Multiple sequence alignment - TraesCS1D01G152100

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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 TraesCS1D01G152100 chr1D 100.000 2276 0 0 1 2276 211715476 211713201 0.000000e+00 4204.0
1 TraesCS1D01G152100 chr3A 95.318 1303 60 1 2 1303 65986236 65987538 0.000000e+00 2067.0
2 TraesCS1D01G152100 chr3A 89.286 56 6 0 1510 1565 83238810 83238865 1.130000e-08 71.3
3 TraesCS1D01G152100 chr3A 95.238 42 2 0 1524 1565 83301998 83302039 1.460000e-07 67.6
4 TraesCS1D01G152100 chr6A 95.320 1282 59 1 22 1302 38871356 38872637 0.000000e+00 2034.0
5 TraesCS1D01G152100 chr7A 94.547 1302 71 0 1 1302 246326942 246328243 0.000000e+00 2012.0
6 TraesCS1D01G152100 chr7A 87.288 118 13 2 1491 1606 652278490 652278373 1.420000e-27 134.0
7 TraesCS1D01G152100 chr7A 87.288 118 12 3 1492 1606 232531396 232531279 5.100000e-27 132.0
8 TraesCS1D01G152100 chr7A 89.286 56 6 0 1510 1565 96529839 96529894 1.130000e-08 71.3
9 TraesCS1D01G152100 chr3D 92.043 930 72 2 373 1302 111891323 111892250 0.000000e+00 1306.0
10 TraesCS1D01G152100 chr4B 84.061 1305 204 4 1 1303 4601646 4602948 0.000000e+00 1254.0
11 TraesCS1D01G152100 chr4B 97.436 39 1 0 2238 2276 262709919 262709881 1.460000e-07 67.6
12 TraesCS1D01G152100 chr7D 84.153 1281 189 11 32 1303 630260439 630259164 0.000000e+00 1229.0
13 TraesCS1D01G152100 chr7D 86.058 416 32 14 1303 1698 585187180 585186771 7.520000e-115 424.0
14 TraesCS1D01G152100 chr7D 78.571 574 89 28 1726 2275 401776208 401776771 4.650000e-92 348.0
15 TraesCS1D01G152100 chr7D 84.810 316 21 7 1915 2208 585186774 585186464 2.210000e-75 292.0
16 TraesCS1D01G152100 chr7D 83.755 277 31 12 1745 2015 565912457 565912189 1.350000e-62 250.0
17 TraesCS1D01G152100 chr7D 85.638 188 23 3 2089 2276 489165430 489165247 6.410000e-46 195.0
18 TraesCS1D01G152100 chr7D 88.618 123 5 7 1491 1606 565950714 565950594 8.480000e-30 141.0
19 TraesCS1D01G152100 chr3B 83.614 1306 205 9 1 1303 762024656 762025955 0.000000e+00 1218.0
20 TraesCS1D01G152100 chr3B 83.597 1262 199 8 56 1313 497424161 497422904 0.000000e+00 1177.0
21 TraesCS1D01G152100 chr3B 93.990 416 19 5 1491 1903 73026648 73026236 1.920000e-175 625.0
22 TraesCS1D01G152100 chr3B 94.872 39 0 2 1562 1599 130628719 130628756 2.440000e-05 60.2
23 TraesCS1D01G152100 chr7B 84.160 1250 194 4 56 1303 678278849 678280096 0.000000e+00 1208.0
24 TraesCS1D01G152100 chr7B 84.324 370 47 9 1649 2012 119320179 119320543 3.600000e-93 351.0
25 TraesCS1D01G152100 chr7B 97.143 35 1 0 2242 2276 749106222 749106188 2.440000e-05 60.2
26 TraesCS1D01G152100 chr4A 84.783 368 47 8 1650 2012 8855730 8856093 5.980000e-96 361.0
27 TraesCS1D01G152100 chr4A 80.574 453 65 18 1650 2089 9054530 9054972 6.060000e-86 327.0
28 TraesCS1D01G152100 chr5B 77.055 584 68 36 1750 2276 273895091 273894517 2.230000e-70 276.0
29 TraesCS1D01G152100 chr6B 83.571 280 41 5 1740 2015 288129576 288129298 8.070000e-65 257.0
30 TraesCS1D01G152100 chr6B 83.544 79 11 2 1491 1568 64858773 64858850 3.140000e-09 73.1
31 TraesCS1D01G152100 chr6D 82.918 281 39 9 1731 2007 54236150 54236425 6.280000e-61 244.0
32 TraesCS1D01G152100 chr5D 85.047 214 26 6 1808 2019 377860777 377860986 1.770000e-51 213.0
33 TraesCS1D01G152100 chr5D 82.065 184 18 6 2095 2266 104083529 104083349 2.360000e-30 143.0


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 TraesCS1D01G152100 chr1D 211713201 211715476 2275 True 4204 4204 100.000 1 2276 1 chr1D.!!$R1 2275
1 TraesCS1D01G152100 chr3A 65986236 65987538 1302 False 2067 2067 95.318 2 1303 1 chr3A.!!$F1 1301
2 TraesCS1D01G152100 chr6A 38871356 38872637 1281 False 2034 2034 95.320 22 1302 1 chr6A.!!$F1 1280
3 TraesCS1D01G152100 chr7A 246326942 246328243 1301 False 2012 2012 94.547 1 1302 1 chr7A.!!$F2 1301
4 TraesCS1D01G152100 chr3D 111891323 111892250 927 False 1306 1306 92.043 373 1302 1 chr3D.!!$F1 929
5 TraesCS1D01G152100 chr4B 4601646 4602948 1302 False 1254 1254 84.061 1 1303 1 chr4B.!!$F1 1302
6 TraesCS1D01G152100 chr7D 630259164 630260439 1275 True 1229 1229 84.153 32 1303 1 chr7D.!!$R4 1271
7 TraesCS1D01G152100 chr7D 585186464 585187180 716 True 358 424 85.434 1303 2208 2 chr7D.!!$R5 905
8 TraesCS1D01G152100 chr7D 401776208 401776771 563 False 348 348 78.571 1726 2275 1 chr7D.!!$F1 549
9 TraesCS1D01G152100 chr3B 762024656 762025955 1299 False 1218 1218 83.614 1 1303 1 chr3B.!!$F2 1302
10 TraesCS1D01G152100 chr3B 497422904 497424161 1257 True 1177 1177 83.597 56 1313 1 chr3B.!!$R2 1257
11 TraesCS1D01G152100 chr7B 678278849 678280096 1247 False 1208 1208 84.160 56 1303 1 chr7B.!!$F2 1247
12 TraesCS1D01G152100 chr5B 273894517 273895091 574 True 276 276 77.055 1750 2276 1 chr5B.!!$R1 526

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
649 650 0.179084 CGTTATGTGGGCGATCTGGT 60.179 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1522 1545 0.724549 TAGCACGTGCAAAATAGGCG 59.275 50.0 39.21 0.0 45.16 5.52 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
19 20 2.415010 CGGGGCTGTCATCTCTCG 59.585 66.667 0.00 0.00 0.00 4.04
66 67 1.827969 ACTCTAGCATGGGTGAGTGAC 59.172 52.381 0.00 0.00 38.22 3.67
153 154 9.307121 CCGGAAGCAGAATCTATACTTAATATG 57.693 37.037 0.00 0.00 0.00 1.78
221 222 3.356529 AAGGAATGGCAACTACTCTGG 57.643 47.619 0.00 0.00 37.61 3.86
226 227 1.604604 TGGCAACTACTCTGGCAAAC 58.395 50.000 0.00 0.00 45.35 2.93
250 251 0.240411 GTACCGTGCTCTCGTGACTT 59.760 55.000 0.00 0.00 0.00 3.01
615 616 3.684305 CACAGTTCACGGATATGCAAAGA 59.316 43.478 0.00 0.00 0.00 2.52
649 650 0.179084 CGTTATGTGGGCGATCTGGT 60.179 55.000 0.00 0.00 0.00 4.00
753 754 1.517238 TGGATATACCCCAAGCTGCA 58.483 50.000 1.02 0.00 38.00 4.41
755 756 1.699634 GGATATACCCCAAGCTGCAGA 59.300 52.381 20.43 0.00 0.00 4.26
758 759 0.921896 ATACCCCAAGCTGCAGATGT 59.078 50.000 20.43 8.00 0.00 3.06
815 816 8.319146 GGATCCGGGAGTGATTAAGATTAATAA 58.681 37.037 0.00 0.00 33.72 1.40
1113 1114 3.128764 AGCTAGCGGCAAATTTTACTTCC 59.871 43.478 9.55 0.00 44.79 3.46
1363 1369 9.667989 TTAAAATTTACGGAAAAGTCTACTTGC 57.332 29.630 0.00 0.00 36.12 4.01
1365 1371 2.806608 ACGGAAAAGTCTACTTGCGA 57.193 45.000 13.25 0.00 38.48 5.10
1381 1389 1.135141 TGCGACCCATTTATGCAAAGC 60.135 47.619 0.00 0.00 31.69 3.51
1383 1391 1.400142 CGACCCATTTATGCAAAGCGA 59.600 47.619 0.00 0.00 0.00 4.93
1384 1392 2.791158 CGACCCATTTATGCAAAGCGAC 60.791 50.000 0.00 0.00 0.00 5.19
1385 1393 1.476488 ACCCATTTATGCAAAGCGACC 59.524 47.619 0.00 0.00 0.00 4.79
1386 1394 1.476085 CCCATTTATGCAAAGCGACCA 59.524 47.619 0.00 0.00 0.00 4.02
1429 1438 1.543429 CCGCTCCAACCTTCAAGTCTT 60.543 52.381 0.00 0.00 0.00 3.01
1496 1519 4.481930 AACGATTGTGTTACACATGTGG 57.518 40.909 28.64 13.84 44.16 4.17
1513 1536 1.729881 GGAGCTTAAATGGGCTGCG 59.270 57.895 0.00 0.00 39.05 5.18
1519 1542 4.003648 AGCTTAAATGGGCTGCGTATATC 58.996 43.478 0.00 0.00 37.41 1.63
1539 1562 1.514014 CCGCCTATTTTGCACGTGC 60.514 57.895 33.11 33.11 42.50 5.34
1616 1641 9.515020 ACATACTTTTGCACATAAATATTTCCG 57.485 29.630 3.39 0.00 0.00 4.30
1638 1663 8.572828 TCCGCATAATAAATAAAGCATGTTTG 57.427 30.769 0.00 0.00 0.00 2.93
1671 1696 9.593134 AAGAACATACTTTTGCACATGTTTTTA 57.407 25.926 0.00 0.00 40.67 1.52
1672 1697 9.762933 AGAACATACTTTTGCACATGTTTTTAT 57.237 25.926 0.00 0.00 40.67 1.40
1701 1726 7.976414 AAATGGATGATCCCTCAAAAACATA 57.024 32.000 9.36 0.00 35.03 2.29
1702 1727 8.557304 AAATGGATGATCCCTCAAAAACATAT 57.443 30.769 9.36 0.00 35.03 1.78
1703 1728 8.557304 AATGGATGATCCCTCAAAAACATATT 57.443 30.769 9.36 0.00 35.03 1.28
1704 1729 7.976414 TGGATGATCCCTCAAAAACATATTT 57.024 32.000 9.36 0.00 35.03 1.40
1705 1730 8.378115 TGGATGATCCCTCAAAAACATATTTT 57.622 30.769 9.36 0.00 36.16 1.82
1706 1731 8.477256 TGGATGATCCCTCAAAAACATATTTTC 58.523 33.333 9.36 0.00 34.59 2.29
1707 1732 7.649306 GGATGATCCCTCAAAAACATATTTTCG 59.351 37.037 0.00 0.00 37.01 3.46
1708 1733 6.329496 TGATCCCTCAAAAACATATTTTCGC 58.671 36.000 0.00 0.00 37.01 4.70
1709 1734 5.713792 TCCCTCAAAAACATATTTTCGCA 57.286 34.783 0.00 0.00 37.01 5.10
1710 1735 5.465935 TCCCTCAAAAACATATTTTCGCAC 58.534 37.500 0.00 0.00 37.01 5.34
1711 1736 5.242838 TCCCTCAAAAACATATTTTCGCACT 59.757 36.000 0.00 0.00 37.01 4.40
1712 1737 5.925969 CCCTCAAAAACATATTTTCGCACTT 59.074 36.000 0.00 0.00 37.01 3.16
1713 1738 7.040340 TCCCTCAAAAACATATTTTCGCACTTA 60.040 33.333 0.00 0.00 37.01 2.24
1714 1739 7.759433 CCCTCAAAAACATATTTTCGCACTTAT 59.241 33.333 0.00 0.00 37.01 1.73
1715 1740 9.139174 CCTCAAAAACATATTTTCGCACTTATT 57.861 29.630 0.00 0.00 37.01 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.283905 ACCAGGTATAACAGTTGGCCC 59.716 52.381 0.00 0.00 32.10 5.80
66 67 9.270640 CAAGACCAATTCTCTTCATCTATAAGG 57.729 37.037 0.00 0.00 31.02 2.69
139 140 4.082408 ACGCAGCGGCATATTAAGTATAGA 60.082 41.667 21.15 0.00 41.24 1.98
175 176 1.134610 GGCCCAAGCAAGGAAATCATG 60.135 52.381 0.00 0.00 42.56 3.07
551 552 0.389391 CCACGTATCGGGATGAAGCT 59.611 55.000 0.00 0.00 28.17 3.74
615 616 5.994054 CCACATAACGGAAATCATCTGAGAT 59.006 40.000 0.00 0.00 37.88 2.75
753 754 6.550163 ACCGTATCCTGGTAGTATAACATCT 58.450 40.000 0.00 0.00 37.83 2.90
755 756 6.014840 CCAACCGTATCCTGGTAGTATAACAT 60.015 42.308 0.00 0.00 37.83 2.71
758 759 5.704354 TCCAACCGTATCCTGGTAGTATAA 58.296 41.667 0.00 0.00 39.29 0.98
815 816 2.895404 ACCAAACTCATTGCTGCATCTT 59.105 40.909 1.84 0.00 37.73 2.40
981 982 2.333688 TGATCACGTGTGAAAACCCA 57.666 45.000 16.51 0.00 43.58 4.51
1113 1114 9.722056 GACCTGCTTACATATTGAATACAAAAG 57.278 33.333 0.00 0.00 39.54 2.27
1126 1127 3.054434 ACATTGGCTGACCTGCTTACATA 60.054 43.478 0.00 0.00 36.63 2.29
1338 1344 8.011106 CGCAAGTAGACTTTTCCGTAAATTTTA 58.989 33.333 0.00 0.00 33.11 1.52
1339 1345 6.854381 CGCAAGTAGACTTTTCCGTAAATTTT 59.146 34.615 0.00 0.00 33.11 1.82
1340 1346 6.203338 TCGCAAGTAGACTTTTCCGTAAATTT 59.797 34.615 0.00 0.00 33.11 1.82
1346 1352 2.401351 GTCGCAAGTAGACTTTTCCGT 58.599 47.619 0.00 0.00 35.84 4.69
1356 1362 2.942376 TGCATAAATGGGTCGCAAGTAG 59.058 45.455 0.00 0.00 39.48 2.57
1361 1367 1.135141 GCTTTGCATAAATGGGTCGCA 60.135 47.619 0.00 0.00 0.00 5.10
1362 1368 1.559831 GCTTTGCATAAATGGGTCGC 58.440 50.000 0.00 0.00 0.00 5.19
1363 1369 1.400142 TCGCTTTGCATAAATGGGTCG 59.600 47.619 0.00 0.00 0.00 4.79
1365 1371 1.476488 GGTCGCTTTGCATAAATGGGT 59.524 47.619 0.00 0.00 0.00 4.51
1381 1389 2.671396 CGTTCCCTGTTAGAATTGGTCG 59.329 50.000 0.00 0.00 0.00 4.79
1383 1391 2.039879 AGCGTTCCCTGTTAGAATTGGT 59.960 45.455 0.00 0.00 0.00 3.67
1384 1392 2.678336 GAGCGTTCCCTGTTAGAATTGG 59.322 50.000 0.00 0.00 0.00 3.16
1385 1393 3.600388 AGAGCGTTCCCTGTTAGAATTG 58.400 45.455 0.00 0.00 0.00 2.32
1386 1394 3.983044 AGAGCGTTCCCTGTTAGAATT 57.017 42.857 0.00 0.00 0.00 2.17
1443 1452 8.988064 ATTAGATATACATACTTGAACCGCTG 57.012 34.615 0.00 0.00 0.00 5.18
1486 1509 4.269183 CCCATTTAAGCTCCACATGTGTA 58.731 43.478 23.79 8.12 0.00 2.90
1496 1519 1.663695 TACGCAGCCCATTTAAGCTC 58.336 50.000 0.00 0.00 37.18 4.09
1513 1536 2.739913 TGCAAAATAGGCGGCGATATAC 59.260 45.455 12.98 0.00 0.00 1.47
1519 1542 2.277247 CGTGCAAAATAGGCGGCG 60.277 61.111 0.51 0.51 0.00 6.46
1522 1545 0.724549 TAGCACGTGCAAAATAGGCG 59.275 50.000 39.21 0.00 45.16 5.52
1595 1620 6.884096 TGCGGAAATATTTATGTGCAAAAG 57.116 33.333 0.00 0.00 0.00 2.27
1616 1641 9.533253 AGTCCAAACATGCTTTATTTATTATGC 57.467 29.630 0.00 0.00 0.00 3.14
1635 1660 6.978080 GCAAAAGTATGTTCTTTGAGTCCAAA 59.022 34.615 0.00 0.00 39.74 3.28
1638 1663 5.915196 GTGCAAAAGTATGTTCTTTGAGTCC 59.085 40.000 0.00 0.00 37.65 3.85
1673 1698 9.659135 TGTTTTTGAGGGATCATCCATTTATAT 57.341 29.630 5.89 0.00 38.64 0.86
1683 1708 6.980397 GCGAAAATATGTTTTTGAGGGATCAT 59.020 34.615 16.68 0.00 39.91 2.45
1686 1711 6.071391 AGTGCGAAAATATGTTTTTGAGGGAT 60.071 34.615 16.68 0.00 39.91 3.85
1687 1712 5.242838 AGTGCGAAAATATGTTTTTGAGGGA 59.757 36.000 16.68 0.66 39.91 4.20
1860 1888 8.726988 ACATTGAACTATACAAATGTGTGTACC 58.273 33.333 0.00 0.00 38.82 3.34
2157 2251 6.706055 TGTTCAAATGTTTGCGTGTTAAAA 57.294 29.167 0.66 0.00 38.05 1.52


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

AutoCloner maintained by Alex Coulton.