Multiple sequence alignment - TraesCS2B01G227300

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 TraesCS2B01G227300 chr2B 100.000 2315 0 0 1 2315 218398588 218400902 0.000000e+00 4276
1 TraesCS2B01G227300 chr2B 95.532 1298 44 1 1032 2315 218447285 218448582 0.000000e+00 2063
2 TraesCS2B01G227300 chr7B 90.334 2338 192 11 1 2315 399856718 399854392 0.000000e+00 3035
3 TraesCS2B01G227300 chr7B 88.844 1497 148 9 834 2315 346696051 346694559 0.000000e+00 1821
4 TraesCS2B01G227300 chr3B 86.459 1765 192 26 581 2315 763007637 763005890 0.000000e+00 1892
5 TraesCS2B01G227300 chr3B 89.139 1510 146 11 821 2315 822804806 822806312 0.000000e+00 1864
6 TraesCS2B01G227300 chr3B 83.752 597 71 21 1 590 763008425 763007848 2.020000e-150 542
7 TraesCS2B01G227300 chr3B 82.940 551 71 17 1 547 215114392 215113861 2.080000e-130 475
8 TraesCS2B01G227300 chr6D 87.336 1674 178 27 664 2314 319012142 319010480 0.000000e+00 1886
9 TraesCS2B01G227300 chr7A 87.255 1687 167 26 657 2315 494280240 494278574 0.000000e+00 1881
10 TraesCS2B01G227300 chr7A 86.033 1704 187 37 642 2315 584378677 584376995 0.000000e+00 1781
11 TraesCS2B01G227300 chr4D 87.011 1686 170 31 657 2315 443736527 443738190 0.000000e+00 1855
12 TraesCS2B01G227300 chr4A 89.863 1460 117 11 1 1451 608351401 608352838 0.000000e+00 1847
13 TraesCS2B01G227300 chr4A 91.084 886 61 5 1446 2315 608361582 608362465 0.000000e+00 1182
14 TraesCS2B01G227300 chr4A 81.849 595 72 27 1 586 504176045 504176612 3.480000e-128 468
15 TraesCS2B01G227300 chr4A 80.968 599 81 28 1 586 8504952 8505530 5.870000e-121 444
16 TraesCS2B01G227300 chr1B 89.029 1504 142 12 828 2315 309928431 309929927 0.000000e+00 1842
17 TraesCS2B01G227300 chr1B 88.801 1518 147 14 813 2315 66183678 66185187 0.000000e+00 1840
18 TraesCS2B01G227300 chr1B 90.741 1242 91 9 1089 2315 251882527 251883759 0.000000e+00 1635
19 TraesCS2B01G227300 chr1B 87.818 1100 120 8 1 1092 251853556 251854649 0.000000e+00 1277
20 TraesCS2B01G227300 chr5A 86.334 1683 180 35 663 2314 705898676 705900339 0.000000e+00 1788
21 TraesCS2B01G227300 chr5A 82.878 549 80 12 1 548 37591612 37591077 4.470000e-132 481
22 TraesCS2B01G227300 chr7D 86.223 1684 177 36 659 2315 322654071 322655726 0.000000e+00 1773
23 TraesCS2B01G227300 chr2D 88.122 1507 145 20 824 2315 71956543 71955056 0.000000e+00 1760
24 TraesCS2B01G227300 chr3A 83.971 549 69 14 1 547 601366009 601365478 2.050000e-140 508


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 TraesCS2B01G227300 chr2B 218398588 218400902 2314 False 4276 4276 100.0000 1 2315 1 chr2B.!!$F1 2314
1 TraesCS2B01G227300 chr2B 218447285 218448582 1297 False 2063 2063 95.5320 1032 2315 1 chr2B.!!$F2 1283
2 TraesCS2B01G227300 chr7B 399854392 399856718 2326 True 3035 3035 90.3340 1 2315 1 chr7B.!!$R2 2314
3 TraesCS2B01G227300 chr7B 346694559 346696051 1492 True 1821 1821 88.8440 834 2315 1 chr7B.!!$R1 1481
4 TraesCS2B01G227300 chr3B 822804806 822806312 1506 False 1864 1864 89.1390 821 2315 1 chr3B.!!$F1 1494
5 TraesCS2B01G227300 chr3B 763005890 763008425 2535 True 1217 1892 85.1055 1 2315 2 chr3B.!!$R2 2314
6 TraesCS2B01G227300 chr3B 215113861 215114392 531 True 475 475 82.9400 1 547 1 chr3B.!!$R1 546
7 TraesCS2B01G227300 chr6D 319010480 319012142 1662 True 1886 1886 87.3360 664 2314 1 chr6D.!!$R1 1650
8 TraesCS2B01G227300 chr7A 494278574 494280240 1666 True 1881 1881 87.2550 657 2315 1 chr7A.!!$R1 1658
9 TraesCS2B01G227300 chr7A 584376995 584378677 1682 True 1781 1781 86.0330 642 2315 1 chr7A.!!$R2 1673
10 TraesCS2B01G227300 chr4D 443736527 443738190 1663 False 1855 1855 87.0110 657 2315 1 chr4D.!!$F1 1658
11 TraesCS2B01G227300 chr4A 608351401 608352838 1437 False 1847 1847 89.8630 1 1451 1 chr4A.!!$F3 1450
12 TraesCS2B01G227300 chr4A 608361582 608362465 883 False 1182 1182 91.0840 1446 2315 1 chr4A.!!$F4 869
13 TraesCS2B01G227300 chr4A 504176045 504176612 567 False 468 468 81.8490 1 586 1 chr4A.!!$F2 585
14 TraesCS2B01G227300 chr4A 8504952 8505530 578 False 444 444 80.9680 1 586 1 chr4A.!!$F1 585
15 TraesCS2B01G227300 chr1B 309928431 309929927 1496 False 1842 1842 89.0290 828 2315 1 chr1B.!!$F4 1487
16 TraesCS2B01G227300 chr1B 66183678 66185187 1509 False 1840 1840 88.8010 813 2315 1 chr1B.!!$F1 1502
17 TraesCS2B01G227300 chr1B 251882527 251883759 1232 False 1635 1635 90.7410 1089 2315 1 chr1B.!!$F3 1226
18 TraesCS2B01G227300 chr1B 251853556 251854649 1093 False 1277 1277 87.8180 1 1092 1 chr1B.!!$F2 1091
19 TraesCS2B01G227300 chr5A 705898676 705900339 1663 False 1788 1788 86.3340 663 2314 1 chr5A.!!$F1 1651
20 TraesCS2B01G227300 chr5A 37591077 37591612 535 True 481 481 82.8780 1 548 1 chr5A.!!$R1 547
21 TraesCS2B01G227300 chr7D 322654071 322655726 1655 False 1773 1773 86.2230 659 2315 1 chr7D.!!$F1 1656
22 TraesCS2B01G227300 chr2D 71955056 71956543 1487 True 1760 1760 88.1220 824 2315 1 chr2D.!!$R1 1491
23 TraesCS2B01G227300 chr3A 601365478 601366009 531 True 508 508 83.9710 1 547 1 chr3A.!!$R1 546

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
130 131 0.107361 ATGGGCTACCGTTGGTAAGC 60.107 55.0 0.0 3.63 37.76 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1454 1848 0.104855 TGCTCATAGGACGATGGCAC 59.895 55.0 0.0 0.0 31.94 5.01 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
39 40 2.340337 GAATGTCCAATTGGTGCAAGC 58.660 47.619 23.76 14.86 36.34 4.01
50 51 1.676635 GTGCAAGCTGGAGCATGGA 60.677 57.895 11.29 0.02 43.44 3.41
118 119 1.138859 CATGGAGTGTTCGATGGGCTA 59.861 52.381 0.00 0.00 36.30 3.93
120 121 0.179081 GGAGTGTTCGATGGGCTACC 60.179 60.000 0.00 0.00 37.24 3.18
123 124 0.390735 GTGTTCGATGGGCTACCGTT 60.391 55.000 0.00 0.00 40.75 4.44
130 131 0.107361 ATGGGCTACCGTTGGTAAGC 60.107 55.000 0.00 3.63 37.76 3.09
205 206 2.636227 CGACGAATTCGGATCGCGG 61.636 63.158 29.79 8.38 44.60 6.46
280 281 2.983433 GAGATGATGTGCTCGGTGG 58.017 57.895 0.00 0.00 0.00 4.61
290 291 1.375523 GCTCGGTGGTGTACAAGGG 60.376 63.158 0.00 0.00 0.00 3.95
291 292 1.823169 GCTCGGTGGTGTACAAGGGA 61.823 60.000 0.00 0.00 0.00 4.20
292 293 0.682852 CTCGGTGGTGTACAAGGGAA 59.317 55.000 0.00 0.00 0.00 3.97
293 294 1.071071 CTCGGTGGTGTACAAGGGAAA 59.929 52.381 0.00 0.00 0.00 3.13
294 295 1.071071 TCGGTGGTGTACAAGGGAAAG 59.929 52.381 0.00 0.00 0.00 2.62
295 296 1.880646 CGGTGGTGTACAAGGGAAAGG 60.881 57.143 0.00 0.00 0.00 3.11
375 381 0.458543 GACTCGTGCATGGACGATGT 60.459 55.000 37.02 32.79 46.72 3.06
382 388 2.102438 CATGGACGATGTGCTGCGT 61.102 57.895 0.00 0.00 44.33 5.24
447 455 2.027192 GGTGACAGGGCTGAACAGATTA 60.027 50.000 5.97 0.00 0.00 1.75
525 534 2.755103 GGCAGAATTTTTCGAGGGACAT 59.245 45.455 0.00 0.00 34.02 3.06
554 563 4.094476 AGGAAAGTAAGGTCAGGATTCGA 58.906 43.478 0.00 0.00 0.00 3.71
619 858 0.400213 TTTGGTCCGCTGGAGATTGT 59.600 50.000 0.00 0.00 29.39 2.71
762 1020 4.913924 CAGAAATCTTTTGCAAGTTCGGAG 59.086 41.667 0.00 0.00 0.00 4.63
799 1061 6.352016 TCTGTAGCAGAGAGAGTTGATTTT 57.648 37.500 0.00 0.00 35.39 1.82
818 1080 7.327214 TGATTTTCTTGTAACAACAAGGCTTT 58.673 30.769 16.01 2.63 45.15 3.51
898 1164 0.179045 GGACTATGGCGTGGCTTCAT 60.179 55.000 0.00 0.00 0.00 2.57
900 1166 2.289694 GGACTATGGCGTGGCTTCATAT 60.290 50.000 0.00 0.00 0.00 1.78
986 1255 1.373590 GGCGGCAACATGTCGGTTAT 61.374 55.000 3.07 0.00 46.90 1.89
1017 1286 4.015406 ATGGCGCCGAGGTTCACA 62.015 61.111 23.90 0.00 0.00 3.58
1024 1293 1.064952 CGCCGAGGTTCACAAAGTTTT 59.935 47.619 0.00 0.00 0.00 2.43
1060 1329 0.470766 TGGCACTGGTAACTTCGGTT 59.529 50.000 0.00 0.00 41.52 4.44
1312 1689 5.163754 GCGACCAATAAGCTGTATTTGAAGT 60.164 40.000 0.00 0.00 0.00 3.01
1327 1704 9.042450 TGTATTTGAAGTAGAAGTTCTATGGGA 57.958 33.333 15.53 1.90 30.76 4.37
1430 1809 3.056821 TGTGAAGATTGACGACGAGGATT 60.057 43.478 0.00 0.00 0.00 3.01
1437 1816 0.248949 GACGACGAGGATTAGGCACC 60.249 60.000 0.00 0.00 0.00 5.01
1442 1824 2.429610 GACGAGGATTAGGCACCACTTA 59.570 50.000 0.00 0.00 0.00 2.24
1451 1845 6.183360 GGATTAGGCACCACTTATTCTTGTTC 60.183 42.308 0.00 0.00 0.00 3.18
1454 1848 2.161609 GCACCACTTATTCTTGTTCCGG 59.838 50.000 0.00 0.00 0.00 5.14
1830 2240 1.135721 GGATGTTGGATTCAGCTTGCC 59.864 52.381 0.00 0.00 0.00 4.52
1838 2249 2.299867 GGATTCAGCTTGCCCTTTTCAA 59.700 45.455 0.00 0.00 0.00 2.69
1936 2350 1.656652 ATCGTGTTGCTGGAGTATGC 58.343 50.000 0.00 0.00 0.00 3.14
2068 2482 4.638421 GGTATGGAATTCCGTTGTGATTGA 59.362 41.667 24.06 0.88 39.43 2.57
2192 2606 5.189736 GGTGGAGCCATGAATATAGTGGATA 59.810 44.000 0.00 0.00 34.94 2.59
2295 2709 3.099905 CCAAGTCCTGAGTACATGGAGA 58.900 50.000 0.00 0.00 37.81 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 1.301558 GATCGCCTCCATGCTCCAG 60.302 63.158 0.00 0.00 0.00 3.86
50 51 4.592192 CCGCATCCACGATCGCCT 62.592 66.667 16.60 0.00 34.06 5.52
104 105 0.390735 AACGGTAGCCCATCGAACAC 60.391 55.000 0.00 0.00 0.00 3.32
105 106 0.390603 CAACGGTAGCCCATCGAACA 60.391 55.000 0.00 0.00 0.00 3.18
130 131 2.407846 ATCGCCACGTCTAGCCGATG 62.408 60.000 0.00 0.00 34.71 3.84
159 160 3.758554 GCCACATCTTCAACAACCACTAT 59.241 43.478 0.00 0.00 0.00 2.12
205 206 3.371063 TCTGGTCGCCGGTCTGAC 61.371 66.667 1.90 9.22 0.00 3.51
271 272 1.369692 CCTTGTACACCACCGAGCA 59.630 57.895 0.00 0.00 0.00 4.26
280 281 0.958876 CCGCCCTTTCCCTTGTACAC 60.959 60.000 0.00 0.00 0.00 2.90
310 311 2.024868 CGACACAATCCGTCCGCAA 61.025 57.895 0.00 0.00 0.00 4.85
337 338 2.203728 TGCCGTACCCTGGTCACT 60.204 61.111 0.00 0.00 0.00 3.41
382 388 1.070134 GCCATAATAGTCGCCACCTCA 59.930 52.381 0.00 0.00 0.00 3.86
447 455 4.326826 TCTGATTTTGATTCTTCGCCAGT 58.673 39.130 0.00 0.00 0.00 4.00
525 534 4.962995 CCTGACCTTACTTTCCTCTATCCA 59.037 45.833 0.00 0.00 0.00 3.41
619 858 4.919168 GCGCACGTATATCCAATACAGTAA 59.081 41.667 0.30 0.00 0.00 2.24
762 1020 2.933056 GCTACAGAAGTGCTCCACCTTC 60.933 54.545 0.00 0.00 34.49 3.46
818 1080 0.902516 CCCTTTGGAAAATCCCCGCA 60.903 55.000 0.00 0.00 35.03 5.69
898 1164 2.823747 CACCGATCCCGTATTCCTCATA 59.176 50.000 0.00 0.00 0.00 2.15
900 1166 1.037493 CACCGATCCCGTATTCCTCA 58.963 55.000 0.00 0.00 0.00 3.86
1017 1286 9.492973 CCATCAAATTTCTCCACATAAAACTTT 57.507 29.630 0.00 0.00 0.00 2.66
1024 1293 5.125900 CAGTGCCATCAAATTTCTCCACATA 59.874 40.000 0.00 0.00 0.00 2.29
1060 1329 3.582647 TCCTTGACTCTTGTCTGCCATAA 59.417 43.478 0.00 0.00 43.29 1.90
1312 1689 6.327365 TGCATCTTCATCCCATAGAACTTCTA 59.673 38.462 0.86 0.86 32.87 2.10
1327 1704 0.842635 GACCCCTCCTGCATCTTCAT 59.157 55.000 0.00 0.00 0.00 2.57
1376 1753 4.036852 CGCTAGATCTGTGACCAACTGATA 59.963 45.833 5.18 0.00 44.78 2.15
1430 1809 4.585879 GGAACAAGAATAAGTGGTGCCTA 58.414 43.478 0.00 0.00 0.00 3.93
1437 1816 2.161609 GGCACCGGAACAAGAATAAGTG 59.838 50.000 9.46 0.00 0.00 3.16
1442 1824 1.463674 GATGGCACCGGAACAAGAAT 58.536 50.000 9.46 0.00 0.00 2.40
1451 1845 1.300931 CATAGGACGATGGCACCGG 60.301 63.158 6.07 0.00 0.00 5.28
1454 1848 0.104855 TGCTCATAGGACGATGGCAC 59.895 55.000 0.00 0.00 31.94 5.01
1830 2240 0.602562 TTGGGCATCGCTTGAAAAGG 59.397 50.000 0.00 0.00 46.35 3.11
1838 2249 2.045926 GTCCTGTTGGGCATCGCT 60.046 61.111 0.00 0.00 38.01 4.93
2192 2606 0.829333 CTCCACTGCTACTCCTGCAT 59.171 55.000 0.00 0.00 39.86 3.96


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

AutoCloner maintained by Alex Coulton.