACAAATTGTCTGAGGATGCGAG 58.994 45.455 0.00 0.00 0.00 5.03
756 832 0.177836 GGCTGCCACACAACCTTTTT 59.822 50.000 15.17 0.00 31.28 1.94
892 968 4.202245 TCTTTGGTACAGATGTGGTAGC 57.798 45.455 0.00 0.00 42.39 3.58
920 996 3.943381 CGGGTCACCACGCTATATATAGA 59.057 47.826 21.65 0.00 36.13 1.98
987 1076 3.009695 CGGGGGCCATGGTATTCTATTAA 59.990 47.826 14.67 0.00 0.00 1.40
993 1082 2.597510 GCGGGGGCCATGGTATTC 60.598 66.667 14.67 0.00 0.00 1.75
1211 1321 6.594159 CGAGGATGGGTTTGGTTATATACATC 59.406 42.308 0.00 0.00 34.33 3.06
1339 1625 4.960938 TGCTAGAATAAATCAGACGGCAT 58.039 39.130 0.00 0.00 0.00 4.40
1342 1628 6.851222 ACAATGCTAGAATAAATCAGACGG 57.149 37.500 0.00 0.00 0.00 4.79
1463 1761 1.073284 GAGGGGTGGCAAGTAAGACAA 59.927 52.381 0.00 0.00 0.00 3.18
1636 1934 1.285641 GTCGGTGCACCCAAACATG 59.714 57.895 29.95 14.08 0.00 3.21
1872 2183 0.319383 CAGAGTCGTGCAGCAGAGTT 60.319 55.000 0.00 0.00 0.00 3.01
1876 2201 1.226686 AAAGCAGAGTCGTGCAGCAG 61.227 55.000 14.37 0.00 46.60 4.24
1877 2202 1.224069 GAAAGCAGAGTCGTGCAGCA 61.224 55.000 14.37 0.00 46.60 4.41
1878 2203 1.495069 GAAAGCAGAGTCGTGCAGC 59.505 57.895 14.37 0.00 46.60 5.25
1879 2204 1.621301 CCGAAAGCAGAGTCGTGCAG 61.621 60.000 14.37 5.45 46.60 4.41
1880 2205 1.664649 CCGAAAGCAGAGTCGTGCA 60.665 57.895 14.37 0.00 46.60 4.57
1881 2206 1.372997 TCCGAAAGCAGAGTCGTGC 60.373 57.895 6.49 6.49 44.35 5.34
1882 2207 1.009389 GGTCCGAAAGCAGAGTCGTG 61.009 60.000 0.00 0.00 35.48 4.35
1883 2208 1.289380 GGTCCGAAAGCAGAGTCGT 59.711 57.895 0.00 0.00 35.48 4.34
1884 2209 1.801913 CGGTCCGAAAGCAGAGTCG 60.802 63.158 4.91 0.00 37.01 4.18
1885 2210 1.446272 CCGGTCCGAAAGCAGAGTC 60.446 63.158 14.39 0.00 0.00 3.36
1886 2211 1.878656 CTCCGGTCCGAAAGCAGAGT 61.879 60.000 14.39 0.00 0.00 3.24
1887 2212 1.153745 CTCCGGTCCGAAAGCAGAG 60.154 63.158 14.39 5.69 0.00 3.35
1888 2213 2.970639 CTCCGGTCCGAAAGCAGA 59.029 61.111 14.39 0.00 0.00 4.26
1897 2222 1.339727 ACAAAAGGTATGCTCCGGTCC 60.340 52.381 0.00 0.00 0.00 4.46
2429 9180 1.325640 CGTGACGAAGATGAATGCCAG 59.674 52.381 0.00 0.00 0.00 4.85
2443 9194 4.222886 TGAATTTGTTTATTGCCGTGACG 58.777 39.130 0.00 0.00 0.00 4.35
2492 9247 9.121517 GGAAGTCATGCAAAAATAATATCGATG 57.878 33.333 8.54 0.00 0.00 3.84
2499 9254 8.851541 ATTTGTGGAAGTCATGCAAAAATAAT 57.148 26.923 0.00 0.00 43.25 1.28
2614 11016 4.092091 CAGCTCGAGTGAACAGTTAAATCC 59.908 45.833 15.13 0.00 0.00 3.01
2620 11024 2.430546 CTCAGCTCGAGTGAACAGTT 57.569 50.000 15.13 0.00 36.94 3.16
2675 11998 8.889717 CAGACCAACAAAAGTTCTTTAGTAAGA 58.110 33.333 0.00 0.00 38.61 2.10
2765 12088 6.148976 GGGATGTACAAGGAAAGTTCTACAAC 59.851 42.308 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.